{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE:\n", "Wed Nov 20 11:53:55 PST 2019\n", "------------\n", "\n", "Distributor ID:\tUbuntu\n", "Description:\tUbuntu 16.04.6 LTS\n", "Release:\t16.04\n", "Codename:\txenial\n", "\n", "------------\n", "HOSTNAME: \n", "swoose\n", "\n", "------------\n", "Computer Specs:\n", "\n", "Architecture: x86_64\n", "CPU op-mode(s): 32-bit, 64-bit\n", "Byte Order: Little Endian\n", "CPU(s): 24\n", "On-line CPU(s) list: 0-23\n", "Thread(s) per core: 2\n", "Core(s) per socket: 6\n", "Socket(s): 2\n", "NUMA node(s): 1\n", "Vendor ID: GenuineIntel\n", "CPU family: 6\n", "Model: 44\n", "Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz\n", "Stepping: 2\n", "CPU MHz: 2925.971\n", "BogoMIPS: 5851.97\n", "Virtualization: VT-x\n", "L1d cache: 32K\n", "L1i cache: 32K\n", "L2 cache: 256K\n", "L3 cache: 12288K\n", "NUMA node0 CPU(s): 0-23\n", "Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb ssbd ibrs ibpb stibp kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_l1d\n", "\n", "------------\n", "\n", "Memory Specs\n", "\n", " total used free shared buff/cache available\n", "Mem: 70G 39G 1.1G 969M 30G 29G\n", "Swap: 4.7G 917M 3.8G\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "No LSB modules are available.\n" ] } ], "source": [ "%%bash\n", "echo \"TODAY'S DATE:\"\n", "date\n", "echo \"------------\"\n", "echo \"\"\n", "#Display operating system info\n", "lsb_release -a\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"HOSTNAME: \"; hostname \n", "echo \"\"\n", "echo \"------------\"\n", "echo \"Computer Specs:\"\n", "echo \"\"\n", "lscpu\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"\"\n", "echo \"Memory Specs\"\n", "echo \"\"\n", "free -mh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Set variables\n", "`%env` variables are good for passing to bash cells" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "env: wd=/home/sam/analyses/20191120_swoose_pgen_v074_renaming\n", "env: old_fa_index=Pgenerosa_v074.fa.fai\n", "env: base_cov_url=https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed\n" ] } ], "source": [ "# Set workding directory\n", "%env wd=/home/sam/analyses/20191120_swoose_pgen_v074_renaming\n", "wd=\"/home/sam/analyses/20191120_swoose_pgen_v074_renaming\"\n", "\n", "%env old_fa_index=Pgenerosa_v074.fa.fai\n", "%env base_cov_url=https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--recursive --accept deduplicated.bismark.cov.gz --no-parent --no-directories --quietly --no-check-certificate\n" ] } ], "source": [ "%%bash\n", "echo ${wget_options}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Create necessary directories" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "%%bash\n", "mkdir --parents ${wd}" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/sam/analyses/20191120_swoose_pgen_v074_renaming\n" ] } ], "source": [ "cd {wd}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Download Pgen_v074 files\n" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0807/\n", "Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0807-003/\n", "Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0807-004/\n", "Downloading coverage files from https://gannet.fish.washington.edu/seashell/bu-mox/scrubbed/0809-005/\n", "total 2.5G\n", "-rw-rw-r-- 1 sam sam 57M Aug 12 14:29 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 68M Aug 12 14:57 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 64M Aug 12 15:24 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 62M Aug 12 15:49 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 69M Aug 12 16:18 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 62M Aug 12 16:43 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 58M Aug 12 17:05 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 61M Aug 12 17:29 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 61M Aug 12 17:55 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 62M Aug 12 18:20 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 55M Aug 12 18:41 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 61M Aug 12 19:05 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 49M Aug 7 08:39 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 53M Aug 7 09:00 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 44M Aug 7 09:16 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 47M Aug 7 09:32 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 36M Aug 7 09:43 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 53M Aug 7 10:04 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 44M Aug 7 10:17 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Aug 7 10:32 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 53M Aug 7 10:50 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 45M Aug 7 11:06 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Aug 7 11:21 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 49M Aug 7 11:37 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 53M Aug 8 05:03 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 63M Aug 8 05:28 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 53M Aug 8 05:49 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 62M Aug 8 06:15 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 44M Aug 8 06:29 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 25M Aug 8 06:36 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 47M Aug 8 06:53 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Aug 8 07:07 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 50M Aug 8 07:25 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 57M Aug 8 07:48 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 33M Aug 8 07:58 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 45M Aug 8 08:14 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 33M Aug 8 10:04 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Aug 8 10:19 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 51M Aug 8 10:37 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 54M Aug 8 10:58 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 55M Aug 8 11:19 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Aug 8 11:37 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 34M Aug 8 11:47 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 36M Aug 8 11:59 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 29M Aug 8 12:07 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 33M Aug 8 12:17 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Aug 8 12:30 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 47M Aug 8 12:47 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Aug 12 19:20 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 48M Aug 12 19:39 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Aug 12 19:54 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 31M Aug 12 20:04 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "rm: cannot remove '*.html*': No such file or directory\n" ] } ], "source": [ "%%bash\n", "url_array=(\"${base_cov_url}\"/0807/ \"${base_cov_url}\"/0807-003/ \"${base_cov_url}\"/0807-004/ \"${base_cov_url}\"/0809-005/)\n", "\n", "# Downlaod Bismark coverage files\n", "for url in \"${url_array[@]}\"\n", "do\n", " echo \"Downloading coverage files from ${url}\"\n", " \n", " wget \\\n", " --recursive \\\n", " --accept deduplicated.bismark.cov.gz \\\n", " --no-parent \\\n", " --no-directories \\\n", " --quiet \\\n", " --no-check-certificate \\\n", " \"${url}\"\n", "done\n", "\n", "\n", "# Remove index files\n", "rm *.html*\n", "\n", "# Download Pgen_074 FastA Index file\n", "wget --quiet http://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v074.fa.fai\n", " \n", "ls -lh" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "PGA_scaffold1__77_contigs__length_89643857\t54\t54\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t72\t72\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t96\t96\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t119\t119\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t202\t202\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t209\t209\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t213\t213\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t221\t221\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t238\t238\t0\t0\t1\n", "PGA_scaffold1__77_contigs__length_89643857\t1254\t1254\t0\t0\t1\n" ] } ], "source": [ "%%bash\n", "\n", "zcat EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz | head" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Change scaffold names" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Decompressing EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "\n", "Decompressing EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "Generating EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Now removing EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov\n", "\n", "Compressing EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp to EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "total 19G\n", "-rw-rw-r-- 1 sam sam 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai\n", "-rw-rw-r-- 1 sam sam 380M Nov 20 13:46 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 56M Nov 20 13:46 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 440M Nov 20 13:47 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 66M Nov 20 13:48 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 416M Nov 20 13:49 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 63M Nov 20 13:49 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 404M Nov 20 13:50 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 13:50 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 445M Nov 20 13:51 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 67M Nov 20 13:51 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 404M Nov 20 13:52 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 13:53 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 380M Nov 20 13:54 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 57M Nov 20 13:54 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 394M Nov 20 13:55 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 59M Nov 20 13:55 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 392M Nov 20 13:56 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 59M Nov 20 13:56 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 400M Nov 20 13:57 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 60M Nov 20 13:57 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 363M Nov 20 13:58 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 54M Nov 20 13:59 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 395M Nov 20 13:59 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 59M Nov 20 14:00 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 323M Nov 20 14:00 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 48M Nov 20 14:01 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 347M Nov 20 14:02 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:02 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 289M Nov 20 14:02 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 43M Nov 20 14:03 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 312M Nov 20 14:03 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 46M Nov 20 14:04 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 244M Nov 20 14:04 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 35M Nov 20 14:04 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 346M Nov 20 14:05 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:05 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 294M Nov 20 14:06 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 43M Nov 20 14:06 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 288M Nov 20 14:07 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:07 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 354M Nov 20 14:08 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:08 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 300M Nov 20 14:09 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 44M Nov 20 14:09 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 283M Nov 20 14:10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 326M Nov 20 14:11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 48M Nov 20 14:11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 346M Nov 20 14:12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 51M Nov 20 14:12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 408M Nov 20 14:13 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 14:14 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 350M Nov 20 14:14 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:15 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 404M Nov 20 14:16 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 14:16 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 294M Nov 20 14:17 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 43M Nov 20 14:17 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 169M Nov 20 14:17 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 24M Nov 20 14:17 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 306M Nov 20 14:18 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 45M Nov 20 14:18 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 279M Nov 20 14:19 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 41M Nov 20 14:19 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 329M Nov 20 14:20 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 49M Nov 20 14:20 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 374M Nov 20 14:21 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 56M Nov 20 14:21 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 223M Nov 20 14:22 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 32M Nov 20 14:22 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 295M Nov 20 14:23 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 44M Nov 20 14:23 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 221M Nov 20 14:23 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 32M Nov 20 14:23 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 286M Nov 20 14:24 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:24 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 336M Nov 20 14:25 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 50M Nov 20 14:25 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 349M Nov 20 14:26 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:26 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 364M Nov 20 14:27 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 54M Nov 20 14:28 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 275M Nov 20 14:28 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 41M Nov 20 14:28 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 227M Nov 20 14:29 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 33M Nov 20 14:29 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 242M Nov 20 14:30 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 35M Nov 20 14:30 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 194M Nov 20 14:30 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 28M Nov 20 14:31 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 224M Nov 20 14:31 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 32M Nov 20 14:31 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 277M Nov 20 14:32 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 41M Nov 20 14:32 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 311M Nov 20 14:33 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 46M Nov 20 14:33 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 288M Nov 20 14:34 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:34 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 312M Nov 20 14:35 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 47M Nov 20 14:35 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 285M Nov 20 14:36 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:36 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 206M Nov 20 14:36 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.tmp\n", "-rw-rw-r-- 1 sam sam 30M Nov 20 14:36 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n" ] } ], "source": [ "%%bash\n", "# Array of old scaffold names\n", "# Uses first column of FastA index file to get scaffold names\n", "mapfile -t orig_scaffold_names < <(awk '{print $1}' \"${old_fa_index}\")\n", "\n", "# Array of new scaffold names\n", "mapfile -t new_scaffold_names < <(for number in {01..18}; do echo \"Scaffold_${number}\"; done)\n", "\n", "\n", "for gzfile in *cov.gz\n", "do\n", " # Save gunzipped filename (via parameter substitution - removes .gz from input filename)\n", " name=\"${gzfile%.*}\"\n", "\n", " # Gunzip the gzipped file\n", " echo \"\"\n", " echo \"Decompressing ${gzfile}\"\n", " echo \"Generating ${name}\"\n", " gunzip \"${gzfile}\"\n", "\n", "\n", " # sed substitution\n", " # creates sed script to find original scaffold names and replace them with new scafold names\n", " # and passes to sed via stdin\n", " for index in \"${!orig_scaffold_names[@]}\"\n", " do\n", " printf \"s/%s/%s/\\n\" \"${orig_scaffold_names[index]}\" \"${new_scaffold_names[index]}\"\n", " done | sed --file - \"${name}\" \\\n", " >> \"${name}\".tmp\n", "\n", " # Remove the gunzipped file, now that a .tmp file exists\n", " echo \"\"\n", " echo \"Now removing ${name}\"\n", " rm \"${name}\"\n", "\n", " # Compress .tmp coverage files\n", " echo \"\"\n", " echo \"Compressing ${name}.tmp to ${name}.gz\"\n", " gzip --to-stdout \"${name}\".tmp > \"${name}\".gz\n", "done\n", "\n", "ls -ltrh" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Scaffold_01\t54\t54\t0\t0\t1\n", "Scaffold_01\t72\t72\t0\t0\t1\n", "Scaffold_01\t96\t96\t0\t0\t1\n", "Scaffold_01\t119\t119\t0\t0\t1\n", "Scaffold_01\t202\t202\t0\t0\t1\n", "Scaffold_01\t209\t209\t0\t0\t1\n", "Scaffold_01\t213\t213\t0\t0\t1\n", "Scaffold_01\t221\t221\t0\t0\t1\n", "Scaffold_01\t238\t238\t0\t0\t1\n", "Scaffold_01\t1254\t1254\t0\t0\t1\n", "Scaffold_18\t27722766\t27722766\t100\t1\t0\n", "Scaffold_18\t27722918\t27722918\t100\t1\t0\n", "Scaffold_18\t27722923\t27722923\t0\t0\t1\n", "Scaffold_18\t27722925\t27722925\t100\t2\t0\n", "Scaffold_18\t27726479\t27726479\t0\t0\t1\n", "Scaffold_18\t27726498\t27726498\t100\t1\t0\n", "Scaffold_18\t27727720\t27727720\t0\t0\t2\n", "Scaffold_18\t27727726\t27727726\t0\t0\t2\n", "Scaffold_18\t27727766\t27727766\t0\t0\t2\n", "Scaffold_18\t27730103\t27730103\t33.3333333333333\t1\t2\n" ] } ], "source": [ "%%bash\n", "zcat EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz | head\n", "zcat EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz | tail" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Clean up" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 2.4G\n", "-rw-rw-r-- 1 sam sam 56M Nov 20 13:46 EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 66M Nov 20 13:48 EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 63M Nov 20 13:49 EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 13:50 EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 67M Nov 20 13:51 EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 13:53 EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 57M Nov 20 13:54 EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 59M Nov 20 13:55 EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 59M Nov 20 13:56 EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 60M Nov 20 13:57 EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 54M Nov 20 13:59 EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 59M Nov 20 14:00 EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 48M Nov 20 14:01 EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:02 EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Nov 20 14:03 EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 46M Nov 20 14:04 EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 35M Nov 20 14:04 EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:05 EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Nov 20 14:06 EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:07 EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:08 EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 44M Nov 20 14:09 EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:10 EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 48M Nov 20 14:11 EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 51M Nov 20 14:12 EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 14:14 EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:15 EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 61M Nov 20 14:16 EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 43M Nov 20 14:17 EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 24M Nov 20 14:17 EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 45M Nov 20 14:18 EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 41M Nov 20 14:19 EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 49M Nov 20 14:20 EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 56M Nov 20 14:21 EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 32M Nov 20 14:22 EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 44M Nov 20 14:23 EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 32M Nov 20 14:23 EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:24 EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 50M Nov 20 14:25 EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 52M Nov 20 14:26 EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 54M Nov 20 14:28 EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 41M Nov 20 14:28 EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 33M Nov 20 14:29 EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 35M Nov 20 14:30 EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 28M Nov 20 14:31 EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 32M Nov 20 14:31 EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 41M Nov 20 14:32 EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 46M Nov 20 14:33 EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:34 EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 47M Nov 20 14:35 EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 42M Nov 20 14:36 EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n", "-rw-rw-r-- 1 sam sam 30M Nov 20 14:36 EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz\n" ] } ], "source": [ "%%bash\n", "rm *.tmp \"${old_fa_index}\"\n", "\n", "ls -lh" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.8" } }, "nbformat": 4, "nbformat_minor": 4 }