{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wed Apr 6 13:35:35 PDT 2016\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Software:\n", "\n", " System Software Overview:\n", "\n", " System Version: OS X 10.9.5 (13F34)\n", " Kernel Version: Darwin 13.4.0\n", " Boot Volume: Hummingbird\n", " Boot Mode: Normal\n", " Computer Name: hummingbird\n", " User Name: Sam (Sam)\n", " Secure Virtual Memory: Enabled\n", " Time since boot: 137 days 22:26\n", "\n" ] } ], "source": [ "%%bash\n", "system_profiler SPSoftwareDataType" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/usr/local/bioinformatics/stacks-1.37\n" ] } ], "source": [ "cd /usr/local/bioinformatics/stacks-1.37" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "ChangeLog README config.h \u001b[31mcstacks\u001b[m\u001b[m* \u001b[34mphp\u001b[m\u001b[m/ \u001b[34mscripts\u001b[m\u001b[m/ \u001b[31mustacks\u001b[m\u001b[m*\r\n", "INSTALL acinclude.m4 config.h.in \u001b[31mestacks\u001b[m\u001b[m* \u001b[31mpopulations\u001b[m\u001b[m* \u001b[34msql\u001b[m\u001b[m/\r\n", "LICENSE aclocal.m4 config.log \u001b[31mgenotypes\u001b[m\u001b[m* \u001b[31mprocess_radtags\u001b[m\u001b[m* \u001b[34msrc\u001b[m\u001b[m/\r\n", "Makefile \u001b[31mautogen.sh\u001b[m\u001b[m* \u001b[31mconfig.status\u001b[m\u001b[m* \u001b[31mhstacks\u001b[m\u001b[m* \u001b[31mprocess_shortreads\u001b[m\u001b[m* \u001b[31msstacks\u001b[m\u001b[m*\r\n", "Makefile.am \u001b[31mclone_filter\u001b[m\u001b[m* \u001b[31mconfigure\u001b[m\u001b[m* \u001b[31mkmer_filter\u001b[m\u001b[m* \u001b[31mpstacks\u001b[m\u001b[m* stamp-h1\r\n", "Makefile.in \u001b[34mconfig\u001b[m\u001b[m/ configure.ac \u001b[31mphasedstacks\u001b[m\u001b[m* \u001b[31mrxstacks\u001b[m\u001b[m* \u001b[34mtests\u001b[m\u001b[m/\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Test out STACKS process_radtags command to see what happens" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "No barcodes specified, files will not be demultiplexed.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_10A_1.fq.gz]\n", " Reading data from:\n", " /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_1.fq.gz and\n", " /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " 6373130 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -364015 low quality reads; 6009115 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6373130 total sequences;\n", " 0 ambiguous barcode drops;\n", " 364015 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6009115 retained reads.\n", "\n", "real\t1m41.004s\n", "user\t0m52.858s\n", "sys\t0m12.562s\n" ] } ], "source": [ "%%bash\n", "time process_radtags -1 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_1.fq.gz -2 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_2.fq.gz \\\n", "-o /Volumes/owl/temp/ -e apeKI -c -q -i gzfastq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### List process_radtags output files" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_1.fq 1HL_10A_1.rem.fq 1HL_10A_2.fq 1HL_10A_2.rem.fq process_radtags.log\r\n" ] } ], "source": [ "ls /Volumes/owl/temp/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Look at process_radtags log file" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "process_radtags -1 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_1.fq.gz -2 /Volumes/nightingales/O_lurida/20160223_gbs/1HL_10A_2.fq.gz -o /Volumes/owl/temp/ -e apeKI -c -q -i gzfastq\n", "process_radtags executed 2016-04-06 13:43:04\n", "\n", "File\tRetained Reads\tLow Quality\tAmbiguous Barcodes\tAmbiguous RAD-Tag\tTotal\n", "1HL_10A_1.fq.gz\t6009115\t364015\t0\t0\t6373130\n", "\n", "Total Sequences\t6373130\n", "Ambiguous Barcodes\t0\n", "Low Quality\t364015\n", "Ambiguous RAD-Tag\t0\n" ] } ], "source": [ "%%bash\n", "head /Volumes/owl/temp/process_radtags.log" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Move to directory with GBS FASTQ files" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/nightingales/O_lurida/20160223_gbs\n" ] } ], "source": [ "cd /Volumes/nightingales/O_lurida/20160223_gbs/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Generate a list of each pair of FASTQ files for subsequent processing" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_1.fq.gz 1HL_11A_1.fq.gz 1HL_12A_1.fq.gz 1HL_13A_1.fq.gz 1HL_14A_1.fq.gz 1HL_15A_1.fq.gz 1HL_16A_1.fq.gz 1HL_17A_1.fq.gz 1HL_19A_1.fq.gz 1HL_1A_1.fq.gz 1HL_20A_1.fq.gz 1HL_21A_1.fq.gz 1HL_22A_1.fq.gz 1HL_23A_1.fq.gz 1HL_24A_1.fq.gz 1HL_25A_1.fq.gz 1HL_26A_1.fq.gz 1HL_27A_1.fq.gz 1HL_28A_1.fq.gz 1HL_29A_1.fq.gz 1HL_2A_1.fq.gz 1HL_31A_1.fq.gz 1HL_33A_1.fq.gz 1HL_34A_1.fq.gz 1HL_35A_1.fq.gz 1HL_3A_1.fq.gz 1HL_4A_1.fq.gz 1HL_5A_1.fq.gz 1HL_6A_1.fq.gz 1HL_7A_1.fq.gz 1HL_8A_1.fq.gz 1HL_9A_1.fq.gz 1NF_10A_1.fq.gz 1NF_11A_1.fq.gz 1NF_12A_1.fq.gz 1NF_13A_1.fq.gz 1NF_14A_1.fq.gz 1NF_15A_1.fq.gz 1NF_16A_1.fq.gz 1NF_17A_1.fq.gz 1NF_18A_1.fq.gz 1NF_19A_1.fq.gz 1NF_1A_1.fq.gz 1NF_20A_1.fq.gz 1NF_21A_1.fq.gz 1NF_22A_1.fq.gz 1NF_23A_1.fq.gz 1NF_24A_1.fq.gz 1NF_25A_1.fq.gz 1NF_26A_1.fq.gz 1NF_27A_1.fq.gz 1NF_28A_1.fq.gz 1NF_29A_1.fq.gz 1NF_2A_1.fq.gz 1NF_30A_1.fq.gz 1NF_31A_1.fq.gz 1NF_32A_1.fq.gz 1NF_33A_1.fq.gz 1NF_4A_1.fq.gz 1NF_5A_1.fq.gz 1NF_6A_1.fq.gz 1NF_7A_1.fq.gz 1NF_8A_1.fq.gz 1NF_9A_1.fq.gz 1SN_10A_1.fq.gz 1SN_11A_1.fq.gz 1SN_12A_1.fq.gz 1SN_13A_1.fq.gz 1SN_14A_1.fq.gz 1SN_15A_1.fq.gz 1SN_16A_1.fq.gz 1SN_17A_1.fq.gz 1SN_18A_1.fq.gz 1SN_19A_1.fq.gz 1SN_1A_1.fq.gz 1SN_20A_1.fq.gz 1SN_21A_1.fq.gz 1SN_22A_1.fq.gz 1SN_23A_1.fq.gz 1SN_24A_1.fq.gz 1SN_25A_1.fq.gz 1SN_26A_1.fq.gz 1SN_27A_1.fq.gz 1SN_28A_1.fq.gz 1SN_29A_1.fq.gz 1SN_2A_1.fq.gz 1SN_30A_1.fq.gz 1SN_31A_1.fq.gz 1SN_32A_1.fq.gz 1SN_3A_1.fq.gz 1SN_4A_1.fq.gz 1SN_5A_1.fq.gz 1SN_6A_1.fq.gz 1SN_7A_1.fq.gz 1SN_8A_1.fq.gz 1SN_9A_1.fq.gz UnKnow_1.fq.gz\n" ] } ], "source": [ "%%bash\n", "echo *_1.fq.gz" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_2.fq.gz 1HL_11A_2.fq.gz 1HL_12A_2.fq.gz 1HL_13A_2.fq.gz 1HL_14A_2.fq.gz 1HL_15A_2.fq.gz 1HL_16A_2.fq.gz 1HL_17A_2.fq.gz 1HL_19A_2.fq.gz 1HL_1A_2.fq.gz 1HL_20A_2.fq.gz 1HL_21A_2.fq.gz 1HL_22A_2.fq.gz 1HL_23A_2.fq.gz 1HL_24A_2.fq.gz 1HL_25A_2.fq.gz 1HL_26A_2.fq.gz 1HL_27A_2.fq.gz 1HL_28A_2.fq.gz 1HL_29A_2.fq.gz 1HL_2A_2.fq.gz 1HL_31A_2.fq.gz 1HL_33A_2.fq.gz 1HL_34A_2.fq.gz 1HL_35A_2.fq.gz 1HL_3A_2.fq.gz 1HL_4A_2.fq.gz 1HL_5A_2.fq.gz 1HL_6A_2.fq.gz 1HL_7A_2.fq.gz 1HL_8A_2.fq.gz 1HL_9A_2.fq.gz 1NF_10A_2.fq.gz 1NF_11A_2.fq.gz 1NF_12A_2.fq.gz 1NF_13A_2.fq.gz 1NF_14A_2.fq.gz 1NF_15A_2.fq.gz 1NF_16A_2.fq.gz 1NF_17A_2.fq.gz 1NF_18A_2.fq.gz 1NF_19A_2.fq.gz 1NF_1A_2.fq.gz 1NF_20A_2.fq.gz 1NF_21A_2.fq.gz 1NF_22A_2.fq.gz 1NF_23A_2.fq.gz 1NF_24A_2.fq.gz 1NF_25A_2.fq.gz 1NF_26A_2.fq.gz 1NF_27A_2.fq.gz 1NF_28A_2.fq.gz 1NF_29A_2.fq.gz 1NF_2A_2.fq.gz 1NF_30A_2.fq.gz 1NF_31A_2.fq.gz 1NF_32A_2.fq.gz 1NF_33A_2.fq.gz 1NF_4A_2.fq.gz 1NF_5A_2.fq.gz 1NF_6A_2.fq.gz 1NF_7A_2.fq.gz 1NF_8A_2.fq.gz 1NF_9A_2.fq.gz 1SN_10A_2.fq.gz 1SN_11A_2.fq.gz 1SN_12A_2.fq.gz 1SN_13A_2.fq.gz 1SN_14A_2.fq.gz 1SN_15A_2.fq.gz 1SN_16A_2.fq.gz 1SN_17A_2.fq.gz 1SN_18A_2.fq.gz 1SN_19A_2.fq.gz 1SN_1A_2.fq.gz 1SN_20A_2.fq.gz 1SN_21A_2.fq.gz 1SN_22A_2.fq.gz 1SN_23A_2.fq.gz 1SN_24A_2.fq.gz 1SN_25A_2.fq.gz 1SN_26A_2.fq.gz 1SN_27A_2.fq.gz 1SN_28A_2.fq.gz 1SN_29A_2.fq.gz 1SN_2A_2.fq.gz 1SN_30A_2.fq.gz 1SN_31A_2.fq.gz 1SN_32A_2.fq.gz 1SN_3A_2.fq.gz 1SN_4A_2.fq.gz 1SN_5A_2.fq.gz 1SN_6A_2.fq.gz 1SN_7A_2.fq.gz 1SN_8A_2.fq.gz 1SN_9A_2.fq.gz UnKnow_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "echo *_2.fq.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Use the two lists generated above for cell below to automate running process_radtags on all 96 individuals that were sequenced. \n", "#####Cell below creates two lists, loops through an array and assigns the corresponding FASTQ pairs to the values \"i\" and \"j\". \n", "#####The values in \"i\" and \"j\" are used in the process_radtags command." ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_10A_1.fq.gz]\n", " Reading data from:\n", " 1HL_10A_1.fq.gz and\n", " 1HL_10A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " 6373130 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -364015 low quality reads; 6009115 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6373130 total sequences;\n", " 0 ambiguous barcode drops;\n", " 364015 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6009115 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_11A_1.fq.gz]\n", " Reading data from:\n", " 1HL_11A_1.fq.gz and\n", " 1HL_11A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " 7137006 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -406623 low quality reads; 6730383 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7137006 total sequences;\n", " 0 ambiguous barcode drops;\n", " 406623 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6730383 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_12A_1.fq.gz]\n", " Reading data from:\n", " 1HL_12A_1.fq.gz and\n", " 1HL_12A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " 5049626 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -287923 low quality reads; 4761703 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5049626 total sequences;\n", " 0 ambiguous barcode drops;\n", " 287923 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4761703 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_13A_1.fq.gz]\n", " Reading data from:\n", " 1HL_13A_1.fq.gz and\n", " 1HL_13A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " 5352850 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -304892 low quality reads; 5047958 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5352850 total sequences;\n", " 0 ambiguous barcode drops;\n", " 304892 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5047958 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_14A_1.fq.gz]\n", " Reading data from:\n", " 1HL_14A_1.fq.gz and\n", " 1HL_14A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " 4031222 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -230119 low quality reads; 3801103 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4031222 total sequences;\n", " 0 ambiguous barcode drops;\n", " 230119 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "3801103 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_15A_1.fq.gz]\n", " Reading data from:\n", " 1HL_15A_1.fq.gz and\n", " 1HL_15A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " 4392648 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -250237 low quality reads; 4142411 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4392648 total sequences;\n", " 0 ambiguous barcode drops;\n", " 250237 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4142411 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_16A_1.fq.gz]\n", " Reading data from:\n", " 1HL_16A_1.fq.gz and\n", " 1HL_16A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " 4666316 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -266126 low quality reads; 4400190 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4666316 total sequences;\n", " 0 ambiguous barcode drops;\n", " 266126 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4400190 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_17A_1.fq.gz]\n", " Reading data from:\n", " 1HL_17A_1.fq.gz and\n", " 1HL_17A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " Processing RAD-Tag 3610000 \r", " Processing RAD-Tag 3620000 \r", " Processing RAD-Tag 3630000 \r", " Processing RAD-Tag 3640000 \r", " Processing RAD-Tag 3650000 \r", " 7307522 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -418495 low quality reads; 6889027 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7307522 total sequences;\n", " 0 ambiguous barcode drops;\n", " 418495 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6889027 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_19A_1.fq.gz]\n", " Reading data from:\n", " 1HL_19A_1.fq.gz and\n", " 1HL_19A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " Processing RAD-Tag 3610000 \r", " 7235968 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -412078 low quality reads; 6823890 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7235968 total sequences;\n", " 0 ambiguous barcode drops;\n", " 412078 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6823890 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_1A_1.fq.gz]\n", " Reading data from:\n", " 1HL_1A_1.fq.gz and\n", " 1HL_1A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " 4520860 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -256112 low quality reads; 4264748 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4520860 total sequences;\n", " 0 ambiguous barcode drops;\n", " 256112 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4264748 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_20A_1.fq.gz]\n", " Reading data from:\n", " 1HL_20A_1.fq.gz and\n", " 1HL_20A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " 5817876 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -330533 low quality reads; 5487343 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5817876 total sequences;\n", " 0 ambiguous barcode drops;\n", " 330533 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5487343 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_21A_1.fq.gz]\n", " Reading data from:\n", " 1HL_21A_1.fq.gz and\n", " 1HL_21A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " 5183690 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -295100 low quality reads; 4888590 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5183690 total sequences;\n", " 0 ambiguous barcode drops;\n", " 295100 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4888590 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_22A_1.fq.gz]\n", " Reading data from:\n", " 1HL_22A_1.fq.gz and\n", " 1HL_22A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " 4148458 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -235614 low quality reads; 3912844 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4148458 total sequences;\n", " 0 ambiguous barcode drops;\n", " 235614 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "3912844 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_23A_1.fq.gz]\n", " Reading data from:\n", " 1HL_23A_1.fq.gz and\n", " 1HL_23A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " 7219588 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -412125 low quality reads; 6807463 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7219588 total sequences;\n", " 0 ambiguous barcode drops;\n", " 412125 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6807463 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_24A_1.fq.gz]\n", " Reading data from:\n", " 1HL_24A_1.fq.gz and\n", " 1HL_24A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " 5443616 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -309887 low quality reads; 5133729 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5443616 total sequences;\n", " 0 ambiguous barcode drops;\n", " 309887 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5133729 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_25A_1.fq.gz]\n", " Reading data from:\n", " 1HL_25A_1.fq.gz and\n", " 1HL_25A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " 5915748 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -335814 low quality reads; 5579934 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5915748 total sequences;\n", " 0 ambiguous barcode drops;\n", " 335814 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5579934 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_26A_1.fq.gz]\n", " Reading data from:\n", " 1HL_26A_1.fq.gz and\n", " 1HL_26A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " 6284738 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -358195 low quality reads; 5926543 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6284738 total sequences;\n", " 0 ambiguous barcode drops;\n", " 358195 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5926543 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_27A_1.fq.gz]\n", " Reading data from:\n", " 1HL_27A_1.fq.gz and\n", " 1HL_27A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " 6399298 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -365037 low quality reads; 6034261 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6399298 total sequences;\n", " 0 ambiguous barcode drops;\n", " 365037 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6034261 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_28A_1.fq.gz]\n", " Reading data from:\n", " 1HL_28A_1.fq.gz and\n", " 1HL_28A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " Processing RAD-Tag 3610000 \r", " Processing RAD-Tag 3620000 \r", " Processing RAD-Tag 3630000 \r", " Processing RAD-Tag 3640000 \r", " Processing RAD-Tag 3650000 \r", " Processing RAD-Tag 3660000 \r", " Processing RAD-Tag 3670000 \r", " Processing RAD-Tag 3680000 \r", " Processing RAD-Tag 3690000 \r", " Processing RAD-Tag 3700000 \r", " Processing RAD-Tag 3710000 \r", " Processing RAD-Tag 3720000 \r", " Processing RAD-Tag 3730000 \r", " Processing RAD-Tag 3740000 \r", " Processing RAD-Tag 3750000 \r", " Processing RAD-Tag 3760000 \r", " Processing RAD-Tag 3770000 \r", " 7540476 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -430416 low quality reads; 7110060 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7540476 total sequences;\n", " 0 ambiguous barcode drops;\n", " 430416 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "7110060 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_29A_1.fq.gz]\n", " Reading data from:\n", " 1HL_29A_1.fq.gz and\n", " 1HL_29A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " 6142410 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -351000 low quality reads; 5791410 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6142410 total sequences;\n", " 0 ambiguous barcode drops;\n", " 351000 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5791410 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_2A_1.fq.gz]\n", " Reading data from:\n", " 1HL_2A_1.fq.gz and\n", " 1HL_2A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " 5516300 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -314684 low quality reads; 5201616 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5516300 total sequences;\n", " 0 ambiguous barcode drops;\n", " 314684 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5201616 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_31A_1.fq.gz]\n", " Reading data from:\n", " 1HL_31A_1.fq.gz and\n", " 1HL_31A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " 4907506 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -280081 low quality reads; 4627425 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4907506 total sequences;\n", " 0 ambiguous barcode drops;\n", " 280081 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4627425 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_33A_1.fq.gz]\n", " Reading data from:\n", " 1HL_33A_1.fq.gz and\n", " 1HL_33A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " 5417886 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -308571 low quality reads; 5109315 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5417886 total sequences;\n", " 0 ambiguous barcode drops;\n", " 308571 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5109315 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_34A_1.fq.gz]\n", " Reading data from:\n", " 1HL_34A_1.fq.gz and\n", " 1HL_34A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " 5798038 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -328771 low quality reads; 5469267 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5798038 total sequences;\n", " 0 ambiguous barcode drops;\n", " 328771 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5469267 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_35A_1.fq.gz]\n", " Reading data from:\n", " 1HL_35A_1.fq.gz and\n", " 1HL_35A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " 5260626 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -299671 low quality reads; 4960955 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5260626 total sequences;\n", " 0 ambiguous barcode drops;\n", " 299671 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4960955 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_3A_1.fq.gz]\n", " Reading data from:\n", " 1HL_3A_1.fq.gz and\n", " 1HL_3A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " 4422802 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -252661 low quality reads; 4170141 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4422802 total sequences;\n", " 0 ambiguous barcode drops;\n", " 252661 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4170141 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_4A_1.fq.gz]\n", " Reading data from:\n", " 1HL_4A_1.fq.gz and\n", " 1HL_4A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " 5142062 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -293734 low quality reads; 4848328 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5142062 total sequences;\n", " 0 ambiguous barcode drops;\n", " 293734 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4848328 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_5A_1.fq.gz]\n", " Reading data from:\n", " 1HL_5A_1.fq.gz and\n", " 1HL_5A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " 3961332 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -225899 low quality reads; 3735433 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "3961332 total sequences;\n", " 0 ambiguous barcode drops;\n", " 225899 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "3735433 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_6A_1.fq.gz]\n", " Reading data from:\n", " 1HL_6A_1.fq.gz and\n", " 1HL_6A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " 4140102 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -235725 low quality reads; 3904377 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4140102 total sequences;\n", " 0 ambiguous barcode drops;\n", " 235725 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "3904377 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_7A_1.fq.gz]\n", " Reading data from:\n", " 1HL_7A_1.fq.gz and\n", " 1HL_7A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " 5587088 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -318275 low quality reads; 5268813 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5587088 total sequences;\n", " 0 ambiguous barcode drops;\n", " 318275 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5268813 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_8A_1.fq.gz]\n", " Reading data from:\n", " 1HL_8A_1.fq.gz and\n", " 1HL_8A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " 5088026 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -289492 low quality reads; 4798534 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5088026 total sequences;\n", " 0 ambiguous barcode drops;\n", " 289492 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4798534 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1HL_9A_1.fq.gz]\n", " Reading data from:\n", " 1HL_9A_1.fq.gz and\n", " 1HL_9A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " 5665890 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -323536 low quality reads; 5342354 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5665890 total sequences;\n", " 0 ambiguous barcode drops;\n", " 323536 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5342354 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_10A_1.fq.gz]\n", " Reading data from:\n", " 1NF_10A_1.fq.gz and\n", " 1NF_10A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " 4298602 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -246007 low quality reads; 4052595 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4298602 total sequences;\n", " 0 ambiguous barcode drops;\n", " 246007 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4052595 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_11A_1.fq.gz]\n", " Reading data from:\n", " 1NF_11A_1.fq.gz and\n", " 1NF_11A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " 4533294 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -258322 low quality reads; 4274972 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4533294 total sequences;\n", " 0 ambiguous barcode drops;\n", " 258322 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4274972 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_12A_1.fq.gz]\n", " Reading data from:\n", " 1NF_12A_1.fq.gz and\n", " 1NF_12A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " 4359846 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -248582 low quality reads; 4111264 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4359846 total sequences;\n", " 0 ambiguous barcode drops;\n", " 248582 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4111264 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_13A_1.fq.gz]\n", " Reading data from:\n", " 1NF_13A_1.fq.gz and\n", " 1NF_13A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " Processing RAD-Tag 3610000 \r", " Processing RAD-Tag 3620000 \r", " Processing RAD-Tag 3630000 \r", " Processing RAD-Tag 3640000 \r", " Processing RAD-Tag 3650000 \r", " Processing RAD-Tag 3660000 \r", " Processing RAD-Tag 3670000 \r", " Processing RAD-Tag 3680000 \r", " Processing RAD-Tag 3690000 \r", " Processing RAD-Tag 3700000 \r", " Processing RAD-Tag 3710000 \r", " Processing RAD-Tag 3720000 \r", " Processing RAD-Tag 3730000 \r", " Processing RAD-Tag 3740000 \r", " Processing RAD-Tag 3750000 \r", " Processing RAD-Tag 3760000 \r", " Processing RAD-Tag 3770000 \r", " Processing RAD-Tag 3780000 \r", " Processing RAD-Tag 3790000 \r", " Processing RAD-Tag 3800000 \r", " Processing RAD-Tag 3810000 \r", " Processing RAD-Tag 3820000 \r", " Processing RAD-Tag 3830000 \r", " Processing RAD-Tag 3840000 \r", " Processing RAD-Tag 3850000 \r", " Processing RAD-Tag 3860000 \r", " Processing RAD-Tag 3870000 \r", " Processing RAD-Tag 3880000 \r", " Processing RAD-Tag 3890000 \r", " 7780236 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -443383 low quality reads; 7336853 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7780236 total sequences;\n", " 0 ambiguous barcode drops;\n", " 443383 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "7336853 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_14A_1.fq.gz]\n", " Reading data from:\n", " 1NF_14A_1.fq.gz and\n", " 1NF_14A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " 5438396 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -309623 low quality reads; 5128773 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5438396 total sequences;\n", " 0 ambiguous barcode drops;\n", " 309623 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5128773 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_15A_1.fq.gz]\n", " Reading data from:\n", " 1NF_15A_1.fq.gz and\n", " 1NF_15A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " 5108648 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -291298 low quality reads; 4817350 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5108648 total sequences;\n", " 0 ambiguous barcode drops;\n", " 291298 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4817350 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_16A_1.fq.gz]\n", " Reading data from:\n", " 1NF_16A_1.fq.gz and\n", " 1NF_16A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " 5365896 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -306723 low quality reads; 5059173 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5365896 total sequences;\n", " 0 ambiguous barcode drops;\n", " 306723 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5059173 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_17A_1.fq.gz]\n", " Reading data from:\n", " 1NF_17A_1.fq.gz and\n", " 1NF_17A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " 6238656 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -356398 low quality reads; 5882258 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6238656 total sequences;\n", " 0 ambiguous barcode drops;\n", " 356398 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5882258 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_18A_1.fq.gz]\n", " Reading data from:\n", " 1NF_18A_1.fq.gz and\n", " 1NF_18A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " 3500140 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -199756 low quality reads; 3300384 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "3500140 total sequences;\n", " 0 ambiguous barcode drops;\n", " 199756 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "3300384 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_19A_1.fq.gz]\n", " Reading data from:\n", " 1NF_19A_1.fq.gz and\n", " 1NF_19A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " 4073280 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -232401 low quality reads; 3840879 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4073280 total sequences;\n", " 0 ambiguous barcode drops;\n", " 232401 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "3840879 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_1A_1.fq.gz]\n", " Reading data from:\n", " 1NF_1A_1.fq.gz and\n", " 1NF_1A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " 2711520 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -154238 low quality reads; 2557282 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "2711520 total sequences;\n", " 0 ambiguous barcode drops;\n", " 154238 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "2557282 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_20A_1.fq.gz]\n", " Reading data from:\n", " 1NF_20A_1.fq.gz and\n", " 1NF_20A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " 4914052 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -280471 low quality reads; 4633581 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4914052 total sequences;\n", " 0 ambiguous barcode drops;\n", " 280471 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4633581 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_21A_1.fq.gz]\n", " Reading data from:\n", " 1NF_21A_1.fq.gz and\n", " 1NF_21A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " 6093874 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -347585 low quality reads; 5746289 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6093874 total sequences;\n", " 0 ambiguous barcode drops;\n", " 347585 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5746289 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_22A_1.fq.gz]\n", " Reading data from:\n", " 1NF_22A_1.fq.gz and\n", " 1NF_22A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " 5790352 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -330821 low quality reads; 5459531 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5790352 total sequences;\n", " 0 ambiguous barcode drops;\n", " 330821 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5459531 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_23A_1.fq.gz]\n", " Reading data from:\n", " 1NF_23A_1.fq.gz and\n", " 1NF_23A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " 6413484 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -367079 low quality reads; 6046405 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6413484 total sequences;\n", " 0 ambiguous barcode drops;\n", " 367079 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6046405 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_24A_1.fq.gz]\n", " Reading data from:\n", " 1NF_24A_1.fq.gz and\n", " 1NF_24A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " 6077252 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -345939 low quality reads; 5731313 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6077252 total sequences;\n", " 0 ambiguous barcode drops;\n", " 345939 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5731313 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_25A_1.fq.gz]\n", " Reading data from:\n", " 1NF_25A_1.fq.gz and\n", " 1NF_25A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " 4406458 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -251905 low quality reads; 4154553 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4406458 total sequences;\n", " 0 ambiguous barcode drops;\n", " 251905 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4154553 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_26A_1.fq.gz]\n", " Reading data from:\n", " 1NF_26A_1.fq.gz and\n", " 1NF_26A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " 5869588 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -335792 low quality reads; 5533796 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5869588 total sequences;\n", " 0 ambiguous barcode drops;\n", " 335792 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5533796 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_27A_1.fq.gz]\n", " Reading data from:\n", " 1NF_27A_1.fq.gz and\n", " 1NF_27A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " 4545304 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -259372 low quality reads; 4285932 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4545304 total sequences;\n", " 0 ambiguous barcode drops;\n", " 259372 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4285932 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_28A_1.fq.gz]\n", " Reading data from:\n", " 1NF_28A_1.fq.gz and\n", " 1NF_28A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " 4689526 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -267109 low quality reads; 4422417 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4689526 total sequences;\n", " 0 ambiguous barcode drops;\n", " 267109 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4422417 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_29A_1.fq.gz]\n", " Reading data from:\n", " 1NF_29A_1.fq.gz and\n", " 1NF_29A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " Processing RAD-Tag 3610000 \r", " Processing RAD-Tag 3620000 \r", " Processing RAD-Tag 3630000 \r", " Processing RAD-Tag 3640000 \r", " Processing RAD-Tag 3650000 \r", " Processing RAD-Tag 3660000 \r", " Processing RAD-Tag 3670000 \r", " Processing RAD-Tag 3680000 \r", " Processing RAD-Tag 3690000 \r", " Processing RAD-Tag 3700000 \r", " Processing RAD-Tag 3710000 \r", " Processing RAD-Tag 3720000 \r", " Processing RAD-Tag 3730000 \r", " Processing RAD-Tag 3740000 \r", " Processing RAD-Tag 3750000 \r", " Processing RAD-Tag 3760000 \r", " Processing RAD-Tag 3770000 \r", " Processing RAD-Tag 3780000 \r", " Processing RAD-Tag 3790000 \r", " Processing RAD-Tag 3800000 \r", " Processing RAD-Tag 3810000 \r", " Processing RAD-Tag 3820000 \r", " 7659962 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -437212 low quality reads; 7222750 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7659962 total sequences;\n", " 0 ambiguous barcode drops;\n", " 437212 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "7222750 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_2A_1.fq.gz]\n", " Reading data from:\n", " 1NF_2A_1.fq.gz and\n", " 1NF_2A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " 6905862 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -394012 low quality reads; 6511850 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6905862 total sequences;\n", " 0 ambiguous barcode drops;\n", " 394012 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6511850 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_30A_1.fq.gz]\n", " Reading data from:\n", " 1NF_30A_1.fq.gz and\n", " 1NF_30A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " 5402094 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -308424 low quality reads; 5093670 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5402094 total sequences;\n", " 0 ambiguous barcode drops;\n", " 308424 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5093670 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_31A_1.fq.gz]\n", " Reading data from:\n", " 1NF_31A_1.fq.gz and\n", " 1NF_31A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " 7123148 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -404772 low quality reads; 6718376 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7123148 total sequences;\n", " 0 ambiguous barcode drops;\n", " 404772 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6718376 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_32A_1.fq.gz]\n", " Reading data from:\n", " 1NF_32A_1.fq.gz and\n", " 1NF_32A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " 6955972 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -395341 low quality reads; 6560631 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6955972 total sequences;\n", " 0 ambiguous barcode drops;\n", " 395341 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6560631 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_33A_1.fq.gz]\n", " Reading data from:\n", " 1NF_33A_1.fq.gz and\n", " 1NF_33A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " 5205902 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -297588 low quality reads; 4908314 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5205902 total sequences;\n", " 0 ambiguous barcode drops;\n", " 297588 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4908314 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_4A_1.fq.gz]\n", " Reading data from:\n", " 1NF_4A_1.fq.gz and\n", " 1NF_4A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " 7165798 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -408033 low quality reads; 6757765 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7165798 total sequences;\n", " 0 ambiguous barcode drops;\n", " 408033 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6757765 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_5A_1.fq.gz]\n", " Reading data from:\n", " 1NF_5A_1.fq.gz and\n", " 1NF_5A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " 5531968 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -314477 low quality reads; 5217491 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5531968 total sequences;\n", " 0 ambiguous barcode drops;\n", " 314477 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5217491 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_6A_1.fq.gz]\n", " Reading data from:\n", " 1NF_6A_1.fq.gz and\n", " 1NF_6A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " 4847776 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -276286 low quality reads; 4571490 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4847776 total sequences;\n", " 0 ambiguous barcode drops;\n", " 276286 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4571490 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_7A_1.fq.gz]\n", " Reading data from:\n", " 1NF_7A_1.fq.gz and\n", " 1NF_7A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " 5181014 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -296076 low quality reads; 4884938 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5181014 total sequences;\n", " 0 ambiguous barcode drops;\n", " 296076 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4884938 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_8A_1.fq.gz]\n", " Reading data from:\n", " 1NF_8A_1.fq.gz and\n", " 1NF_8A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " 5545160 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -316222 low quality reads; 5228938 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5545160 total sequences;\n", " 0 ambiguous barcode drops;\n", " 316222 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5228938 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1NF_9A_1.fq.gz]\n", " Reading data from:\n", " 1NF_9A_1.fq.gz and\n", " 1NF_9A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " 6760996 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -385656 low quality reads; 6375340 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6760996 total sequences;\n", " 0 ambiguous barcode drops;\n", " 385656 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6375340 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_10A_1.fq.gz]\n", " Reading data from:\n", " 1SN_10A_1.fq.gz and\n", " 1SN_10A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " 5117334 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -291812 low quality reads; 4825522 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5117334 total sequences;\n", " 0 ambiguous barcode drops;\n", " 291812 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4825522 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_11A_1.fq.gz]\n", " Reading data from:\n", " 1SN_11A_1.fq.gz and\n", " 1SN_11A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " 5167984 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -295139 low quality reads; 4872845 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5167984 total sequences;\n", " 0 ambiguous barcode drops;\n", " 295139 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4872845 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_12A_1.fq.gz]\n", " Reading data from:\n", " 1SN_12A_1.fq.gz and\n", " 1SN_12A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " 6847804 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -390395 low quality reads; 6457409 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6847804 total sequences;\n", " 0 ambiguous barcode drops;\n", " 390395 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6457409 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_13A_1.fq.gz]\n", " Reading data from:\n", " 1SN_13A_1.fq.gz and\n", " 1SN_13A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " 5913982 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -336735 low quality reads; 5577247 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5913982 total sequences;\n", " 0 ambiguous barcode drops;\n", " 336735 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5577247 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_14A_1.fq.gz]\n", " Reading data from:\n", " 1SN_14A_1.fq.gz and\n", " 1SN_14A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " 7088580 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -403741 low quality reads; 6684839 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7088580 total sequences;\n", " 0 ambiguous barcode drops;\n", " 403741 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6684839 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_15A_1.fq.gz]\n", " Reading data from:\n", " 1SN_15A_1.fq.gz and\n", " 1SN_15A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " 5012650 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -285801 low quality reads; 4726849 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5012650 total sequences;\n", " 0 ambiguous barcode drops;\n", " 285801 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4726849 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_16A_1.fq.gz]\n", " Reading data from:\n", " 1SN_16A_1.fq.gz and\n", " 1SN_16A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " 5233932 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -298373 low quality reads; 4935559 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5233932 total sequences;\n", " 0 ambiguous barcode drops;\n", " 298373 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4935559 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_17A_1.fq.gz]\n", " Reading data from:\n", " 1SN_17A_1.fq.gz and\n", " 1SN_17A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " 5966802 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -339721 low quality reads; 5627081 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5966802 total sequences;\n", " 0 ambiguous barcode drops;\n", " 339721 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5627081 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_18A_1.fq.gz]\n", " Reading data from:\n", " 1SN_18A_1.fq.gz and\n", " 1SN_18A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " 6497024 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -371120 low quality reads; 6125904 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6497024 total sequences;\n", " 0 ambiguous barcode drops;\n", " 371120 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6125904 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_19A_1.fq.gz]\n", " Reading data from:\n", " 1SN_19A_1.fq.gz and\n", " 1SN_19A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " 6072926 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -344632 low quality reads; 5728294 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6072926 total sequences;\n", " 0 ambiguous barcode drops;\n", " 344632 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5728294 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_1A_1.fq.gz]\n", " Reading data from:\n", " 1SN_1A_1.fq.gz and\n", " 1SN_1A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " 6081074 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -344640 low quality reads; 5736434 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6081074 total sequences;\n", " 0 ambiguous barcode drops;\n", " 344640 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5736434 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_20A_1.fq.gz]\n", " Reading data from:\n", " 1SN_20A_1.fq.gz and\n", " 1SN_20A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " 4310354 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -247242 low quality reads; 4063112 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4310354 total sequences;\n", " 0 ambiguous barcode drops;\n", " 247242 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4063112 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_21A_1.fq.gz]\n", " Reading data from:\n", " 1SN_21A_1.fq.gz and\n", " 1SN_21A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " 7081236 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -402346 low quality reads; 6678890 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7081236 total sequences;\n", " 0 ambiguous barcode drops;\n", " 402346 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6678890 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_22A_1.fq.gz]\n", " Reading data from:\n", " 1SN_22A_1.fq.gz and\n", " 1SN_22A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " 6120730 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -347346 low quality reads; 5773384 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6120730 total sequences;\n", " 0 ambiguous barcode drops;\n", " 347346 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5773384 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_23A_1.fq.gz]\n", " Reading data from:\n", " 1SN_23A_1.fq.gz and\n", " 1SN_23A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " Processing RAD-Tag 3610000 \r", " Processing RAD-Tag 3620000 \r", " Processing RAD-Tag 3630000 \r", " Processing RAD-Tag 3640000 \r", " Processing RAD-Tag 3650000 \r", " Processing RAD-Tag 3660000 \r", " Processing RAD-Tag 3670000 \r", " Processing RAD-Tag 3680000 \r", " Processing RAD-Tag 3690000 \r", " 7392514 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -421778 low quality reads; 6970736 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7392514 total sequences;\n", " 0 ambiguous barcode drops;\n", " 421778 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6970736 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_24A_1.fq.gz]\n", " Reading data from:\n", " 1SN_24A_1.fq.gz and\n", " 1SN_24A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " 3770530 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -213919 low quality reads; 3556611 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "3770530 total sequences;\n", " 0 ambiguous barcode drops;\n", " 213919 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "3556611 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_25A_1.fq.gz]\n", " Reading data from:\n", " 1SN_25A_1.fq.gz and\n", " 1SN_25A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " 6074178 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -346564 low quality reads; 5727614 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6074178 total sequences;\n", " 0 ambiguous barcode drops;\n", " 346564 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5727614 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_26A_1.fq.gz]\n", " Reading data from:\n", " 1SN_26A_1.fq.gz and\n", " 1SN_26A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " 5517746 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -314306 low quality reads; 5203440 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5517746 total sequences;\n", " 0 ambiguous barcode drops;\n", " 314306 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5203440 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_27A_1.fq.gz]\n", " Reading data from:\n", " 1SN_27A_1.fq.gz and\n", " 1SN_27A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " 5215618 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -297965 low quality reads; 4917653 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5215618 total sequences;\n", " 0 ambiguous barcode drops;\n", " 297965 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4917653 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_28A_1.fq.gz]\n", " Reading data from:\n", " 1SN_28A_1.fq.gz and\n", " 1SN_28A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " 5683174 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -323400 low quality reads; 5359774 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5683174 total sequences;\n", " 0 ambiguous barcode drops;\n", " 323400 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5359774 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_29A_1.fq.gz]\n", " Reading data from:\n", " 1SN_29A_1.fq.gz and\n", " 1SN_29A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " 4514548 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -256147 low quality reads; 4258401 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4514548 total sequences;\n", " 0 ambiguous barcode drops;\n", " 256147 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4258401 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_2A_1.fq.gz]\n", " Reading data from:\n", " 1SN_2A_1.fq.gz and\n", " 1SN_2A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " 6160214 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -351022 low quality reads; 5809192 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6160214 total sequences;\n", " 0 ambiguous barcode drops;\n", " 351022 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5809192 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_30A_1.fq.gz]\n", " Reading data from:\n", " 1SN_30A_1.fq.gz and\n", " 1SN_30A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " Processing RAD-Tag 3360000 \r", " Processing RAD-Tag 3370000 \r", " Processing RAD-Tag 3380000 \r", " Processing RAD-Tag 3390000 \r", " Processing RAD-Tag 3400000 \r", " Processing RAD-Tag 3410000 \r", " Processing RAD-Tag 3420000 \r", " Processing RAD-Tag 3430000 \r", " Processing RAD-Tag 3440000 \r", " Processing RAD-Tag 3450000 \r", " Processing RAD-Tag 3460000 \r", " Processing RAD-Tag 3470000 \r", " Processing RAD-Tag 3480000 \r", " Processing RAD-Tag 3490000 \r", " Processing RAD-Tag 3500000 \r", " Processing RAD-Tag 3510000 \r", " Processing RAD-Tag 3520000 \r", " Processing RAD-Tag 3530000 \r", " Processing RAD-Tag 3540000 \r", " Processing RAD-Tag 3550000 \r", " Processing RAD-Tag 3560000 \r", " Processing RAD-Tag 3570000 \r", " Processing RAD-Tag 3580000 \r", " Processing RAD-Tag 3590000 \r", " Processing RAD-Tag 3600000 \r", " Processing RAD-Tag 3610000 \r", " Processing RAD-Tag 3620000 \r", " Processing RAD-Tag 3630000 \r", " Processing RAD-Tag 3640000 \r", " Processing RAD-Tag 3650000 \r", " Processing RAD-Tag 3660000 \r", " Processing RAD-Tag 3670000 \r", " Processing RAD-Tag 3680000 \r", " Processing RAD-Tag 3690000 \r", " Processing RAD-Tag 3700000 \r", " Processing RAD-Tag 3710000 \r", " Processing RAD-Tag 3720000 \r", " Processing RAD-Tag 3730000 \r", " Processing RAD-Tag 3740000 \r", " Processing RAD-Tag 3750000 \r", " Processing RAD-Tag 3760000 \r", " Processing RAD-Tag 3770000 \r", " Processing RAD-Tag 3780000 \r", " Processing RAD-Tag 3790000 \r", " Processing RAD-Tag 3800000 \r", " Processing RAD-Tag 3810000 \r", " Processing RAD-Tag 3820000 \r", " Processing RAD-Tag 3830000 \r", " Processing RAD-Tag 3840000 \r", " 7680406 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -437786 low quality reads; 7242620 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "7680406 total sequences;\n", " 0 ambiguous barcode drops;\n", " 437786 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "7242620 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_31A_1.fq.gz]\n", " Reading data from:\n", " 1SN_31A_1.fq.gz and\n", " 1SN_31A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " 6707430 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -382160 low quality reads; 6325270 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6707430 total sequences;\n", " 0 ambiguous barcode drops;\n", " 382160 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6325270 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_32A_1.fq.gz]\n", " Reading data from:\n", " 1SN_32A_1.fq.gz and\n", " 1SN_32A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " 5105270 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -290816 low quality reads; 4814454 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5105270 total sequences;\n", " 0 ambiguous barcode drops;\n", " 290816 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4814454 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_3A_1.fq.gz]\n", " Reading data from:\n", " 1SN_3A_1.fq.gz and\n", " 1SN_3A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " 4884978 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -278712 low quality reads; 4606266 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "4884978 total sequences;\n", " 0 ambiguous barcode drops;\n", " 278712 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "4606266 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_4A_1.fq.gz]\n", " Reading data from:\n", " 1SN_4A_1.fq.gz and\n", " 1SN_4A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " 6589742 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -375779 low quality reads; 6213963 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6589742 total sequences;\n", " 0 ambiguous barcode drops;\n", " 375779 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6213963 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_5A_1.fq.gz]\n", " Reading data from:\n", " 1SN_5A_1.fq.gz and\n", " 1SN_5A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " 6001704 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -342355 low quality reads; 5659349 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6001704 total sequences;\n", " 0 ambiguous barcode drops;\n", " 342355 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5659349 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_6A_1.fq.gz]\n", " Reading data from:\n", " 1SN_6A_1.fq.gz and\n", " 1SN_6A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " Processing RAD-Tag 3270000 \r", " Processing RAD-Tag 3280000 \r", " Processing RAD-Tag 3290000 \r", " Processing RAD-Tag 3300000 \r", " Processing RAD-Tag 3310000 \r", " Processing RAD-Tag 3320000 \r", " Processing RAD-Tag 3330000 \r", " Processing RAD-Tag 3340000 \r", " Processing RAD-Tag 3350000 \r", " 6708620 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -383346 low quality reads; 6325274 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6708620 total sequences;\n", " 0 ambiguous barcode drops;\n", " 383346 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6325274 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_7A_1.fq.gz]\n", " Reading data from:\n", " 1SN_7A_1.fq.gz and\n", " 1SN_7A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " 5929188 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -339301 low quality reads; 5589887 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "5929188 total sequences;\n", " 0 ambiguous barcode drops;\n", " 339301 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5589887 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_8A_1.fq.gz]\n", " Reading data from:\n", " 1SN_8A_1.fq.gz and\n", " 1SN_8A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " Processing RAD-Tag 3180000 \r", " Processing RAD-Tag 3190000 \r", " Processing RAD-Tag 3200000 \r", " Processing RAD-Tag 3210000 \r", " Processing RAD-Tag 3220000 \r", " Processing RAD-Tag 3230000 \r", " Processing RAD-Tag 3240000 \r", " Processing RAD-Tag 3250000 \r", " Processing RAD-Tag 3260000 \r", " 6539620 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -372582 low quality reads; 6167038 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6539620 total sequences;\n", " 0 ambiguous barcode drops;\n", " 372582 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "6167038 retained reads.\n", "No barcodes specified, files will not be demultiplexed.\n", "Processing paired-end data.\n", "Using Phred+33 encoding for quality scores.\n", "Found 1 paired input file(s).\n", "Barcode type unspecified, assuming unbarcoded data.\n", "Processing file 1 of 1 [1SN_9A_1.fq.gz]\n", " Reading data from:\n", " 1SN_9A_1.fq.gz and\n", " 1SN_9A_2.fq.gz\n", " Processing RAD-Tag 10000 \r", " Processing RAD-Tag 20000 \r", " Processing RAD-Tag 30000 \r", " Processing RAD-Tag 40000 \r", " Processing RAD-Tag 50000 \r", " Processing RAD-Tag 60000 \r", " Processing RAD-Tag 70000 \r", " Processing RAD-Tag 80000 \r", " Processing RAD-Tag 90000 \r", " Processing RAD-Tag 100000 \r", " Processing RAD-Tag 110000 \r", " Processing RAD-Tag 120000 \r", " Processing RAD-Tag 130000 \r", " Processing RAD-Tag 140000 \r", " Processing RAD-Tag 150000 \r", " Processing RAD-Tag 160000 \r", " Processing RAD-Tag 170000 \r", " Processing RAD-Tag 180000 \r", " Processing RAD-Tag 190000 \r", " Processing RAD-Tag 200000 \r", " Processing RAD-Tag 210000 \r", " Processing RAD-Tag 220000 \r", " Processing RAD-Tag 230000 \r", " Processing RAD-Tag 240000 \r", " Processing RAD-Tag 250000 \r", " Processing RAD-Tag 260000 \r", " Processing RAD-Tag 270000 \r", " Processing RAD-Tag 280000 \r", " Processing RAD-Tag 290000 \r", " Processing RAD-Tag 300000 \r", " Processing RAD-Tag 310000 \r", " Processing RAD-Tag 320000 \r", " Processing RAD-Tag 330000 \r", " Processing RAD-Tag 340000 \r", " Processing RAD-Tag 350000 \r", " Processing RAD-Tag 360000 \r", " Processing RAD-Tag 370000 \r", " Processing RAD-Tag 380000 \r", " Processing RAD-Tag 390000 \r", " Processing RAD-Tag 400000 \r", " Processing RAD-Tag 410000 \r", " Processing RAD-Tag 420000 \r", " Processing RAD-Tag 430000 \r", " Processing RAD-Tag 440000 \r", " Processing RAD-Tag 450000 \r", " Processing RAD-Tag 460000 \r", " Processing RAD-Tag 470000 \r", " Processing RAD-Tag 480000 \r", " Processing RAD-Tag 490000 \r", " Processing RAD-Tag 500000 \r", " Processing RAD-Tag 510000 \r", " Processing RAD-Tag 520000 \r", " Processing RAD-Tag 530000 \r", " Processing RAD-Tag 540000 \r", " Processing RAD-Tag 550000 \r", " Processing RAD-Tag 560000 \r", " Processing RAD-Tag 570000 \r", " Processing RAD-Tag 580000 \r", " Processing RAD-Tag 590000 \r", " Processing RAD-Tag 600000 \r", " Processing RAD-Tag 610000 \r", " Processing RAD-Tag 620000 \r", " Processing RAD-Tag 630000 \r", " Processing RAD-Tag 640000 \r", " Processing RAD-Tag 650000 \r", " Processing RAD-Tag 660000 \r", " Processing RAD-Tag 670000 \r", " Processing RAD-Tag 680000 \r", " Processing RAD-Tag 690000 \r", " Processing RAD-Tag 700000 \r", " Processing RAD-Tag 710000 \r", " Processing RAD-Tag 720000 \r", " Processing RAD-Tag 730000 \r", " Processing RAD-Tag 740000 \r", " Processing RAD-Tag 750000 \r", " Processing RAD-Tag 760000 \r", " Processing RAD-Tag 770000 \r", " Processing RAD-Tag 780000 \r", " Processing RAD-Tag 790000 \r", " Processing RAD-Tag 800000 \r", " Processing RAD-Tag 810000 \r", " Processing RAD-Tag 820000 \r", " Processing RAD-Tag 830000 \r", " Processing RAD-Tag 840000 \r", " Processing RAD-Tag 850000 \r", " Processing RAD-Tag 860000 \r", " Processing RAD-Tag 870000 \r", " Processing RAD-Tag 880000 \r", " Processing RAD-Tag 890000 \r", " Processing RAD-Tag 900000 \r", " Processing RAD-Tag 910000 \r", " Processing RAD-Tag 920000 \r", " Processing RAD-Tag 930000 \r", " Processing RAD-Tag 940000 \r", " Processing RAD-Tag 950000 \r", " Processing RAD-Tag 960000 \r", " Processing RAD-Tag 970000 \r", " Processing RAD-Tag 980000 \r", " Processing RAD-Tag 990000 \r", " Processing RAD-Tag 1000000 \r", " Processing RAD-Tag 1010000 \r", " Processing RAD-Tag 1020000 \r", " Processing RAD-Tag 1030000 \r", " Processing RAD-Tag 1040000 \r", " Processing RAD-Tag 1050000 \r", " Processing RAD-Tag 1060000 \r", " Processing RAD-Tag 1070000 \r", " Processing RAD-Tag 1080000 \r", " Processing RAD-Tag 1090000 \r", " Processing RAD-Tag 1100000 \r", " Processing RAD-Tag 1110000 \r", " Processing RAD-Tag 1120000 \r", " Processing RAD-Tag 1130000 \r", " Processing RAD-Tag 1140000 \r", " Processing RAD-Tag 1150000 \r", " Processing RAD-Tag 1160000 \r", " Processing RAD-Tag 1170000 \r", " Processing RAD-Tag 1180000 \r", " Processing RAD-Tag 1190000 \r", " Processing RAD-Tag 1200000 \r", " Processing RAD-Tag 1210000 \r", " Processing RAD-Tag 1220000 \r", " Processing RAD-Tag 1230000 \r", " Processing RAD-Tag 1240000 \r", " Processing RAD-Tag 1250000 \r", " Processing RAD-Tag 1260000 \r", " Processing RAD-Tag 1270000 \r", " Processing RAD-Tag 1280000 \r", " Processing RAD-Tag 1290000 \r", " Processing RAD-Tag 1300000 \r", " Processing RAD-Tag 1310000 \r", " Processing RAD-Tag 1320000 \r", " Processing RAD-Tag 1330000 \r", " Processing RAD-Tag 1340000 \r", " Processing RAD-Tag 1350000 \r", " Processing RAD-Tag 1360000 \r", " Processing RAD-Tag 1370000 \r", " Processing RAD-Tag 1380000 \r", " Processing RAD-Tag 1390000 \r", " Processing RAD-Tag 1400000 \r", " Processing RAD-Tag 1410000 \r", " Processing RAD-Tag 1420000 \r", " Processing RAD-Tag 1430000 \r", " Processing RAD-Tag 1440000 \r", " Processing RAD-Tag 1450000 \r", " Processing RAD-Tag 1460000 \r", " Processing RAD-Tag 1470000 \r", " Processing RAD-Tag 1480000 \r", " Processing RAD-Tag 1490000 \r", " Processing RAD-Tag 1500000 \r", " Processing RAD-Tag 1510000 \r", " Processing RAD-Tag 1520000 \r", " Processing RAD-Tag 1530000 \r", " Processing RAD-Tag 1540000 \r", " Processing RAD-Tag 1550000 \r", " Processing RAD-Tag 1560000 \r", " Processing RAD-Tag 1570000 \r", " Processing RAD-Tag 1580000 \r", " Processing RAD-Tag 1590000 \r", " Processing RAD-Tag 1600000 \r", " Processing RAD-Tag 1610000 \r", " Processing RAD-Tag 1620000 \r", " Processing RAD-Tag 1630000 \r", " Processing RAD-Tag 1640000 \r", " Processing RAD-Tag 1650000 \r", " Processing RAD-Tag 1660000 \r", " Processing RAD-Tag 1670000 \r", " Processing RAD-Tag 1680000 \r", " Processing RAD-Tag 1690000 \r", " Processing RAD-Tag 1700000 \r", " Processing RAD-Tag 1710000 \r", " Processing RAD-Tag 1720000 \r", " Processing RAD-Tag 1730000 \r", " Processing RAD-Tag 1740000 \r", " Processing RAD-Tag 1750000 \r", " Processing RAD-Tag 1760000 \r", " Processing RAD-Tag 1770000 \r", " Processing RAD-Tag 1780000 \r", " Processing RAD-Tag 1790000 \r", " Processing RAD-Tag 1800000 \r", " Processing RAD-Tag 1810000 \r", " Processing RAD-Tag 1820000 \r", " Processing RAD-Tag 1830000 \r", " Processing RAD-Tag 1840000 \r", " Processing RAD-Tag 1850000 \r", " Processing RAD-Tag 1860000 \r", " Processing RAD-Tag 1870000 \r", " Processing RAD-Tag 1880000 \r", " Processing RAD-Tag 1890000 \r", " Processing RAD-Tag 1900000 \r", " Processing RAD-Tag 1910000 \r", " Processing RAD-Tag 1920000 \r", " Processing RAD-Tag 1930000 \r", " Processing RAD-Tag 1940000 \r", " Processing RAD-Tag 1950000 \r", " Processing RAD-Tag 1960000 \r", " Processing RAD-Tag 1970000 \r", " Processing RAD-Tag 1980000 \r", " Processing RAD-Tag 1990000 \r", " Processing RAD-Tag 2000000 \r", " Processing RAD-Tag 2010000 \r", " Processing RAD-Tag 2020000 \r", " Processing RAD-Tag 2030000 \r", " Processing RAD-Tag 2040000 \r", " Processing RAD-Tag 2050000 \r", " Processing RAD-Tag 2060000 \r", " Processing RAD-Tag 2070000 \r", " Processing RAD-Tag 2080000 \r", " Processing RAD-Tag 2090000 \r", " Processing RAD-Tag 2100000 \r", " Processing RAD-Tag 2110000 \r", " Processing RAD-Tag 2120000 \r", " Processing RAD-Tag 2130000 \r", " Processing RAD-Tag 2140000 \r", " Processing RAD-Tag 2150000 \r", " Processing RAD-Tag 2160000 \r", " Processing RAD-Tag 2170000 \r", " Processing RAD-Tag 2180000 \r", " Processing RAD-Tag 2190000 \r", " Processing RAD-Tag 2200000 \r", " Processing RAD-Tag 2210000 \r", " Processing RAD-Tag 2220000 \r", " Processing RAD-Tag 2230000 \r", " Processing RAD-Tag 2240000 \r", " Processing RAD-Tag 2250000 \r", " Processing RAD-Tag 2260000 \r", " Processing RAD-Tag 2270000 \r", " Processing RAD-Tag 2280000 \r", " Processing RAD-Tag 2290000 \r", " Processing RAD-Tag 2300000 \r", " Processing RAD-Tag 2310000 \r", " Processing RAD-Tag 2320000 \r", " Processing RAD-Tag 2330000 \r", " Processing RAD-Tag 2340000 \r", " Processing RAD-Tag 2350000 \r", " Processing RAD-Tag 2360000 \r", " Processing RAD-Tag 2370000 \r", " Processing RAD-Tag 2380000 \r", " Processing RAD-Tag 2390000 \r", " Processing RAD-Tag 2400000 \r", " Processing RAD-Tag 2410000 \r", " Processing RAD-Tag 2420000 \r", " Processing RAD-Tag 2430000 \r", " Processing RAD-Tag 2440000 \r", " Processing RAD-Tag 2450000 \r", " Processing RAD-Tag 2460000 \r", " Processing RAD-Tag 2470000 \r", " Processing RAD-Tag 2480000 \r", " Processing RAD-Tag 2490000 \r", " Processing RAD-Tag 2500000 \r", " Processing RAD-Tag 2510000 \r", " Processing RAD-Tag 2520000 \r", " Processing RAD-Tag 2530000 \r", " Processing RAD-Tag 2540000 \r", " Processing RAD-Tag 2550000 \r", " Processing RAD-Tag 2560000 \r", " Processing RAD-Tag 2570000 \r", " Processing RAD-Tag 2580000 \r", " Processing RAD-Tag 2590000 \r", " Processing RAD-Tag 2600000 \r", " Processing RAD-Tag 2610000 \r", " Processing RAD-Tag 2620000 \r", " Processing RAD-Tag 2630000 \r", " Processing RAD-Tag 2640000 \r", " Processing RAD-Tag 2650000 \r", " Processing RAD-Tag 2660000 \r", " Processing RAD-Tag 2670000 \r", " Processing RAD-Tag 2680000 \r", " Processing RAD-Tag 2690000 \r", " Processing RAD-Tag 2700000 \r", " Processing RAD-Tag 2710000 \r", " Processing RAD-Tag 2720000 \r", " Processing RAD-Tag 2730000 \r", " Processing RAD-Tag 2740000 \r", " Processing RAD-Tag 2750000 \r", " Processing RAD-Tag 2760000 \r", " Processing RAD-Tag 2770000 \r", " Processing RAD-Tag 2780000 \r", " Processing RAD-Tag 2790000 \r", " Processing RAD-Tag 2800000 \r", " Processing RAD-Tag 2810000 \r", " Processing RAD-Tag 2820000 \r", " Processing RAD-Tag 2830000 \r", " Processing RAD-Tag 2840000 \r", " Processing RAD-Tag 2850000 \r", " Processing RAD-Tag 2860000 \r", " Processing RAD-Tag 2870000 \r", " Processing RAD-Tag 2880000 \r", " Processing RAD-Tag 2890000 \r", " Processing RAD-Tag 2900000 \r", " Processing RAD-Tag 2910000 \r", " Processing RAD-Tag 2920000 \r", " Processing RAD-Tag 2930000 \r", " Processing RAD-Tag 2940000 \r", " Processing RAD-Tag 2950000 \r", " Processing RAD-Tag 2960000 \r", " Processing RAD-Tag 2970000 \r", " Processing RAD-Tag 2980000 \r", " Processing RAD-Tag 2990000 \r", " Processing RAD-Tag 3000000 \r", " Processing RAD-Tag 3010000 \r", " Processing RAD-Tag 3020000 \r", " Processing RAD-Tag 3030000 \r", " Processing RAD-Tag 3040000 \r", " Processing RAD-Tag 3050000 \r", " Processing RAD-Tag 3060000 \r", " Processing RAD-Tag 3070000 \r", " Processing RAD-Tag 3080000 \r", " Processing RAD-Tag 3090000 \r", " Processing RAD-Tag 3100000 \r", " Processing RAD-Tag 3110000 \r", " Processing RAD-Tag 3120000 \r", " Processing RAD-Tag 3130000 \r", " Processing RAD-Tag 3140000 \r", " Processing RAD-Tag 3150000 \r", " Processing RAD-Tag 3160000 \r", " Processing RAD-Tag 3170000 \r", " 6354410 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -361967 low quality reads; 5992443 retained reads.\n", "Closing files, flushing buffers...\n", "Outputing details to log: '/Volumes/owl/temp/process_radtags.log'\n", "\n", "6354410 total sequences;\n", " 0 ambiguous barcode drops;\n", " 361967 low quality read drops;\n", " 0 ambiguous RAD-Tag drops;\n", "5992443 retained reads.\n" ] } ], "source": [ "%%bash\n", "list1=( 1HL_10A_1.fq.gz 1HL_11A_1.fq.gz 1HL_12A_1.fq.gz 1HL_13A_1.fq.gz 1HL_14A_1.fq.gz 1HL_15A_1.fq.gz 1HL_16A_1.fq.gz 1HL_17A_1.fq.gz 1HL_19A_1.fq.gz 1HL_1A_1.fq.gz 1HL_20A_1.fq.gz 1HL_21A_1.fq.gz 1HL_22A_1.fq.gz 1HL_23A_1.fq.gz 1HL_24A_1.fq.gz 1HL_25A_1.fq.gz 1HL_26A_1.fq.gz 1HL_27A_1.fq.gz 1HL_28A_1.fq.gz 1HL_29A_1.fq.gz 1HL_2A_1.fq.gz 1HL_31A_1.fq.gz 1HL_33A_1.fq.gz 1HL_34A_1.fq.gz 1HL_35A_1.fq.gz 1HL_3A_1.fq.gz 1HL_4A_1.fq.gz 1HL_5A_1.fq.gz 1HL_6A_1.fq.gz 1HL_7A_1.fq.gz 1HL_8A_1.fq.gz 1HL_9A_1.fq.gz 1NF_10A_1.fq.gz 1NF_11A_1.fq.gz 1NF_12A_1.fq.gz 1NF_13A_1.fq.gz 1NF_14A_1.fq.gz 1NF_15A_1.fq.gz 1NF_16A_1.fq.gz 1NF_17A_1.fq.gz 1NF_18A_1.fq.gz 1NF_19A_1.fq.gz 1NF_1A_1.fq.gz 1NF_20A_1.fq.gz 1NF_21A_1.fq.gz 1NF_22A_1.fq.gz 1NF_23A_1.fq.gz 1NF_24A_1.fq.gz 1NF_25A_1.fq.gz 1NF_26A_1.fq.gz 1NF_27A_1.fq.gz 1NF_28A_1.fq.gz 1NF_29A_1.fq.gz 1NF_2A_1.fq.gz 1NF_30A_1.fq.gz 1NF_31A_1.fq.gz 1NF_32A_1.fq.gz 1NF_33A_1.fq.gz 1NF_4A_1.fq.gz 1NF_5A_1.fq.gz 1NF_6A_1.fq.gz 1NF_7A_1.fq.gz 1NF_8A_1.fq.gz 1NF_9A_1.fq.gz 1SN_10A_1.fq.gz 1SN_11A_1.fq.gz 1SN_12A_1.fq.gz 1SN_13A_1.fq.gz 1SN_14A_1.fq.gz 1SN_15A_1.fq.gz 1SN_16A_1.fq.gz 1SN_17A_1.fq.gz 1SN_18A_1.fq.gz 1SN_19A_1.fq.gz 1SN_1A_1.fq.gz 1SN_20A_1.fq.gz 1SN_21A_1.fq.gz 1SN_22A_1.fq.gz 1SN_23A_1.fq.gz 1SN_24A_1.fq.gz 1SN_25A_1.fq.gz 1SN_26A_1.fq.gz 1SN_27A_1.fq.gz 1SN_28A_1.fq.gz 1SN_29A_1.fq.gz 1SN_2A_1.fq.gz 1SN_30A_1.fq.gz 1SN_31A_1.fq.gz 1SN_32A_1.fq.gz 1SN_3A_1.fq.gz 1SN_4A_1.fq.gz 1SN_5A_1.fq.gz 1SN_6A_1.fq.gz 1SN_7A_1.fq.gz 1SN_8A_1.fq.gz 1SN_9A_1.fq.gz )\n", "list2=( 1HL_10A_2.fq.gz 1HL_11A_2.fq.gz 1HL_12A_2.fq.gz 1HL_13A_2.fq.gz 1HL_14A_2.fq.gz 1HL_15A_2.fq.gz 1HL_16A_2.fq.gz 1HL_17A_2.fq.gz 1HL_19A_2.fq.gz 1HL_1A_2.fq.gz 1HL_20A_2.fq.gz 1HL_21A_2.fq.gz 1HL_22A_2.fq.gz 1HL_23A_2.fq.gz 1HL_24A_2.fq.gz 1HL_25A_2.fq.gz 1HL_26A_2.fq.gz 1HL_27A_2.fq.gz 1HL_28A_2.fq.gz 1HL_29A_2.fq.gz 1HL_2A_2.fq.gz 1HL_31A_2.fq.gz 1HL_33A_2.fq.gz 1HL_34A_2.fq.gz 1HL_35A_2.fq.gz 1HL_3A_2.fq.gz 1HL_4A_2.fq.gz 1HL_5A_2.fq.gz 1HL_6A_2.fq.gz 1HL_7A_2.fq.gz 1HL_8A_2.fq.gz 1HL_9A_2.fq.gz 1NF_10A_2.fq.gz 1NF_11A_2.fq.gz 1NF_12A_2.fq.gz 1NF_13A_2.fq.gz 1NF_14A_2.fq.gz 1NF_15A_2.fq.gz 1NF_16A_2.fq.gz 1NF_17A_2.fq.gz 1NF_18A_2.fq.gz 1NF_19A_2.fq.gz 1NF_1A_2.fq.gz 1NF_20A_2.fq.gz 1NF_21A_2.fq.gz 1NF_22A_2.fq.gz 1NF_23A_2.fq.gz 1NF_24A_2.fq.gz 1NF_25A_2.fq.gz 1NF_26A_2.fq.gz 1NF_27A_2.fq.gz 1NF_28A_2.fq.gz 1NF_29A_2.fq.gz 1NF_2A_2.fq.gz 1NF_30A_2.fq.gz 1NF_31A_2.fq.gz 1NF_32A_2.fq.gz 1NF_33A_2.fq.gz 1NF_4A_2.fq.gz 1NF_5A_2.fq.gz 1NF_6A_2.fq.gz 1NF_7A_2.fq.gz 1NF_8A_2.fq.gz 1NF_9A_2.fq.gz 1SN_10A_2.fq.gz 1SN_11A_2.fq.gz 1SN_12A_2.fq.gz 1SN_13A_2.fq.gz 1SN_14A_2.fq.gz 1SN_15A_2.fq.gz 1SN_16A_2.fq.gz 1SN_17A_2.fq.gz 1SN_18A_2.fq.gz 1SN_19A_2.fq.gz 1SN_1A_2.fq.gz 1SN_20A_2.fq.gz 1SN_21A_2.fq.gz 1SN_22A_2.fq.gz 1SN_23A_2.fq.gz 1SN_24A_2.fq.gz 1SN_25A_2.fq.gz 1SN_26A_2.fq.gz 1SN_27A_2.fq.gz 1SN_28A_2.fq.gz 1SN_29A_2.fq.gz 1SN_2A_2.fq.gz 1SN_30A_2.fq.gz 1SN_31A_2.fq.gz 1SN_32A_2.fq.gz 1SN_3A_2.fq.gz 1SN_4A_2.fq.gz 1SN_5A_2.fq.gz 1SN_6A_2.fq.gz 1SN_7A_2.fq.gz 1SN_8A_2.fq.gz 1SN_9A_2.fq.gz )\n", "for pair in \"${!list1[@]}\"; do\n", " i=${list1[$pair]}\n", " j=${list2[$pair]}\n", " /usr/local/bioinformatics/stacks-1.37/process_radtags -1 $i -2 $j \\\n", "-o /Volumes/owl/temp/ -e apeKI -c -q -i gzfastq\n", "done" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Concatenate output files into single FASTQ file." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Create four lists - each of the four output files generated per individual" ] }, { "cell_type": "code", "execution_count": 28, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/owl/temp\n" ] } ], "source": [ "cd /Volumes/owl/temp/" ] }, { "cell_type": "code", "execution_count": 29, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_1.1.fq.gz 1HL_11A_1.1.fq.gz 1HL_12A_1.1.fq.gz 1HL_13A_1.1.fq.gz 1HL_14A_1.1.fq.gz 1HL_15A_1.1.fq.gz 1HL_16A_1.1.fq.gz 1HL_17A_1.1.fq.gz 1HL_19A_1.1.fq.gz 1HL_1A_1.1.fq.gz 1HL_20A_1.1.fq.gz 1HL_21A_1.1.fq.gz 1HL_22A_1.1.fq.gz 1HL_23A_1.1.fq.gz 1HL_24A_1.1.fq.gz 1HL_25A_1.1.fq.gz 1HL_26A_1.1.fq.gz 1HL_27A_1.1.fq.gz 1HL_28A_1.1.fq.gz 1HL_29A_1.1.fq.gz 1HL_2A_1.1.fq.gz 1HL_31A_1.1.fq.gz 1HL_33A_1.1.fq.gz 1HL_34A_1.1.fq.gz 1HL_35A_1.1.fq.gz 1HL_3A_1.1.fq.gz 1HL_4A_1.1.fq.gz 1HL_5A_1.1.fq.gz 1HL_6A_1.1.fq.gz 1HL_7A_1.1.fq.gz 1HL_8A_1.1.fq.gz 1HL_9A_1.1.fq.gz 1NF_10A_1.1.fq.gz 1NF_11A_1.1.fq.gz 1NF_12A_1.1.fq.gz 1NF_13A_1.1.fq.gz 1NF_14A_1.1.fq.gz 1NF_15A_1.1.fq.gz 1NF_16A_1.1.fq.gz 1NF_17A_1.1.fq.gz 1NF_18A_1.1.fq.gz 1NF_19A_1.1.fq.gz 1NF_1A_1.1.fq.gz 1NF_20A_1.1.fq.gz 1NF_21A_1.1.fq.gz 1NF_22A_1.1.fq.gz 1NF_23A_1.1.fq.gz 1NF_24A_1.1.fq.gz 1NF_25A_1.1.fq.gz 1NF_26A_1.1.fq.gz 1NF_27A_1.1.fq.gz 1NF_28A_1.1.fq.gz 1NF_29A_1.1.fq.gz 1NF_2A_1.1.fq.gz 1NF_30A_1.1.fq.gz 1NF_31A_1.1.fq.gz 1NF_32A_1.1.fq.gz 1NF_33A_1.1.fq.gz 1NF_4A_1.1.fq.gz 1NF_5A_1.1.fq.gz 1NF_6A_1.1.fq.gz 1NF_7A_1.1.fq.gz 1NF_8A_1.1.fq.gz 1NF_9A_1.1.fq.gz 1SN_10A_1.1.fq.gz 1SN_11A_1.1.fq.gz 1SN_12A_1.1.fq.gz 1SN_13A_1.1.fq.gz 1SN_14A_1.1.fq.gz 1SN_15A_1.1.fq.gz 1SN_16A_1.1.fq.gz 1SN_17A_1.1.fq.gz 1SN_18A_1.1.fq.gz 1SN_19A_1.1.fq.gz 1SN_1A_1.1.fq.gz 1SN_20A_1.1.fq.gz 1SN_21A_1.1.fq.gz 1SN_22A_1.1.fq.gz 1SN_23A_1.1.fq.gz 1SN_24A_1.1.fq.gz 1SN_25A_1.1.fq.gz 1SN_26A_1.1.fq.gz 1SN_27A_1.1.fq.gz 1SN_28A_1.1.fq.gz 1SN_29A_1.1.fq.gz 1SN_2A_1.1.fq.gz 1SN_30A_1.1.fq.gz 1SN_31A_1.1.fq.gz 1SN_32A_1.1.fq.gz 1SN_3A_1.1.fq.gz 1SN_4A_1.1.fq.gz 1SN_5A_1.1.fq.gz 1SN_6A_1.1.fq.gz 1SN_7A_1.1.fq.gz 1SN_8A_1.1.fq.gz 1SN_9A_1.1.fq.gz\n" ] } ], "source": [ "%%bash\n", "echo *A_1.1.fq.gz" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_1.rem.1.fq.gz 1HL_11A_1.rem.1.fq.gz 1HL_12A_1.rem.1.fq.gz 1HL_13A_1.rem.1.fq.gz 1HL_14A_1.rem.1.fq.gz 1HL_15A_1.rem.1.fq.gz 1HL_16A_1.rem.1.fq.gz 1HL_17A_1.rem.1.fq.gz 1HL_19A_1.rem.1.fq.gz 1HL_1A_1.rem.1.fq.gz 1HL_20A_1.rem.1.fq.gz 1HL_21A_1.rem.1.fq.gz 1HL_22A_1.rem.1.fq.gz 1HL_23A_1.rem.1.fq.gz 1HL_24A_1.rem.1.fq.gz 1HL_25A_1.rem.1.fq.gz 1HL_26A_1.rem.1.fq.gz 1HL_27A_1.rem.1.fq.gz 1HL_28A_1.rem.1.fq.gz 1HL_29A_1.rem.1.fq.gz 1HL_2A_1.rem.1.fq.gz 1HL_31A_1.rem.1.fq.gz 1HL_33A_1.rem.1.fq.gz 1HL_34A_1.rem.1.fq.gz 1HL_35A_1.rem.1.fq.gz 1HL_3A_1.rem.1.fq.gz 1HL_4A_1.rem.1.fq.gz 1HL_5A_1.rem.1.fq.gz 1HL_6A_1.rem.1.fq.gz 1HL_7A_1.rem.1.fq.gz 1HL_8A_1.rem.1.fq.gz 1HL_9A_1.rem.1.fq.gz 1NF_10A_1.rem.1.fq.gz 1NF_11A_1.rem.1.fq.gz 1NF_12A_1.rem.1.fq.gz 1NF_13A_1.rem.1.fq.gz 1NF_14A_1.rem.1.fq.gz 1NF_15A_1.rem.1.fq.gz 1NF_16A_1.rem.1.fq.gz 1NF_17A_1.rem.1.fq.gz 1NF_18A_1.rem.1.fq.gz 1NF_19A_1.rem.1.fq.gz 1NF_1A_1.rem.1.fq.gz 1NF_20A_1.rem.1.fq.gz 1NF_21A_1.rem.1.fq.gz 1NF_22A_1.rem.1.fq.gz 1NF_23A_1.rem.1.fq.gz 1NF_24A_1.rem.1.fq.gz 1NF_25A_1.rem.1.fq.gz 1NF_26A_1.rem.1.fq.gz 1NF_27A_1.rem.1.fq.gz 1NF_28A_1.rem.1.fq.gz 1NF_29A_1.rem.1.fq.gz 1NF_2A_1.rem.1.fq.gz 1NF_30A_1.rem.1.fq.gz 1NF_31A_1.rem.1.fq.gz 1NF_32A_1.rem.1.fq.gz 1NF_33A_1.rem.1.fq.gz 1NF_4A_1.rem.1.fq.gz 1NF_5A_1.rem.1.fq.gz 1NF_6A_1.rem.1.fq.gz 1NF_7A_1.rem.1.fq.gz 1NF_8A_1.rem.1.fq.gz 1NF_9A_1.rem.1.fq.gz 1SN_10A_1.rem.1.fq.gz 1SN_11A_1.rem.1.fq.gz 1SN_12A_1.rem.1.fq.gz 1SN_13A_1.rem.1.fq.gz 1SN_14A_1.rem.1.fq.gz 1SN_15A_1.rem.1.fq.gz 1SN_16A_1.rem.1.fq.gz 1SN_17A_1.rem.1.fq.gz 1SN_18A_1.rem.1.fq.gz 1SN_19A_1.rem.1.fq.gz 1SN_1A_1.rem.1.fq.gz 1SN_20A_1.rem.1.fq.gz 1SN_21A_1.rem.1.fq.gz 1SN_22A_1.rem.1.fq.gz 1SN_23A_1.rem.1.fq.gz 1SN_24A_1.rem.1.fq.gz 1SN_25A_1.rem.1.fq.gz 1SN_26A_1.rem.1.fq.gz 1SN_27A_1.rem.1.fq.gz 1SN_28A_1.rem.1.fq.gz 1SN_29A_1.rem.1.fq.gz 1SN_2A_1.rem.1.fq.gz 1SN_30A_1.rem.1.fq.gz 1SN_31A_1.rem.1.fq.gz 1SN_32A_1.rem.1.fq.gz 1SN_3A_1.rem.1.fq.gz 1SN_4A_1.rem.1.fq.gz 1SN_5A_1.rem.1.fq.gz 1SN_6A_1.rem.1.fq.gz 1SN_7A_1.rem.1.fq.gz 1SN_8A_1.rem.1.fq.gz 1SN_9A_1.rem.1.fq.gz\n" ] } ], "source": [ "%%bash\n", "echo *A_1.rem.1.fq.gz" ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_2.2.fq.gz 1HL_11A_2.2.fq.gz 1HL_12A_2.2.fq.gz 1HL_13A_2.2.fq.gz 1HL_14A_2.2.fq.gz 1HL_15A_2.2.fq.gz 1HL_16A_2.2.fq.gz 1HL_17A_2.2.fq.gz 1HL_19A_2.2.fq.gz 1HL_1A_2.2.fq.gz 1HL_20A_2.2.fq.gz 1HL_21A_2.2.fq.gz 1HL_22A_2.2.fq.gz 1HL_23A_2.2.fq.gz 1HL_24A_2.2.fq.gz 1HL_25A_2.2.fq.gz 1HL_26A_2.2.fq.gz 1HL_27A_2.2.fq.gz 1HL_28A_2.2.fq.gz 1HL_29A_2.2.fq.gz 1HL_2A_2.2.fq.gz 1HL_31A_2.2.fq.gz 1HL_33A_2.2.fq.gz 1HL_34A_2.2.fq.gz 1HL_35A_2.2.fq.gz 1HL_3A_2.2.fq.gz 1HL_4A_2.2.fq.gz 1HL_5A_2.2.fq.gz 1HL_6A_2.2.fq.gz 1HL_7A_2.2.fq.gz 1HL_8A_2.2.fq.gz 1HL_9A_2.2.fq.gz 1NF_10A_2.2.fq.gz 1NF_11A_2.2.fq.gz 1NF_12A_2.2.fq.gz 1NF_13A_2.2.fq.gz 1NF_14A_2.2.fq.gz 1NF_15A_2.2.fq.gz 1NF_16A_2.2.fq.gz 1NF_17A_2.2.fq.gz 1NF_18A_2.2.fq.gz 1NF_19A_2.2.fq.gz 1NF_1A_2.2.fq.gz 1NF_20A_2.2.fq.gz 1NF_21A_2.2.fq.gz 1NF_22A_2.2.fq.gz 1NF_23A_2.2.fq.gz 1NF_24A_2.2.fq.gz 1NF_25A_2.2.fq.gz 1NF_26A_2.2.fq.gz 1NF_27A_2.2.fq.gz 1NF_28A_2.2.fq.gz 1NF_29A_2.2.fq.gz 1NF_2A_2.2.fq.gz 1NF_30A_2.2.fq.gz 1NF_31A_2.2.fq.gz 1NF_32A_2.2.fq.gz 1NF_33A_2.2.fq.gz 1NF_4A_2.2.fq.gz 1NF_5A_2.2.fq.gz 1NF_6A_2.2.fq.gz 1NF_7A_2.2.fq.gz 1NF_8A_2.2.fq.gz 1NF_9A_2.2.fq.gz 1SN_10A_2.2.fq.gz 1SN_11A_2.2.fq.gz 1SN_12A_2.2.fq.gz 1SN_13A_2.2.fq.gz 1SN_14A_2.2.fq.gz 1SN_15A_2.2.fq.gz 1SN_16A_2.2.fq.gz 1SN_17A_2.2.fq.gz 1SN_18A_2.2.fq.gz 1SN_19A_2.2.fq.gz 1SN_1A_2.2.fq.gz 1SN_20A_2.2.fq.gz 1SN_21A_2.2.fq.gz 1SN_22A_2.2.fq.gz 1SN_23A_2.2.fq.gz 1SN_24A_2.2.fq.gz 1SN_25A_2.2.fq.gz 1SN_26A_2.2.fq.gz 1SN_27A_2.2.fq.gz 1SN_28A_2.2.fq.gz 1SN_29A_2.2.fq.gz 1SN_2A_2.2.fq.gz 1SN_30A_2.2.fq.gz 1SN_31A_2.2.fq.gz 1SN_32A_2.2.fq.gz 1SN_3A_2.2.fq.gz 1SN_4A_2.2.fq.gz 1SN_5A_2.2.fq.gz 1SN_6A_2.2.fq.gz 1SN_7A_2.2.fq.gz 1SN_8A_2.2.fq.gz 1SN_9A_2.2.fq.gz\n" ] } ], "source": [ "%%bash\n", "echo *A_2.2.fq.gz" ] }, { "cell_type": "code", "execution_count": 32, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A_2.rem.2.fq.gz 1HL_11A_2.rem.2.fq.gz 1HL_12A_2.rem.2.fq.gz 1HL_13A_2.rem.2.fq.gz 1HL_14A_2.rem.2.fq.gz 1HL_15A_2.rem.2.fq.gz 1HL_16A_2.rem.2.fq.gz 1HL_17A_2.rem.2.fq.gz 1HL_19A_2.rem.2.fq.gz 1HL_1A_2.rem.2.fq.gz 1HL_20A_2.rem.2.fq.gz 1HL_21A_2.rem.2.fq.gz 1HL_22A_2.rem.2.fq.gz 1HL_23A_2.rem.2.fq.gz 1HL_24A_2.rem.2.fq.gz 1HL_25A_2.rem.2.fq.gz 1HL_26A_2.rem.2.fq.gz 1HL_27A_2.rem.2.fq.gz 1HL_28A_2.rem.2.fq.gz 1HL_29A_2.rem.2.fq.gz 1HL_2A_2.rem.2.fq.gz 1HL_31A_2.rem.2.fq.gz 1HL_33A_2.rem.2.fq.gz 1HL_34A_2.rem.2.fq.gz 1HL_35A_2.rem.2.fq.gz 1HL_3A_2.rem.2.fq.gz 1HL_4A_2.rem.2.fq.gz 1HL_5A_2.rem.2.fq.gz 1HL_6A_2.rem.2.fq.gz 1HL_7A_2.rem.2.fq.gz 1HL_8A_2.rem.2.fq.gz 1HL_9A_2.rem.2.fq.gz 1NF_10A_2.rem.2.fq.gz 1NF_11A_2.rem.2.fq.gz 1NF_12A_2.rem.2.fq.gz 1NF_13A_2.rem.2.fq.gz 1NF_14A_2.rem.2.fq.gz 1NF_15A_2.rem.2.fq.gz 1NF_16A_2.rem.2.fq.gz 1NF_17A_2.rem.2.fq.gz 1NF_18A_2.rem.2.fq.gz 1NF_19A_2.rem.2.fq.gz 1NF_1A_2.rem.2.fq.gz 1NF_20A_2.rem.2.fq.gz 1NF_21A_2.rem.2.fq.gz 1NF_22A_2.rem.2.fq.gz 1NF_23A_2.rem.2.fq.gz 1NF_24A_2.rem.2.fq.gz 1NF_25A_2.rem.2.fq.gz 1NF_26A_2.rem.2.fq.gz 1NF_27A_2.rem.2.fq.gz 1NF_28A_2.rem.2.fq.gz 1NF_29A_2.rem.2.fq.gz 1NF_2A_2.rem.2.fq.gz 1NF_30A_2.rem.2.fq.gz 1NF_31A_2.rem.2.fq.gz 1NF_32A_2.rem.2.fq.gz 1NF_33A_2.rem.2.fq.gz 1NF_4A_2.rem.2.fq.gz 1NF_5A_2.rem.2.fq.gz 1NF_6A_2.rem.2.fq.gz 1NF_7A_2.rem.2.fq.gz 1NF_8A_2.rem.2.fq.gz 1NF_9A_2.rem.2.fq.gz 1SN_10A_2.rem.2.fq.gz 1SN_11A_2.rem.2.fq.gz 1SN_12A_2.rem.2.fq.gz 1SN_13A_2.rem.2.fq.gz 1SN_14A_2.rem.2.fq.gz 1SN_15A_2.rem.2.fq.gz 1SN_16A_2.rem.2.fq.gz 1SN_17A_2.rem.2.fq.gz 1SN_18A_2.rem.2.fq.gz 1SN_19A_2.rem.2.fq.gz 1SN_1A_2.rem.2.fq.gz 1SN_20A_2.rem.2.fq.gz 1SN_21A_2.rem.2.fq.gz 1SN_22A_2.rem.2.fq.gz 1SN_23A_2.rem.2.fq.gz 1SN_24A_2.rem.2.fq.gz 1SN_25A_2.rem.2.fq.gz 1SN_26A_2.rem.2.fq.gz 1SN_27A_2.rem.2.fq.gz 1SN_28A_2.rem.2.fq.gz 1SN_29A_2.rem.2.fq.gz 1SN_2A_2.rem.2.fq.gz 1SN_30A_2.rem.2.fq.gz 1SN_31A_2.rem.2.fq.gz 1SN_32A_2.rem.2.fq.gz 1SN_3A_2.rem.2.fq.gz 1SN_4A_2.rem.2.fq.gz 1SN_5A_2.rem.2.fq.gz 1SN_6A_2.rem.2.fq.gz 1SN_7A_2.rem.2.fq.gz 1SN_8A_2.rem.2.fq.gz 1SN_9A_2.rem.2.fq.gz\n" ] } ], "source": [ "%%bash\n", "echo *A_2.rem.2.fq.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Store the four lists generated above as variables\n", "##### Loop through each component of each list as arrays and store the value from each list in independent variables\n", "##### Concatenate the four corresponding files into a single FASTQ GZIP file\n", "##### Use parameter expansion to adjust name of output file by replacing \"_1.1\" from list1 filenames with nothing (i.e. delete \"_1.1\")." ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "list1=( 1HL_10A_1.1.fq.gz 1HL_11A_1.1.fq.gz 1HL_12A_1.1.fq.gz 1HL_13A_1.1.fq.gz 1HL_14A_1.1.fq.gz 1HL_15A_1.1.fq.gz 1HL_16A_1.1.fq.gz 1HL_17A_1.1.fq.gz 1HL_19A_1.1.fq.gz 1HL_1A_1.1.fq.gz 1HL_20A_1.1.fq.gz 1HL_21A_1.1.fq.gz 1HL_22A_1.1.fq.gz 1HL_23A_1.1.fq.gz 1HL_24A_1.1.fq.gz 1HL_25A_1.1.fq.gz 1HL_26A_1.1.fq.gz 1HL_27A_1.1.fq.gz 1HL_28A_1.1.fq.gz 1HL_29A_1.1.fq.gz 1HL_2A_1.1.fq.gz 1HL_31A_1.1.fq.gz 1HL_33A_1.1.fq.gz 1HL_34A_1.1.fq.gz 1HL_35A_1.1.fq.gz 1HL_3A_1.1.fq.gz 1HL_4A_1.1.fq.gz 1HL_5A_1.1.fq.gz 1HL_6A_1.1.fq.gz 1HL_7A_1.1.fq.gz 1HL_8A_1.1.fq.gz 1HL_9A_1.1.fq.gz 1NF_10A_1.1.fq.gz 1NF_11A_1.1.fq.gz 1NF_12A_1.1.fq.gz 1NF_13A_1.1.fq.gz 1NF_14A_1.1.fq.gz 1NF_15A_1.1.fq.gz 1NF_16A_1.1.fq.gz 1NF_17A_1.1.fq.gz 1NF_18A_1.1.fq.gz 1NF_19A_1.1.fq.gz 1NF_1A_1.1.fq.gz 1NF_20A_1.1.fq.gz 1NF_21A_1.1.fq.gz 1NF_22A_1.1.fq.gz 1NF_23A_1.1.fq.gz 1NF_24A_1.1.fq.gz 1NF_25A_1.1.fq.gz 1NF_26A_1.1.fq.gz 1NF_27A_1.1.fq.gz 1NF_28A_1.1.fq.gz 1NF_29A_1.1.fq.gz 1NF_2A_1.1.fq.gz 1NF_30A_1.1.fq.gz 1NF_31A_1.1.fq.gz 1NF_32A_1.1.fq.gz 1NF_33A_1.1.fq.gz 1NF_4A_1.1.fq.gz 1NF_5A_1.1.fq.gz 1NF_6A_1.1.fq.gz 1NF_7A_1.1.fq.gz 1NF_8A_1.1.fq.gz 1NF_9A_1.1.fq.gz 1SN_10A_1.1.fq.gz 1SN_11A_1.1.fq.gz 1SN_12A_1.1.fq.gz 1SN_13A_1.1.fq.gz 1SN_14A_1.1.fq.gz 1SN_15A_1.1.fq.gz 1SN_16A_1.1.fq.gz 1SN_17A_1.1.fq.gz 1SN_18A_1.1.fq.gz 1SN_19A_1.1.fq.gz 1SN_1A_1.1.fq.gz 1SN_20A_1.1.fq.gz 1SN_21A_1.1.fq.gz 1SN_22A_1.1.fq.gz 1SN_23A_1.1.fq.gz 1SN_24A_1.1.fq.gz 1SN_25A_1.1.fq.gz 1SN_26A_1.1.fq.gz 1SN_27A_1.1.fq.gz 1SN_28A_1.1.fq.gz 1SN_29A_1.1.fq.gz 1SN_2A_1.1.fq.gz 1SN_30A_1.1.fq.gz 1SN_31A_1.1.fq.gz 1SN_32A_1.1.fq.gz 1SN_3A_1.1.fq.gz 1SN_4A_1.1.fq.gz 1SN_5A_1.1.fq.gz 1SN_6A_1.1.fq.gz 1SN_7A_1.1.fq.gz 1SN_8A_1.1.fq.gz 1SN_9A_1.1.fq.gz )\n", "list2=( 1HL_10A_1.rem.1.fq.gz 1HL_11A_1.rem.1.fq.gz 1HL_12A_1.rem.1.fq.gz 1HL_13A_1.rem.1.fq.gz 1HL_14A_1.rem.1.fq.gz 1HL_15A_1.rem.1.fq.gz 1HL_16A_1.rem.1.fq.gz 1HL_17A_1.rem.1.fq.gz 1HL_19A_1.rem.1.fq.gz 1HL_1A_1.rem.1.fq.gz 1HL_20A_1.rem.1.fq.gz 1HL_21A_1.rem.1.fq.gz 1HL_22A_1.rem.1.fq.gz 1HL_23A_1.rem.1.fq.gz 1HL_24A_1.rem.1.fq.gz 1HL_25A_1.rem.1.fq.gz 1HL_26A_1.rem.1.fq.gz 1HL_27A_1.rem.1.fq.gz 1HL_28A_1.rem.1.fq.gz 1HL_29A_1.rem.1.fq.gz 1HL_2A_1.rem.1.fq.gz 1HL_31A_1.rem.1.fq.gz 1HL_33A_1.rem.1.fq.gz 1HL_34A_1.rem.1.fq.gz 1HL_35A_1.rem.1.fq.gz 1HL_3A_1.rem.1.fq.gz 1HL_4A_1.rem.1.fq.gz 1HL_5A_1.rem.1.fq.gz 1HL_6A_1.rem.1.fq.gz 1HL_7A_1.rem.1.fq.gz 1HL_8A_1.rem.1.fq.gz 1HL_9A_1.rem.1.fq.gz 1NF_10A_1.rem.1.fq.gz 1NF_11A_1.rem.1.fq.gz 1NF_12A_1.rem.1.fq.gz 1NF_13A_1.rem.1.fq.gz 1NF_14A_1.rem.1.fq.gz 1NF_15A_1.rem.1.fq.gz 1NF_16A_1.rem.1.fq.gz 1NF_17A_1.rem.1.fq.gz 1NF_18A_1.rem.1.fq.gz 1NF_19A_1.rem.1.fq.gz 1NF_1A_1.rem.1.fq.gz 1NF_20A_1.rem.1.fq.gz 1NF_21A_1.rem.1.fq.gz 1NF_22A_1.rem.1.fq.gz 1NF_23A_1.rem.1.fq.gz 1NF_24A_1.rem.1.fq.gz 1NF_25A_1.rem.1.fq.gz 1NF_26A_1.rem.1.fq.gz 1NF_27A_1.rem.1.fq.gz 1NF_28A_1.rem.1.fq.gz 1NF_29A_1.rem.1.fq.gz 1NF_2A_1.rem.1.fq.gz 1NF_30A_1.rem.1.fq.gz 1NF_31A_1.rem.1.fq.gz 1NF_32A_1.rem.1.fq.gz 1NF_33A_1.rem.1.fq.gz 1NF_4A_1.rem.1.fq.gz 1NF_5A_1.rem.1.fq.gz 1NF_6A_1.rem.1.fq.gz 1NF_7A_1.rem.1.fq.gz 1NF_8A_1.rem.1.fq.gz 1NF_9A_1.rem.1.fq.gz 1SN_10A_1.rem.1.fq.gz 1SN_11A_1.rem.1.fq.gz 1SN_12A_1.rem.1.fq.gz 1SN_13A_1.rem.1.fq.gz 1SN_14A_1.rem.1.fq.gz 1SN_15A_1.rem.1.fq.gz 1SN_16A_1.rem.1.fq.gz 1SN_17A_1.rem.1.fq.gz 1SN_18A_1.rem.1.fq.gz 1SN_19A_1.rem.1.fq.gz 1SN_1A_1.rem.1.fq.gz 1SN_20A_1.rem.1.fq.gz 1SN_21A_1.rem.1.fq.gz 1SN_22A_1.rem.1.fq.gz 1SN_23A_1.rem.1.fq.gz 1SN_24A_1.rem.1.fq.gz 1SN_25A_1.rem.1.fq.gz 1SN_26A_1.rem.1.fq.gz 1SN_27A_1.rem.1.fq.gz 1SN_28A_1.rem.1.fq.gz 1SN_29A_1.rem.1.fq.gz 1SN_2A_1.rem.1.fq.gz 1SN_30A_1.rem.1.fq.gz 1SN_31A_1.rem.1.fq.gz 1SN_32A_1.rem.1.fq.gz 1SN_3A_1.rem.1.fq.gz 1SN_4A_1.rem.1.fq.gz 1SN_5A_1.rem.1.fq.gz 1SN_6A_1.rem.1.fq.gz 1SN_7A_1.rem.1.fq.gz 1SN_8A_1.rem.1.fq.gz 1SN_9A_1.rem.1.fq.gz )\n", "list3=( 1HL_10A_2.2.fq.gz 1HL_11A_2.2.fq.gz 1HL_12A_2.2.fq.gz 1HL_13A_2.2.fq.gz 1HL_14A_2.2.fq.gz 1HL_15A_2.2.fq.gz 1HL_16A_2.2.fq.gz 1HL_17A_2.2.fq.gz 1HL_19A_2.2.fq.gz 1HL_1A_2.2.fq.gz 1HL_20A_2.2.fq.gz 1HL_21A_2.2.fq.gz 1HL_22A_2.2.fq.gz 1HL_23A_2.2.fq.gz 1HL_24A_2.2.fq.gz 1HL_25A_2.2.fq.gz 1HL_26A_2.2.fq.gz 1HL_27A_2.2.fq.gz 1HL_28A_2.2.fq.gz 1HL_29A_2.2.fq.gz 1HL_2A_2.2.fq.gz 1HL_31A_2.2.fq.gz 1HL_33A_2.2.fq.gz 1HL_34A_2.2.fq.gz 1HL_35A_2.2.fq.gz 1HL_3A_2.2.fq.gz 1HL_4A_2.2.fq.gz 1HL_5A_2.2.fq.gz 1HL_6A_2.2.fq.gz 1HL_7A_2.2.fq.gz 1HL_8A_2.2.fq.gz 1HL_9A_2.2.fq.gz 1NF_10A_2.2.fq.gz 1NF_11A_2.2.fq.gz 1NF_12A_2.2.fq.gz 1NF_13A_2.2.fq.gz 1NF_14A_2.2.fq.gz 1NF_15A_2.2.fq.gz 1NF_16A_2.2.fq.gz 1NF_17A_2.2.fq.gz 1NF_18A_2.2.fq.gz 1NF_19A_2.2.fq.gz 1NF_1A_2.2.fq.gz 1NF_20A_2.2.fq.gz 1NF_21A_2.2.fq.gz 1NF_22A_2.2.fq.gz 1NF_23A_2.2.fq.gz 1NF_24A_2.2.fq.gz 1NF_25A_2.2.fq.gz 1NF_26A_2.2.fq.gz 1NF_27A_2.2.fq.gz 1NF_28A_2.2.fq.gz 1NF_29A_2.2.fq.gz 1NF_2A_2.2.fq.gz 1NF_30A_2.2.fq.gz 1NF_31A_2.2.fq.gz 1NF_32A_2.2.fq.gz 1NF_33A_2.2.fq.gz 1NF_4A_2.2.fq.gz 1NF_5A_2.2.fq.gz 1NF_6A_2.2.fq.gz 1NF_7A_2.2.fq.gz 1NF_8A_2.2.fq.gz 1NF_9A_2.2.fq.gz 1SN_10A_2.2.fq.gz 1SN_11A_2.2.fq.gz 1SN_12A_2.2.fq.gz 1SN_13A_2.2.fq.gz 1SN_14A_2.2.fq.gz 1SN_15A_2.2.fq.gz 1SN_16A_2.2.fq.gz 1SN_17A_2.2.fq.gz 1SN_18A_2.2.fq.gz 1SN_19A_2.2.fq.gz 1SN_1A_2.2.fq.gz 1SN_20A_2.2.fq.gz 1SN_21A_2.2.fq.gz 1SN_22A_2.2.fq.gz 1SN_23A_2.2.fq.gz 1SN_24A_2.2.fq.gz 1SN_25A_2.2.fq.gz 1SN_26A_2.2.fq.gz 1SN_27A_2.2.fq.gz 1SN_28A_2.2.fq.gz 1SN_29A_2.2.fq.gz 1SN_2A_2.2.fq.gz 1SN_30A_2.2.fq.gz 1SN_31A_2.2.fq.gz 1SN_32A_2.2.fq.gz 1SN_3A_2.2.fq.gz 1SN_4A_2.2.fq.gz 1SN_5A_2.2.fq.gz 1SN_6A_2.2.fq.gz 1SN_7A_2.2.fq.gz 1SN_8A_2.2.fq.gz 1SN_9A_2.2.fq.gz )\n", "list4=( 1HL_10A_2.rem.2.fq.gz 1HL_11A_2.rem.2.fq.gz 1HL_12A_2.rem.2.fq.gz 1HL_13A_2.rem.2.fq.gz 1HL_14A_2.rem.2.fq.gz 1HL_15A_2.rem.2.fq.gz 1HL_16A_2.rem.2.fq.gz 1HL_17A_2.rem.2.fq.gz 1HL_19A_2.rem.2.fq.gz 1HL_1A_2.rem.2.fq.gz 1HL_20A_2.rem.2.fq.gz 1HL_21A_2.rem.2.fq.gz 1HL_22A_2.rem.2.fq.gz 1HL_23A_2.rem.2.fq.gz 1HL_24A_2.rem.2.fq.gz 1HL_25A_2.rem.2.fq.gz 1HL_26A_2.rem.2.fq.gz 1HL_27A_2.rem.2.fq.gz 1HL_28A_2.rem.2.fq.gz 1HL_29A_2.rem.2.fq.gz 1HL_2A_2.rem.2.fq.gz 1HL_31A_2.rem.2.fq.gz 1HL_33A_2.rem.2.fq.gz 1HL_34A_2.rem.2.fq.gz 1HL_35A_2.rem.2.fq.gz 1HL_3A_2.rem.2.fq.gz 1HL_4A_2.rem.2.fq.gz 1HL_5A_2.rem.2.fq.gz 1HL_6A_2.rem.2.fq.gz 1HL_7A_2.rem.2.fq.gz 1HL_8A_2.rem.2.fq.gz 1HL_9A_2.rem.2.fq.gz 1NF_10A_2.rem.2.fq.gz 1NF_11A_2.rem.2.fq.gz 1NF_12A_2.rem.2.fq.gz 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1SN_25A_2.rem.2.fq.gz 1SN_26A_2.rem.2.fq.gz 1SN_27A_2.rem.2.fq.gz 1SN_28A_2.rem.2.fq.gz 1SN_29A_2.rem.2.fq.gz 1SN_2A_2.rem.2.fq.gz 1SN_30A_2.rem.2.fq.gz 1SN_31A_2.rem.2.fq.gz 1SN_32A_2.rem.2.fq.gz 1SN_3A_2.rem.2.fq.gz 1SN_4A_2.rem.2.fq.gz 1SN_5A_2.rem.2.fq.gz 1SN_6A_2.rem.2.fq.gz 1SN_7A_2.rem.2.fq.gz 1SN_8A_2.rem.2.fq.gz 1SN_9A_2.rem.2.fq.gz )\n", "\n", "for index in \"${!list1[@]}\"; do\n", " i=${list1[$index]}\n", " j=${list2[$index]}\n", " k=${list3[$index]}\n", " l=${list4[$index]}\n", " cat $i $j $k $l > ${i/_1.1/}\n", " \n", "done" ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1HL_10A.fq.gz 1HL_11A.fq.gz 1HL_12A.fq.gz 1HL_13A.fq.gz 1HL_14A.fq.gz 1HL_15A.fq.gz 1HL_16A.fq.gz 1HL_17A.fq.gz 1HL_19A.fq.gz 1HL_1A.fq.gz 1HL_20A.fq.gz 1HL_21A.fq.gz 1HL_22A.fq.gz 1HL_23A.fq.gz 1HL_24A.fq.gz 1HL_25A.fq.gz 1HL_26A.fq.gz 1HL_27A.fq.gz 1HL_28A.fq.gz 1HL_29A.fq.gz 1HL_2A.fq.gz 1HL_31A.fq.gz 1HL_33A.fq.gz 1HL_34A.fq.gz 1HL_35A.fq.gz 1HL_3A.fq.gz 1HL_4A.fq.gz 1HL_5A.fq.gz 1HL_6A.fq.gz 1HL_7A.fq.gz 1HL_8A.fq.gz 1HL_9A.fq.gz 1NF_10A.fq.gz 1NF_11A.fq.gz 1NF_12A.fq.gz 1NF_13A.fq.gz 1NF_14A.fq.gz 1NF_15A.fq.gz 1NF_16A.fq.gz 1NF_17A.fq.gz 1NF_18A.fq.gz 1NF_19A.fq.gz 1NF_1A.fq.gz 1NF_20A.fq.gz 1NF_21A.fq.gz 1NF_22A.fq.gz 1NF_23A.fq.gz 1NF_24A.fq.gz 1NF_25A.fq.gz 1NF_26A.fq.gz 1NF_27A.fq.gz 1NF_28A.fq.gz 1NF_29A.fq.gz 1NF_2A.fq.gz 1NF_30A.fq.gz 1NF_31A.fq.gz 1NF_32A.fq.gz 1NF_33A.fq.gz 1NF_4A.fq.gz 1NF_5A.fq.gz 1NF_6A.fq.gz 1NF_7A.fq.gz 1NF_8A.fq.gz 1NF_9A.fq.gz 1SN_10A.fq.gz 1SN_11A.fq.gz 1SN_12A.fq.gz 1SN_13A.fq.gz 1SN_14A.fq.gz 1SN_15A.fq.gz 1SN_16A.fq.gz 1SN_17A.fq.gz 1SN_18A.fq.gz 1SN_19A.fq.gz 1SN_1A.fq.gz 1SN_20A.fq.gz 1SN_21A.fq.gz 1SN_22A.fq.gz 1SN_23A.fq.gz 1SN_24A.fq.gz 1SN_25A.fq.gz 1SN_26A.fq.gz 1SN_27A.fq.gz 1SN_28A.fq.gz 1SN_29A.fq.gz 1SN_2A.fq.gz 1SN_30A.fq.gz 1SN_31A.fq.gz 1SN_32A.fq.gz 1SN_3A.fq.gz 1SN_4A.fq.gz 1SN_5A.fq.gz 1SN_6A.fq.gz 1SN_7A.fq.gz 1SN_8A.fq.gz 1SN_9A.fq.gz\n" ] } ], "source": [ "%%bash\n", "echo *A.fq.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Create de novo stacks" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Volumes/owl/temp\n" ] } ], "source": [ "cd /Volumes/owl/temp/" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "#Runs ustacks and appends sql ID to each file for downstream analysis.\n", "sql_id=0\n", "for i in *A.fq.gz; do\n", " ((sql_id++))\n", " /usr/local/bioinformatics/stacks-1.37/ustacks -t gzfastq -f $i -o ./stacks -i $sql_id -d -r -p 16\n", " \n", "done" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "ls ./stacks/" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "pwd" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Create stacks catalog (cstacks)" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "cd ./stacks/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### List file names and format for subsequent use in cstacks command" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false }, "outputs": [], "source": [ "%%bash\n", "#Uses printf statement to print just the first part of each filename, without the extension, and ads a \"-s\" and a \" \\\"\n", "#to each line for use in the following cstacks command.\n", "for fname in *; do printf \" %s\\n\" \"-s ${fname%%.*} \\\\\" >> tmp.txt; done\n", "cat tmp.txt | uniq\n", "rm tmp.txt" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [], "source": [ "%%bash\n", "#cstacks command.\n", "time /usr/local/bioinformatics/stacks-1.37/cstacks -b 1 -o . \\\n", "-p 16 \\\n", "-s 1HL_10A \\\n", "-s 1HL_11A \\\n", "-s 1HL_12A \\\n", "-s 1HL_13A \\\n", "-s 1HL_14A \\\n", "-s 1HL_15A \\\n", "-s 1HL_16A \\\n", "-s 1HL_17A \\\n", "-s 1HL_19A \\\n", "-s 1HL_1A \\\n", "-s 1HL_20A \\\n", "-s 1HL_21A \\\n", "-s 1HL_22A \\\n", "-s 1HL_23A \\\n", "-s 1HL_24A \\\n", "-s 1HL_25A \\\n", "-s 1HL_26A \\\n", "-s 1HL_27A \\\n", "-s 1HL_28A \\\n", "-s 1HL_29A \\\n", "-s 1HL_2A \\\n", "-s 1HL_31A \\\n", "-s 1HL_33A \\\n", "-s 1HL_34A \\\n", "-s 1HL_35A \\\n", "-s 1HL_3A \\\n", "-s 1HL_4A \\\n", "-s 1HL_5A \\\n", "-s 1HL_6A \\\n", "-s 1HL_7A \\\n", "-s 1HL_8A \\\n", "-s 1HL_9A \\\n", "-s 1NF_10A \\\n", "-s 1NF_11A \\\n", "-s 1NF_12A \\\n", "-s 1NF_13A \\\n", "-s 1NF_14A \\\n", "-s 1NF_15A \\\n", "-s 1NF_16A \\\n", "-s 1NF_17A \\\n", "-s 1NF_18A \\\n", "-s 1NF_19A \\\n", "-s 1NF_1A \\\n", "-s 1NF_20A \\\n", "-s 1NF_21A \\\n", "-s 1NF_22A \\\n", "-s 1NF_23A \\\n", "-s 1NF_24A \\\n", "-s 1NF_25A \\\n", "-s 1NF_26A \\\n", "-s 1NF_27A \\\n", "-s 1NF_28A \\\n", "-s 1NF_29A \\\n", "-s 1NF_2A \\\n", "-s 1NF_30A \\\n", "-s 1NF_31A \\\n", "-s 1NF_32A \\\n", "-s 1NF_33A \\\n", "-s 1NF_4A \\\n", "-s 1NF_5A \\\n", "-s 1NF_6A \\\n", "-s 1NF_7A \\\n", "-s 1NF_8A \\\n", "-s 1NF_9A \\\n", "-s 1SN_10A \\\n", "-s 1SN_11A \\\n", "-s 1SN_12A \\\n", "-s 1SN_13A \\\n", "-s 1SN_14A \\\n", "-s 1SN_15A \\\n", "-s 1SN_16A \\\n", "-s 1SN_17A \\\n", "-s 1SN_18A \\\n", "-s 1SN_19A \\\n", "-s 1SN_1A \\\n", "-s 1SN_20A \\\n", "-s 1SN_21A \\\n", "-s 1SN_22A \\\n", "-s 1SN_23A \\\n", "-s 1SN_24A \\\n", "-s 1SN_25A \\\n", "-s 1SN_26A \\\n", "-s 1SN_27A \\\n", "-s 1SN_28A \\\n", "-s 1SN_29A \\\n", "-s 1SN_2A \\\n", "-s 1SN_30A \\\n", "-s 1SN_31A \\\n", "-s 1SN_32A \\\n", "-s 1SN_3A \\\n", "-s 1SN_4A \\\n", "-s 1SN_5A \\\n", "-s 1SN_6A \\\n", "-s 1SN_7A \\\n", "-s 1SN_8A \\\n", "-s 1SN_9A" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }