{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE\n", "Mon Feb 5 13:50:49 PST 2018\n", "------------\n", "\n", "Distributor ID:\tUbuntu\n", "Description:\tUbuntu 16.04.3 LTS\n", "Release:\t16.04\n", "Codename:\txenial\n", "\n", "------------\n", "HOSTNAME: \n", "roadrunner\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): 16\n", "On-line CPU(s) list: 0-15\n", "Thread(s) per core: 2\n", "Core(s) per socket: 4\n", "Socket(s): 2\n", "NUMA node(s): 1\n", "Vendor ID: GenuineIntel\n", "CPU family: 6\n", "Model: 26\n", "Model name: Intel(R) Xeon(R) CPU E5520 @ 2.27GHz\n", "Stepping: 5\n", "CPU MHz: 1596.000\n", "CPU max MHz: 2394.0000\n", "CPU min MHz: 1596.0000\n", "BogoMIPS: 4521.78\n", "Virtualization: VT-x\n", "L1d cache: 32K\n", "L1i cache: 32K\n", "L2 cache: 256K\n", "L3 cache: 8192K\n", "NUMA node0 CPU(s): 0-15\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 rdtscp lm constant_tsc arch_perfmon pebs bts nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida\n", "\n", "------------\n", "\n", "Memory Specs\n", "\n", " total used free shared buff/cache available\n", "Mem: 47G 1.1G 44G 18M 1.4G 45G\n", "Swap: 47G 0B 47G\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", "lsb_release -a\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"HOSTNAME: \"\n", "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": "code", "execution_count": 2, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/20180205_soap_geoduck" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/20180206_meraculous_geoduck" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/data/geoduck_illumina/trimmed/trimmed_again/20180206_kmergenie" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "mkdir: cannot create directory ‘/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/’: File exists\n" ] } ], "source": [ "%%bash\n", "rmdir /home/sam/data/geoduck_illumina/trimmed/trimmed_again/20180206_kmergenie\n", "mkdir /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/20180206_kmergenie" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "for fastq in /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/*.fq.gz\n", "do\n", "echo \"$fastq\" >> /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/20180206_kmergenie/fastq_list.txt\n", "done\n", "\n", "cat /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/20180206_kmergenie/fastq_list.txt" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "running histogram estimation\n", "list of reads:\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fq.gz\n", "Setting maximum kmer length to: 151 bp\n", "computing histograms (from k=21 to k=121): 51 61 41 31 21 81 71 91 111 101 121 estimation of the best k so far: 121\n", "\n", "ntCard wall-clock time over all k values: 47879 seconds \n", "fitting model to histograms to estimate best k\n", "refining estimation around [115; 121], with a step of 2\n", "running histogram estimation\n", "list of reads:\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fq.gz\n", "/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fq.gz\n", "Setting maximum kmer length to: 151 bp\n", "computing histograms (from k=117 to k=121): 117 119 121 table of predicted num. of genomic k-mers: histograms.dat\n", "recommended coverage cut-off for best k: 4\n", "best k: 117\n", "\n", "ntCard wall-clock time over all k values: 45509 seconds \n", "fitting model to histograms to estimate best k\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t1557m8.632s\n", "user\t5832m21.724s\n", "sys\t359m59.412s\n" ] } ], "source": [ "%%bash\n", "cd /home/shared/kmergenie-1.7044/\n", "time ./kmergenie /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/20180206_kmergenie/fastq_list.txt\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 2044\n", "-rw-r--r-- 1 sam sam 3790 May 3 2017 README\n", "-rw-r--r-- 1 sam sam 2087 May 3 2017 readfq.py\n", "-rw-r--r-- 1 sam sam 2512 May 3 2017 makefile\n", "-rw-r--r-- 1 sam sam 10753 May 3 2017 main.cpp\n", "-rw-r--r-- 1 sam sam 22745 May 3 2017 LICENSE\n", "-rw-r--r-- 1 sam sam 0 May 3 2017 CHANGELOG\n", "-rw-r--r-- 1 sam sam 1948 May 3 2017 wrapper.py\n", "-rw-r--r-- 1 sam sam 874 May 3 2017 setup.py\n", "-rwxr-xr-x 1 sam sam 11102 May 3 2017 kmergenie\n", "-rw-r--r-- 1 sam sam 0 May 3 2017 __init__.py\n", "drwxr-xr-x 3 sam sam 4096 Feb 6 07:27 third_party\n", "drwxr-xr-x 2 sam sam 4096 Feb 6 07:31 minia\n", "-rwxrwxr-x 1 sam sam 118512 Feb 6 07:31 specialk\n", "drwxr-xr-x 5 sam sam 4096 Feb 6 07:31 ntCard\n", "drwxrwxr-x 2 sam sam 4096 Feb 6 07:40 __pycache__\n", "-rw-rw-r-- 1 sam sam 85399 Feb 6 12:10 histograms-k61.histo\n", "-rw-rw-r-- 1 sam sam 87660 Feb 6 12:10 histograms-k51.histo\n", "-rw-rw-r-- 1 sam sam 91393 Feb 6 12:19 histograms-k41.histo\n", "-rw-rw-r-- 1 sam sam 94299 Feb 6 12:25 histograms-k31.histo\n", "-rw-rw-r-- 1 sam sam 98123 Feb 6 12:26 histograms-k21.histo\n", "-rw-rw-r-- 1 sam sam 80894 Feb 6 16:44 histograms-k81.histo\n", "-rw-rw-r-- 1 sam sam 82809 Feb 6 16:44 histograms-k71.histo\n", "-rw-rw-r-- 1 sam sam 79364 Feb 6 16:47 histograms-k91.histo\n", "-rw-rw-r-- 1 sam sam 76319 Feb 6 16:56 histograms-k111.histo\n", "-rw-rw-r-- 1 sam sam 77695 Feb 6 16:56 histograms-k101.histo\n", "drwxr-xr-x 3 sam sam 4096 Feb 6 20:58 scripts\n", "-rw-rw-r-- 1 sam sam 75192 Feb 7 01:10 histograms-k117.histo\n", "-rw-rw-r-- 1 sam sam 74770 Feb 7 05:23 histograms-k119.histo\n", "-rw-rw-r-- 1 sam sam 74665 Feb 7 09:37 histograms-k121.histo\n", "-rw-rw-r-- 1 sam sam 5746 Feb 7 09:37 histograms-k117.histo.pdf\n", "-rw-rw-r-- 1 sam sam 5672 Feb 7 09:37 histograms-k119.histo.pdf\n", "-rw-rw-r-- 1 sam sam 8628 Feb 7 09:37 histograms-k71.histo.pdf\n", "-rw-rw-r-- 1 sam sam 6064 Feb 7 09:37 histograms-k111.histo.pdf\n", "-rw-rw-r-- 1 sam sam 11590 Feb 7 09:37 histograms-k41.histo.pdf\n", "-rw-rw-r-- 1 sam sam 5584 Feb 7 09:37 histograms-k121.histo.pdf\n", "-rw-rw-r-- 1 sam sam 7615 Feb 7 09:37 histograms-k81.histo.pdf\n", "-rw-rw-r-- 1 sam sam 6557 Feb 7 09:37 histograms-k101.histo.pdf\n", "-rw-rw-r-- 1 sam sam 13596 Feb 7 09:37 histograms-k31.histo.pdf\n", "-rw-rw-r-- 1 sam sam 16073 Feb 7 09:37 histograms-k21.histo.pdf\n", "-rw-rw-r-- 1 sam sam 10411 Feb 7 09:37 histograms-k51.histo.pdf\n", "-rw-rw-r-- 1 sam sam 7121 Feb 7 09:37 histograms-k91.histo.pdf\n", "-rw-rw-r-- 1 sam sam 9552 Feb 7 09:37 histograms-k61.histo.pdf\n", "-rw-rw-r-- 1 sam sam 247 Feb 7 09:37 histograms.dat\n", "-rw-rw-r-- 1 sam sam 625084 Feb 7 09:37 histograms_report.html\n", "-rw-rw-r-- 1 sam sam 4546 Feb 7 09:37 histograms.dat.pdf\n" ] } ], "source": [ "%%bash\n", "ls -ltr /home/shared/kmergenie-1.7044/" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv /home/shared/kmergenie-1.7044/histograms* /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/20180206_kmergenie/" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "fastq_list.txt\n", "histograms.dat\n", "histograms.dat.pdf\n", "histograms-k101.histo\n", "histograms-k101.histo.pdf\n", "histograms-k111.histo\n", "histograms-k111.histo.pdf\n", "histograms-k117.histo\n", "histograms-k117.histo.pdf\n", "histograms-k119.histo\n", "histograms-k119.histo.pdf\n", "histograms-k121.histo\n", "histograms-k121.histo.pdf\n", "histograms-k21.histo\n", "histograms-k21.histo.pdf\n", "histograms-k31.histo\n", "histograms-k31.histo.pdf\n", "histograms-k41.histo\n", "histograms-k41.histo.pdf\n", "histograms-k51.histo\n", "histograms-k51.histo.pdf\n", "histograms-k61.histo\n", "histograms-k61.histo.pdf\n", "histograms-k71.histo\n", "histograms-k71.histo.pdf\n", "histograms-k81.histo\n", "histograms-k81.histo.pdf\n", "histograms-k91.histo\n", "histograms-k91.histo.pdf\n", "histograms_report.html\n" ] } ], "source": [ "%%bash\n", "ls /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/20180206_kmergenie/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Concerned about the amount of space left on this drive for the upcoming assembly. Moving to \"toaster\"." ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t88m11.549s\n", "user\t0m10.484s\n", "sys\t14m7.736s\n" ] } ], "source": [ "%%bash\n", "mkdir /media/sam/toaster/geoduck_novaseq_meraculous_assembly\n", "time mv /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/ /media/sam/toaster/geoduck_novaseq_meraculous_assembly" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "20180129_trimmed_again\n" ] } ], "source": [ "%%bash\n", "ls /media/sam/toaster/geoduck_novaseq_meraculous_assembly" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "20180206_kmergenie\n", "AD002_S9_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "AD002_S9_L001_R1_001_val_1_val_1.fq.gz\n", "AD002_S9_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "AD002_S9_L001_R2_001_val_2_val_2.fq.gz\n", "AD002_S9_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "AD002_S9_L002_R1_001_val_1_val_1.fq.gz\n", "AD002_S9_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "AD002_S9_L002_R2_001_val_2_val_2.fq.gz\n", "NR005_S4_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR005_S4_L001_R1_001_val_1_val_1.fq.gz\n", "NR005_S4_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR005_S4_L001_R2_001_val_2_val_2.fq.gz\n", "NR005_S4_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR005_S4_L002_R1_001_val_1_val_1.fq.gz\n", "NR005_S4_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR005_S4_L002_R2_001_val_2_val_2.fq.gz\n", "NR006_S3_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR006_S3_L001_R1_001_val_1_val_1.fq.gz\n", "NR006_S3_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR006_S3_L001_R2_001_val_2_val_2.fq.gz\n", "NR006_S3_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR006_S3_L002_R1_001_val_1_val_1.fq.gz\n", "NR006_S3_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR006_S3_L002_R2_001_val_2_val_2.fq.gz\n", "NR012_S1_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR012_S1_L001_R1_001_val_1_val_1.fq.gz\n", "NR012_S1_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR012_S1_L001_R2_001_val_2_val_2.fq.gz\n", "NR012_S1_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR012_S1_L002_R1_001_val_1_val_1.fq.gz\n", "NR012_S1_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR012_S1_L002_R2_001_val_2_val_2.fq.gz\n", "NR013_AD013_S2_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz\n", "NR013_AD013_S2_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz\n", "NR013_AD013_S2_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz\n", "NR013_AD013_S2_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz\n", "NR014_AD014_S5_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz\n", "NR014_AD014_S5_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz\n", "NR014_AD014_S5_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz\n", "NR014_AD014_S5_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz\n", "NR015_AD015_S6_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz\n", "NR015_AD015_S6_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz\n", "NR015_AD015_S6_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz\n", "NR015_AD015_S6_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz\n", "NR019_S7_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR019_S7_L001_R1_001_val_1_val_1.fq.gz\n", "NR019_S7_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR019_S7_L001_R2_001_val_2_val_2.fq.gz\n", "NR019_S7_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR019_S7_L002_R1_001_val_1_val_1.fq.gz\n", "NR019_S7_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR019_S7_L002_R2_001_val_2_val_2.fq.gz\n", "NR021_S8_L001_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR021_S8_L001_R1_001_val_1_val_1.fq.gz\n", "NR021_S8_L001_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR021_S8_L001_R2_001_val_2_val_2.fq.gz\n", "NR021_S8_L002_R1_001_val_1.fq.gz_trimming_report.txt\n", "NR021_S8_L002_R1_001_val_1_val_1.fq.gz\n", "NR021_S8_L002_R2_001_val_2.fq.gz_trimming_report.txt\n", "NR021_S8_L002_R2_001_val_2_val_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "ls /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fq.gz\n", "/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "ls /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/*.fq.gz" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "echo \\\n", "\"###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.fz AD002 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2*.fq.gz AD002 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2*.fq.gz NR005 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2*.fq.gz NR005 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2*.fq.gz NR006 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2*.fq.gz NR006 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2*.fq.gz NR012 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2*fq.gz NR012 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2*.fq.gz NR013 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2*.fq.gz NR013 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2*.fq.gz NR014 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2*.fq.gz NR014 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2*.fq.gz NR015 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2*.fq.gz NR015 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2*.fq.gz NR019 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2*.fq.gz NR019 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2*.fq.gz NR021 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2*.fq.gz NR021 800 10 150 0 0 0 1 1 0 0\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters \n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\" \\\n", "> /home/sam/20180206_meraculous_geoduck/meraculous.config" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "echo \\\n", "\"###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.fz AD002 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2*.fq.gz AD002 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2*.fq.gz NR005 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2*.fq.gz NR005 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2*.fq.gz NR006 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2*.fq.gz NR006 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2*.fq.gz NR012 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2*fq.gz NR012 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2*.fq.gz NR013 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2*.fq.gz NR013 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2*.fq.gz NR014 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2*.fq.gz NR014 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2*.fq.gz NR015 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2*.fq.gz NR015 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2*.fq.gz NR019 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2*.fq.gz NR019 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2*.fq.gz NR021 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2*.fq.gz NR021 800 10 150 0 0 0 1 1 0 0\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters \n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\" \\\n", "> /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.fz AD002 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2*.fq.gz AD002 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2*.fq.gz NR005 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2*.fq.gz NR005 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2*.fq.gz NR006 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2*.fq.gz NR006 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2*.fq.gz NR012 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2*fq.gz NR012 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2*.fq.gz NR013 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2*.fq.gz NR013 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2*.fq.gz NR014 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2*.fq.gz NR014 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2*.fq.gz NR015 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2*.fq.gz NR015 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2*.fq.gz NR019 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2*.fq.gz NR019 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2*.fq.gz NR021 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2*.fq.gz NR021 800 10 150 0 0 0 1 1 0 0\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters \n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\n" ] } ], "source": [ "%%bash\n", "cat /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "meraculous run exited prematurely: 1\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/09 07:03:40 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/09 07:03:40 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/09 07:03:40 Setting the stage for the new run..\n", "2018/02/09 07:03:40 Error: Multiple user parameter entries for library NR014!\n", "2018/02/09 07:03:40 Unable to load user-defined library info!\n", "2018/02/09 07:03:40 Error: Cannot load library info!\n", "Died at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 527.\n", "\n", "real\t0m0.665s\n", "user\t0m0.148s\n", "sys\t0m0.028s\n" ] } ], "source": [ "%%bash\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh -dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ -c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "echo \\\n", "\"###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.fz AD00201 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2*.fq.gz AD00202 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2*.fq.gz NR00501 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2*.fq.gz NR00502 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2*.fq.gz NR00601 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2*.fq.gz NR00602 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2*.fq.gz NR01201 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2*,fq.gz NR01202 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2*.fq.gz NR01301 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2*.fq.gz NR01302 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2*.fq.gz NR01401 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2*.fq.gz NR01402 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2*.fq.gz NR01501 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2*.fq.gz NR01502 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2*.fq.gz NR01901 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2*.fq.gz NR01902 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2*.fq.gz NR02101 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2*.fq.gz NR02102 800 10 150 0 0 0 1 1 0 0\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters\n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\" \\\n", "> /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "meraculous run exited prematurely: 1\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/09 07:47:41 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/09 07:47:41 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/09 07:47:41 Setting the stage for the new run..\n", "2018/02/09 07:47:41 Prep work complete. From here on will channel all messages to appropriate logs ...\n", "2018/02/09 07:47:41 Logging to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/run_2018-02-09_07h47m41s/log/ ...\n", "\n", "\u001b[34m2018/02/09 07:47:42 meraculous.pl main:: 737> RUNNING STAGE: meraculous_import \u001b[0m\n", "\u001b[35m2018/02/09 09:04:29 meraculous.pl main::run_meraculous_import 985> Error in user parameters: No files found matching /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.fz \u001b[0m\n", "\u001b[35m2018/02/09 09:04:30 meraculous.pl main:: 769> Stage meraculous_import failed (4608.297121 seconds)\u001b[0m\n", "\u001b[35m \u001b[0m\n", "\u001b[34m2018/02/09 09:04:30 meraculous.pl main:: 824> RUN DID NOT COMPLETE ! \u001b[0m\n", "\u001b[34m2018/02/09 09:04:30 meraculous.pl main:: 828> Total run time: 4608.398879 seconds. \u001b[0m\n", "\u001b[34m2018/02/09 09:04:30 meraculous.pl main:: 830> Thank you for running Meraculous! \u001b[0m\n", "\n", "real\t76m48.563s\n", "user\t138m43.424s\n", "sys\t19m20.252s\n" ] } ], "source": [ "%%bash\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh -dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ -c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 22, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "echo \\\n", "\"###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.gz AD00201 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2*.fq.gz AD00202 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2*.fq.gz NR00501 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2*.fq.gz NR00502 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2*.fq.gz NR00601 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2*.fq.gz NR00602 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2*.fq.gz NR01201 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2*,fq.gz NR01202 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2*.fq.gz NR01301 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2*.fq.gz NR01302 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2*.fq.gz NR01401 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2*.fq.gz NR01402 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2*.fq.gz NR01501 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2*.fq.gz NR01502 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2*.fq.gz NR01901 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2*.fq.gz NR01902 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2*.fq.gz NR02101 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2*.fq.gz NR02102 800 10 150 0 0 0 1 1 0 0\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters\n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\" \\\n", "> /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "meraculous run exited prematurely: 1\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/09 09:38:01 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/09 09:38:01 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/09 09:38:01 Setting the stage for the new run..\n", "2018/02/09 09:38:01 Prep work complete. From here on will channel all messages to appropriate logs ...\n", "2018/02/09 09:38:01 Logging to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/run_2018-02-09_09h38m01s/log/ ...\n", "\n", "\u001b[34m2018/02/09 09:38:01 meraculous.pl main:: 737> RUNNING STAGE: meraculous_import \u001b[0m\n", "\u001b[35m2018/02/09 09:57:40 M_Generic_Config.pm M_Generic_Config::config_print_all 1380> Unable to close the configuration file!\u001b[0m\n", "\u001b[35mFile:\t/home/sam/gitrepos/LabDocs/jupyter_nbs/sam/run_2018-02-09_09h38m01s/checkpoints/meraculous_import.local.params \u001b[0m\n", "\u001b[35m2018/02/09 09:57:40 meraculous.pl main::write_stage_params_file 3608> Params file creation failed for stage meraculous_import! \u001b[0m\n", "\u001b[35m2018/02/09 09:57:40 meraculous.pl main:: 769> Stage meraculous_import failed (1178.939498 seconds)\u001b[0m\n", "\u001b[35mDied at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 3609.\u001b[0m\n", "\u001b[35m \u001b[0m\n", "\u001b[34m2018/02/09 09:57:40 meraculous.pl main:: 824> RUN DID NOT COMPLETE ! \u001b[0m\n", "\u001b[34m2018/02/09 09:57:40 meraculous.pl main:: 828> Total run time: 1179.055165 seconds. \u001b[0m\n", "\u001b[34m2018/02/09 09:57:40 meraculous.pl main:: 830> Thank you for running Meraculous! \u001b[0m\n", "\n", "real\t19m39.709s\n", "user\t36m5.940s\n", "sys\t5m7.884s\n", "msmtp: cannot rewind temporary file: No space left on device\n" ] } ], "source": [ "%%bash\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh -dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ -c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "ename": "SyntaxError", "evalue": "invalid syntax (, line 1)", "output_type": "error", "traceback": [ "\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m du -h /home/sam/data/ | grep '[0-9\\.]\\+G'\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "The history saving thread hit an unexpected error (OperationalError('database or disk is full',)).History will not be written to the database.\n" ] } ], "source": [ "du -h /home/sam/data/ | grep '[0-9\\.]\\+G'" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "381G\t/home/sam/data/geoduck_illumina/trimmed\n", "921G\t/home/sam/data/geoduck_illumina\n", "921G\t/home/sam/data/\n" ] } ], "source": [ "%%bash\n", "du -h /home/sam/data/ | grep '[0-9\\.]\\+G'" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 541G\n", "-rwxr-xr-x 1 sam sam 15G Jan 25 09:05 AD002_S9_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 15G Jan 25 09:08 AD002_S9_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 17G Jan 25 09:13 AD002_S9_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 18G Jan 25 09:17 AD002_S9_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 3.4M Jan 25 09:17 NR005_S4_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 3.5M Jan 25 09:17 NR005_S4_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 2.8M Jan 25 09:17 NR005_S4_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 2.9M Jan 25 09:17 NR005_S4_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 262M Jan 25 09:17 NR006_S3_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 271M Jan 25 09:17 NR006_S3_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 217M Jan 25 09:17 NR006_S3_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 226M Jan 25 09:17 NR006_S3_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 25M Jan 25 09:17 NR012_S1_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 27M Jan 25 09:17 NR012_S1_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 28M Jan 25 09:17 NR012_S1_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 29M Jan 25 09:17 NR012_S1_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 26G Jan 25 09:23 NR013_AD013_S2_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 28G Jan 25 09:30 NR013_AD013_S2_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 30G Jan 25 09:37 NR013_AD013_S2_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 32G Jan 25 09:44 NR013_AD013_S2_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 64G Jan 25 10:02 NR014_AD014_S5_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 66G Jan 25 10:20 NR014_AD014_S5_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 70G Jan 25 10:39 NR014_AD014_S5_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 73G Jan 25 11:01 NR014_AD014_S5_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 22G Jan 25 11:07 NR015_AD015_S6_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 23G Jan 25 11:15 NR015_AD015_S6_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 23G Jan 25 11:23 NR015_AD015_S6_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 24G Jan 25 11:31 NR015_AD015_S6_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 4.5M Jan 25 11:31 NR019_S7_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 4.5M Jan 25 11:31 NR019_S7_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 2.5M Jan 25 11:31 NR019_S7_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 2.5M Jan 25 11:31 NR019_S7_L002_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 319M Jan 25 11:31 NR021_S8_L001_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 333M Jan 25 11:31 NR021_S8_L001_R2_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 265M Jan 25 11:31 NR021_S8_L002_R1_001.fastq.gz\n", "-rwxr-xr-x 1 sam sam 276M Jan 25 11:31 NR021_S8_L002_R2_001.fastq.gz\n", "drwxrwxr-x 7 sam sam 12K Feb 9 11:08 trimmed\n" ] } ], "source": [ "%%bash\n", "ls -lh /home/sam/data/geoduck_illumina/" ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "rm /home/sam/data/geoduck_illumina/*.gz" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "meraculous run exited prematurely: 1\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/09 11:14:36 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/09 11:14:36 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/09 11:14:36 Setting the stage for the new run..\n", "2018/02/09 11:14:36 Prep work complete. From here on will channel all messages to appropriate logs ...\n", "2018/02/09 11:14:36 Logging to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/run_2018-02-09_11h14m36s/log/ ...\n", "\n", "\u001b[34m2018/02/09 11:14:36 meraculous.pl main:: 737> RUNNING STAGE: meraculous_import \u001b[0m\n", "\u001b[35m2018/02/09 12:54:39 M_Generic_Config.pm M_Generic_Config::config_print_all 1380> Unable to close the configuration file!\u001b[0m\n", "\u001b[35mFile:\t/home/sam/gitrepos/LabDocs/jupyter_nbs/sam/run_2018-02-09_11h14m36s/checkpoints/meraculous_import.local.params \u001b[0m\n", "\u001b[35m2018/02/09 12:54:39 meraculous.pl main::write_stage_params_file 3608> Params file creation failed for stage meraculous_import! \u001b[0m\n", "\u001b[35m2018/02/09 12:54:39 meraculous.pl main:: 769> Stage meraculous_import failed (6003.4647 seconds)\u001b[0m\n", "\u001b[35mDied at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 3609.\u001b[0m\n", "\u001b[35m \u001b[0m\n", "\u001b[34m2018/02/09 12:54:39 meraculous.pl main:: 824> RUN DID NOT COMPLETE ! \u001b[0m\n", "\u001b[34m2018/02/09 12:54:39 meraculous.pl main:: 828> Total run time: 6003.605069 seconds. \u001b[0m\n", "\u001b[34m2018/02/09 12:54:39 meraculous.pl main:: 830> Thank you for running Meraculous! \u001b[0m\n", "\n", "real\t100m4.039s\n", "user\t177m3.684s\n", "sys\t25m46.032s\n", "msmtp: cannot rewind temporary file: No space left on device\n" ] } ], "source": [ "%%bash\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh -dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ -c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 50M\n", "-rw-rw-r-- 1 sam sam 29K Mar 7 2017 20160203_Olurida_Zymo_Data_Handling.ipynb\n", "-rw-rw-r-- 1 sam sam 24K Mar 7 2017 20160126_Pgenerosa_BGI_data_handling.ipynb\n", "-rw-rw-r-- 1 sam sam 24K Mar 7 2017 20160126_Olurida_BGI_data_handling.ipynb\n", "-rw-rw-r-- 1 sam sam 14K Mar 7 2017 20160114_wasted_space_synologies.ipynb\n", "-rw-rw-r-- 1 sam sam 19K Mar 7 2017 20150521_Cgigas_larvae_OA_Trimmomatic_FASTQC.ipynb\n", "-rw-rw-r-- 1 sam sam 9.3K Mar 7 2017 20150506_Cgigas_larvae_OA_trimmomatic_FASTQC.ipynb\n", "-rw-rw-r-- 1 sam sam 23K Mar 7 2017 20150501_Cgigas_larvae_OA_BLASTn_nt.ipynb\n", "-rw-rw-r-- 1 sam sam 15K Mar 7 2017 20150429_Gigas_larvae_OA_BLASTn.ipynb\n", "-rw-rw-r-- 1 sam sam 73K Mar 7 2017 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb\n", "-rw-rw-r-- 1 sam sam 62K Mar 7 2017 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb\n", "-rw-rw-r-- 1 sam sam 5.1K Mar 7 2017 20150408_Install_Bismark_bisulfite_mapper.ipynb\n", "-rw-rw-r-- 1 sam sam 8.1K Mar 7 2017 20150317_LSU_OilSpill_EpinextAdaptor1_ID.ipynb\n", "-rw-rw-r-- 1 sam sam 14K Mar 7 2017 20150316_LSU_OilSpill_Adapter_ID.ipynb\n", "-rw-rw-r-- 1 sam sam 30K Mar 7 2017 20150313_LSU_Oil_Spill_IndexID_Comparisons.ipynb\n", "-rw-rw-r-- 1 sam sam 31M Mar 7 2017 20160308_find_rename_2bRAD_undetermined_fastqs.ipynb\n", "-rw-rw-r-- 1 sam sam 164K Mar 7 2017 20160406_STACKS_install.ipynb\n", "-rw-rw-r-- 1 sam sam 1.4M Mar 7 2017 20160406_Oly_GBS_STACKS.ipynb\n", "-rw-rw-r-- 1 sam sam 21K Mar 7 2017 20160314_Olurida_GBS_data_management.ipynb\n", "-rw-rw-r-- 1 sam sam 7.3K Mar 7 2017 20160516_Oly_Small_Insert_Library_Genome_Read_Counts.ipynb\n", "-rw-rw-r-- 1 sam sam 12K Mar 7 2017 20160502_Oly_GBS_barcode_repair.ipynb\n", "-rw-rw-r-- 1 sam sam 33K Mar 7 2017 20160428_Oly_GBS_STACKS.ipynb\n", "-rw-rw-r-- 1 sam sam 9.5K Mar 7 2017 20160427_speed_comparison.ipynb\n", "-rw-rw-r-- 1 sam sam 5.3K Mar 7 2017 20160427_Oly_GBS_data_management.ipynb\n", "-rw-rw-r-- 1 sam sam 135K Mar 7 2017 20160418_pyrad_oly_PE-GBS.ipynb\n", "-rw-rw-r-- 1 sam sam 114K Mar 7 2017 20160418_Oly_GBS_PE-Pyrad_populations.ipynb\n", "-rw-rw-r-- 1 sam sam 16K Mar 7 2017 20160411_Concatenate_Oly_MBDseq.ipynb\n", "-rw-rw-r-- 1 sam sam 18K Mar 7 2017 20160525_pyrad_oly_gbs_bgi.ipynb\n", "-rw-rw-r-- 1 sam sam 2.9M Mar 7 2017 20160523_Oly_GBS_Stacks.ipynb\n", "-rw-rw-r-- 1 sam sam 327K Mar 7 2017 20160715_ec2_oly_gbs_pyrad.ipynb\n", "-rw-rw-r-- 1 sam sam 95K Mar 7 2017 20160714_EC2_Oly_GBS_stacks_analysis.ipynb\n", "-rw-rw-r-- 1 sam sam 422K Mar 7 2017 20160609_pyrad_oly_gbs_bgi.ipynb\n", "-rw-rw-r-- 1 sam sam 24K Mar 7 2017 20170104_docker_oly_BGI_genome_corruption_solved.ipynb\n", "-rw-rw-r-- 1 sam sam 37K Mar 7 2017 20161230_docker_geoduck_RRBS_md5_checks.ipynb\n", "-rw-rw-r-- 1 sam sam 22K Mar 7 2017 20161229_docker_genewiz_geoduck_RRBS_data.ipynb\n", "-rw-rw-r-- 1 sam sam 19K Mar 7 2017 20161214_docker_notebook_trimming.ipynb\n", "-rw-rw-r-- 1 sam sam 81K Mar 7 2017 20161214_docker_BGI_data_integrity_check.ipynb\n", "-rw-rw-r-- 1 sam sam 6.4K Mar 7 2017 20161206_docker_BGI_genome_downloads.ipynb\n", "-rw-rw-r-- 1 sam sam 387K Mar 7 2017 20161129_docker_R_magics_failure.ipynb\n", "-rw-rw-r-- 1 sam sam 24K Mar 7 2017 20161117_docker_oly_vcf_analysis.ipynb\n", "-rw-rw-r-- 1 sam sam 23K Mar 7 2017 20161117_docker_oly_genome_fastq_corruption.ipynb\n", "-rw-rw-r-- 1 sam sam 7.4K Mar 7 2017 20161025_Pgenerosa_Small_Library_Genome_Read_Counts.ipynb\n", "-rw-rw-r-- 1 sam sam 677K Mar 7 2017 20160816_oly_gbs_fst_calcs.ipynb\n", "-rwxrwxr-x 1 sam sam 17K Mar 7 2017 PhageNGS.ipynb\n", "-rwxrwxr-x 1 sam sam 112K Mar 7 2017 PhageNGS_ID.ipynb\n", "-rw-rw-r-- 1 sam sam 97K Mar 7 2017 PE-GBS_empirical.ipynb\n", "-rwxrwxr-x 1 sam sam 21K Mar 7 2017 InstallingBLAST.ipynb\n", "-rw-rw-r-- 1 sam sam 338K Mar 7 2017 20170306_docker_fastqc_demultiplexed_bgi_oly_gbs.ipynb\n", "-rw-rw-r-- 1 sam sam 117K Mar 7 2017 20170227_docker_jay_ngs_data_retrieval.ipynb\n", "-rw-rw-r-- 1 sam sam 30K Jan 25 08:15 20170320_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb\n", "-rw-rw-r-- 1 sam sam 93K Jan 25 08:15 20170314_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb\n", "-rw-rw-r-- 1 sam sam 49K Jan 25 08:15 20170301_docker_fastqc_nondemultiplexed_bgi_oly_gbs.ipynb\n", "-rw-rw-r-- 1 sam sam 45K Jan 25 08:15 20170918_docker_pacbio_oly_miniasm0.2.ipynb\n", "-rw-rw-r-- 1 sam sam 44K Jan 25 08:15 20170907_docker_pacbio_oly_minimap2.ipynb\n", "-rw-rw-r-- 1 sam sam 78K Jan 25 08:15 20170622_oly_pacbio_data_management.ipynb\n", "-rw-rw-r-- 1 sam sam 1.3M Jan 25 08:15 20170918_docker_pacbio_oly_racon0.5.0.ipynb\n", "-rw-rw-r-- 1 sam sam 1.3M Jan 25 08:15 20171003_docker_oly_assembly_comparisons.ipynb\n", "-rw-rw-r-- 1 sam sam 3.1M Jan 25 08:15 20171004_docker_oly_redundans.ipynb\n", "-rw-rw-r-- 1 sam sam 291K Jan 25 08:15 20171018_docker_oly_canu.ipynb\n", "-rw-rw-r-- 1 sam sam 1.6M Jan 25 08:15 20171005_docker_oly_redundans.ipynb\n", "-rw-rw-r-- 1 sam sam 240 Jan 25 08:15 README.md\n", "-rw-rw-r-- 1 sam sam 31K Jan 25 08:15 20180103_emu_pbjelly.ipynb\n", "-rw-rw-r-- 1 sam sam 20K Jan 25 08:15 20171130_emu_pbjelly.ipynb\n", "-rw-rw-r-- 1 sam sam 27K Jan 25 08:15 20171114_swoose_oly_assembly_comparisons_quast.ipynb\n", "-rw-rw-r-- 1 sam sam 28K Jan 25 08:15 20171114_emu_pbjelly_BGI_scaffold.ipynb\n", "-rw-rw-r-- 1 sam sam 34K Jan 25 08:15 20171113_emu_pbjelly_22mer_plat.ipynb\n", "-rw-rw-r-- 1 sam sam 17K Jan 25 08:15 20171023_restore_scaphapoda_data.ipynb\n", "-rw-rw-r-- 1 sam sam 35K Jan 25 08:15 20171023_docker_oly_redundans.ipynb\n", "-rw-rw-r-- 1 sam sam 961K Jan 25 08:15 20171023_docker_oly_pacbio_canu_comparisons.ipynb\n", "-rw-rw-r-- 1 sam sam 15K Jan 25 08:55 20180116_swoose_oly_assembly_comparisons_quast.ipynb\n", "-rw-rw-r-- 1 sam sam 1.1K Jan 25 08:58 template_linux.ipynb\n", "-rw-rw-r-- 1 sam sam 1.1M Jan 29 07:43 multiqc_report.html\n", "drwxrwxr-x 2 sam sam 4.0K Jan 29 07:43 multiqc_data\n", "-rw-rw-r-- 1 sam sam 6.3K Jan 29 08:07 stdin_fastqc.zip\n", "-rw-rw-r-- 1 sam sam 927K Feb 5 13:09 20180125_roadrunner_trimming_geoduck_novaseq.ipynb\n", "-rw-rw-r-- 1 sam sam 1.4K Feb 5 14:31 Untitled.ipynb\n", "drwxrwxr-x 3 sam sam 4.0K Feb 9 07:03 run_2018-02-09_07h03m40s\n", "drwxrwxr-x 5 sam sam 4.0K Feb 9 07:47 run_2018-02-09_07h47m41s\n", "drwxrwxr-x 5 sam sam 4.0K Feb 9 09:38 run_2018-02-09_09h38m01s\n", "drwxrwxr-x 5 sam sam 4.0K Feb 9 11:14 run_2018-02-09_11h14m36s\n", "-rw-rw-r-- 1 sam sam 77K Feb 9 11:14 20180205_roadrunner_SoapDeNovo_geoduck_novaseq.ipynb\n" ] } ], "source": [ "%%bash\n", "ls -ltrh" ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "rm -rf run_2018*" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "meraculous run exited prematurely: 1\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/09 16:28:40 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/09 16:28:40 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/09 16:28:40 Setting the stage for the new run..\n", "2018/02/09 16:28:40 Prep work complete. From here on will channel all messages to appropriate logs ...\n", "2018/02/09 16:28:40 Logging to /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-09_16h28m40s/log/ ...\n", "\n", "\u001b[34m2018/02/09 16:28:59 meraculous.pl main:: 737> RUNNING STAGE: meraculous_import \u001b[0m\n", "\u001b[35m2018/02/10 08:00:40 meraculous.pl main::run_meraculous_import 985> Error in user parameters: No files found matching /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-09_16h28m40s/../fq.gz \u001b[0m\n", "\u001b[35m2018/02/10 08:00:40 meraculous.pl main:: 769> Stage meraculous_import failed (55900.91221 seconds)\u001b[0m\n", "\u001b[35m \u001b[0m\n", "\u001b[34m2018/02/10 08:00:40 meraculous.pl main:: 824> RUN DID NOT COMPLETE ! \u001b[0m\n", "\u001b[34m2018/02/10 08:00:40 meraculous.pl main:: 828> Total run time: 55919.270211 seconds. \u001b[0m\n", "\u001b[34m2018/02/10 08:00:40 meraculous.pl main:: 830> Thank you for running Meraculous! \u001b[0m\n", "\n", "real\t931m59.704s\n", "user\t422m36.140s\n", "sys\t82m33.192s\n" ] } ], "source": [ "%%bash\n", "cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh -dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ -c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Giving up on this for the time being. Have emailed the people who made this software to see if they can help." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Mon Feb 12 13:18:59 PST 2018\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "There was typo in the config file - the path to library NR01202 had a comma in it. \n", "\n", "Discovered this after the author pointed out that there's a log file that can be examined (human readable, pretty short).\n", "\n", "Here's the updated config file." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.gz AD00201 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2*.fq.gz AD00202 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2*.fq.gz NR00501 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2*.fq.gz NR00502 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2*.fq.gz NR00601 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2*.fq.gz NR00602 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2*.fq.gz NR01201 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2*.fq.gz NR01202 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2*.fq.gz NR01301 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2*.fq.gz NR01302 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2*.fq.gz NR01401 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2*.fq.gz NR01402 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2*.fq.gz NR01501 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2*.fq.gz NR01502 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2*.fq.gz NR01901 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2*.fq.gz NR01902 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2*.fq.gz NR02101 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2*.fq.gz NR02102 800 10 150 0 0 0 1 1 0 0\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters\n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\n" ] } ], "source": [ "%%bash\n", "cat /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Process is terminated.\n" ] } ], "source": [ "%%bash\n", "cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh -dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ -c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Stopped to change config file, per author's recommendation. Changing to use for contiging." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L001_R2*.fq.gz AD00201 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/AD002_S9_L002_R2*.fq.gz AD00202 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L001_R2*.fq.gz NR00501 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR005_S4_L002_R2*.fq.gz NR00502 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L001_R2*.fq.gz NR00601 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR006_S3_L002_R2*.fq.gz NR00602 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L001_R2*.fq.gz NR01201 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR012_S1_L002_R2*.fq.gz NR01202 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L001_R2*.fq.gz NR01301 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR013_AD013_S2_L002_R2*.fq.gz NR01302 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L001_R2*.fq.gz NR01401 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR014_AD014_S5_L002_R2*.fq.gz NR01402 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L001_R2*.fq.gz NR01501 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR015_AD015_S6_L002_R2*.fq.gz NR01502 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L001_R2*.fq.gz NR01901 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR019_S7_L002_R2*.fq.gz NR01902 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L001_R2*.fq.gz NR02101 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R1*.fq.gz,/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/NR021_S8_L002_R2*.fq.gz NR02102 800 10 150 0 0 1 1 1 0 0\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters\n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\n" ] } ], "source": [ "%%bash\n", "cat /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/12 14:46:24 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/12 14:46:24 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/12 14:46:24 Setting the stage for the new run..\n", "2018/02/12 14:46:24 Prep work complete. From here on will channel all messages to appropriate logs ...\n", "2018/02/12 14:46:24 Logging to /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/log/ ...\n", "\n", "\u001b[34m2018/02/12 14:46:24 meraculous.pl main:: 737> RUNNING STAGE: meraculous_import \u001b[0m\n", "\u001b[35m2018/02/12 16:29:48 M_Utility.pm M_Utility::run_local_cmd 770> Command failed! Return value: (7168) Command: (cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/meraculous_import; /home/shared/meraculous-2.2.5/bin/memtime -f /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/meraculous_import/JOB_SET_DIR.split-validate.NR01502/0.memtime perl /home/shared/meraculous-2.2.5/bin/split_and_validate_reads.pl -f \"/media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/meraculous_import/source_reads/NR01502.fastq.0.F.gz /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/meraculous_import/source_reads/NR01502.fastq.0.R.gz\" -p NR01502.fastq.0 -r 0.0001 -s 3333334 -N > /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/meraculous_import/JOB_SET_DIR.split-validate.NR01502/stdout_files/0/job_set.0.out 2> /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/meraculous_import/NR01502.splitNvalidate.0.err)\u001b[0m\n", "\u001b[35mFor more clues on what went wrong please examine the output and stderr files produced by this command! \u001b[0m\n", "\u001b[35m2018/02/12 16:29:48 meraculous.pl main:: 769> Stage meraculous_import failed (6203.749161 seconds)\u001b[0m\n", "\u001b[35mCannot write to '/media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/log/errors.log': No space left on device at /usr/local/share/perl/5.22.1/Log/Log4perl/Appender/File.pm line 313.\u001b[0m\n", "\u001b[35m \u001b[0m\n", "Cannot write to '/media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/log/errors.log': No space left on device at /usr/local/share/perl/5.22.1/Log/Log4perl/Appender/File.pm line 313.\n", "Can't close /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-12_14h46m24s/log/errors.log (No space left on device) at /usr/local/share/perl/5.22.1/Log/Log4perl/Appender/File.pm line 349 during global destruction.\n", "\n", "real\t103m24.526s\n", "user\t48m55.632s\n", "sys\t9m21.852s\n" ] } ], "source": [ "%%bash\n", "cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh -dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ -c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "20180129_trimmed_again\n", "meraculous.config\n", "run_2018-02-09_16h28m40s\n", "run_2018-02-12_13h40m03s\n", "run_2018-02-12_14h46m24s\n" ] } ], "source": [ "%%bash\n", "ls /media/sam/toaster/geoduck_novaseq_meraculous_assembly/" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "rm -rf /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run*" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ ".\n", "..\n", "20180129_trimmed_again\n", "meraculous.config\n" ] } ], "source": [ "%%bash\n", "ls -a /media/sam/toaster/geoduck_novaseq_meraculous_assembly/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Re-run with ```cleanup``` flag" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/13 06:54:01 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/13 06:54:01 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/13 06:54:01 Setting the stage for the new run..\n", "2018/02/13 06:54:01 Prep work complete. From here on will channel all messages to appropriate logs ...\n", "2018/02/13 06:54:01 Logging to /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/log/ ...\n", "\n", "\u001b[34m2018/02/13 06:54:01 meraculous.pl main:: 737> RUNNING STAGE: meraculous_import \u001b[0m\n", "\u001b[35m2018/02/14 00:53:21 M_Utility.pm M_Utility::run_local_cmd 770> Command failed! Return value: (7168) Command: (cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/meraculous_import; /home/shared/meraculous-2.2.5/bin/memtime -f /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/meraculous_import/JOB_SET_DIR.split-validate.NR01302/0.memtime perl /home/shared/meraculous-2.2.5/bin/split_and_validate_reads.pl -f \"/media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/meraculous_import/source_reads/NR01302.fastq.0.F.gz /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/meraculous_import/source_reads/NR01302.fastq.0.R.gz\" -p NR01302.fastq.0 -r 0.0001 -s 3333334 -N > /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/meraculous_import/JOB_SET_DIR.split-validate.NR01302/stdout_files/0/job_set.0.out 2> /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/meraculous_import/NR01302.splitNvalidate.0.err)\u001b[0m\n", "\u001b[35mFor more clues on what went wrong please examine the output and stderr files produced by this command! \u001b[0m\n", "\u001b[35m2018/02/14 00:53:21 meraculous.pl main:: 769> Stage meraculous_import failed (64759.583242 seconds)\u001b[0m\n", "\u001b[35mCannot write to '/media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/log/errors.log': No space left on device at /usr/local/share/perl/5.22.1/Log/Log4perl/Appender/File.pm line 313.\u001b[0m\n", "\u001b[35m \u001b[0m\n", "Cannot write to '/media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/log/errors.log': No space left on device at /usr/local/share/perl/5.22.1/Log/Log4perl/Appender/File.pm line 313.\n", "Can't close /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/log/errors.log (No space left on device) at /usr/local/share/perl/5.22.1/Log/Log4perl/Appender/File.pm line 349 during global destruction.\n", "\n", "real\t1079m20.569s\n", "user\t504m41.236s\n", "sys\t97m9.556s\n" ] } ], "source": [ "%%bash\n", "cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh \\\n", "-dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ \\\n", "-cleanup_level 1 \\\n", "-c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Filesystem Size Used Avail Use% Mounted on\n", "udev 24G 0 24G 0% /dev\n", "tmpfs 4.8G 490M 4.3G 11% /run\n", "/dev/sdb2 1.8T 493G 1.2T 30% /\n", "tmpfs 24G 308K 24G 1% /dev/shm\n", "tmpfs 5.0M 0 5.0M 0% /run/lock\n", "tmpfs 24G 0 24G 0% /sys/fs/cgroup\n", "/dev/sdb1 511M 3.5M 508M 1% /boot/efi\n", "tmpfs 4.8G 112K 4.8G 1% /run/user/1001\n", "//owl.fish.washington.edu/web 51T 41T 11T 80% /home/sam/owl\n", "/dev/sda1 1.9T 1.9T 0 100% /media/sam/toaster\n" ] } ], "source": [ "%%bash\n", "df -h" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "rm -rf /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-13_06h54m01s/" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Filesystem Size Used Avail Use% Mounted on\n", "udev 24G 0 24G 0% /dev\n", "tmpfs 4.8G 490M 4.3G 11% /run\n", "/dev/sdb2 1.8T 493G 1.2T 30% /\n", "tmpfs 24G 308K 24G 1% /dev/shm\n", "tmpfs 5.0M 0 5.0M 0% /run/lock\n", "tmpfs 24G 0 24G 0% /sys/fs/cgroup\n", "/dev/sdb1 511M 3.5M 508M 1% /boot/efi\n", "tmpfs 4.8G 112K 4.8G 1% /run/user/1001\n", "//owl.fish.washington.edu/web 51T 41T 11T 80% /home/sam/owl\n", "/dev/sda1 1.9T 374G 1.5T 21% /media/sam/toaster\n" ] } ], "source": [ "%%bash\n", "df -h" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "rm: cannot remove '/media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/': Directory not empty\n" ] } ], "source": [ "%%bash\n", "rm -rf /media/sam/toaster/geoduck_novaseq_meraculous_assembly/20180129_trimmed_again/" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Filesystem Size Used Avail Use% Mounted on\n", "udev 24G 0 24G 0% /dev\n", "tmpfs 4.8G 490M 4.3G 11% /run\n", "/dev/sdb2 1.8T 493G 1.2T 30% /\n", "tmpfs 24G 308K 24G 1% /dev/shm\n", "tmpfs 5.0M 0 5.0M 0% /run/lock\n", "tmpfs 24G 0 24G 0% /sys/fs/cgroup\n", "/dev/sdb1 511M 3.5M 508M 1% /boot/efi\n", "tmpfs 4.8G 112K 4.8G 1% /run/user/1001\n", "//owl.fish.washington.edu/web 51T 41T 11T 80% /home/sam/owl\n", "/dev/sda1 1.9T 44G 1.8T 3% /media/sam/toaster\n" ] } ], "source": [ "%%bash\n", "df -h" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/AD002*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/AD002*R2*.fq.gz AD002 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR005*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR005*R2*.fq.gz NR005 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR006*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR006*R2*.fq.gz NR006 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR012*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR012*R2*.fq.gz NR012 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR013*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR013*R2*.fq.gz NR013 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR014*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR014*R2*.fq.gz NR014 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR015*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR015*R2*.fq.gz NR015 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR019*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR019*R2*.fq.gz NR019 800 10 150 0 0 0 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR021*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR021*R2*.fq.gz NR021 800 10 150 0 0 0 1 1 0 0\n", "\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters\n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\n" ] } ], "source": [ "%%bash\n", "cat /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Deleted fastq files from \"toaster\". Changed \"cleanup level\" to highest level (i.e. will delete most intermediate files)." ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "meraculous run exited prematurely: 1\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 929.\n", "Smartmatch is experimental at /home/shared/meraculous-2.2.5/bin/meraculous.pl line 2789.\n", "2018/02/15 11:08:40 Meraculous runtime root directory: /home/shared/meraculous-2.2.5/\n", "2018/02/15 11:08:40 Loading run parameters from /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config ...\n", "2018/02/15 11:08:40 Setting the stage for the new run..\n", "2018/02/15 11:08:40 Prep work complete. From here on will channel all messages to appropriate logs ...\n", "2018/02/15 11:08:40 Logging to /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-15_11h08m40s/log/ ...\n", "\n", "\u001b[34m2018/02/15 11:08:40 meraculous.pl main:: 737> RUNNING STAGE: meraculous_import \u001b[0m\n", "\u001b[35m2018/02/15 20:14:13 meraculous.pl main::run_meraculous_import 1194> ERROR: Can't perform load balancing: /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run_2018-02-15_11h08m40s/meraculous_import/prefixer.sample.info is empty! Please verify that at least one library is selected for contig generation. \u001b[0m\n", "\u001b[35m2018/02/15 20:14:13 meraculous.pl main:: 769> Stage meraculous_import failed (32732.106668 seconds)\u001b[0m\n", "\u001b[35m \u001b[0m\n", "\u001b[34m2018/02/15 20:14:13 meraculous.pl main:: 824> RUN DID NOT COMPLETE ! \u001b[0m\n", "\u001b[34m2018/02/15 20:14:13 meraculous.pl main:: 828> Total run time: 32732.258263 seconds. \u001b[0m\n", "\u001b[34m2018/02/15 20:14:13 meraculous.pl main:: 830> Thank you for running Meraculous! \u001b[0m\n", "\n", "real\t545m33.077s\n", "user\t652m25.780s\n", "sys\t144m16.544s\n" ] } ], "source": [ "%%bash\n", "cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh \\\n", "-dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ \\\n", "-cleanup_level 2 \\\n", "-c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Oh my gosh! I edited the wrong config file and had the wrong contig value in! Grrrr. Edited again and it should be correct, now." ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "###################################\n", "#\n", "# Meraculous params file\n", "#\n", "###################################\n", "\n", "\n", "#######################################\n", "#\n", "# Basic parameters\n", "#\n", "########################################\n", "\n", "\n", "\n", "# Describe the libraries ( one line per library )\n", "# lib_seq [ wildcard ][ prefix ][ insAvg ][ insSdev ][ avgReadLen ][ hasInnieArtifact ][ isRevComped ][ useForContigging ][ onoSetId ][ useForGapClosing ][ 5pWiggleRoom ][3pWiggleRoom]\n", "#\n", "\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/AD002*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/AD002*R2*.fq.gz AD002 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR005*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR005*R2*.fq.gz NR005 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR006*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR006*R2*.fq.gz NR006 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR012*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR012*R2*.fq.gz NR012 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR013*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR013*R2*.fq.gz NR013 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR014*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR014*R2*.fq.gz NR014 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR015*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR015*R2*.fq.gz NR015 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR019*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR019*R2*.fq.gz NR019 800 10 150 0 0 1 1 1 0 0\n", "lib_seq /home/sam/data/geoduck_illumina/trimmed/NR021*R1*.fq.gz,/home/sam/data/geoduck_illumina/trimmed/NR021*R2*.fq.gz NR021 800 10 150 0 0 1 1 1 0 0\n", "\n", "\n", "\n", "genome_size 2.1697\n", "\n", "diploid_mode 1\n", "\n", "mer_size 117\n", "\n", "min_depth_cutoff 7\n", "\n", "num_prefix_blocks 4\n", "\n", "\n", "#################################################\n", "#\n", "# Advanced parameters\n", "#\n", "#################################################\n", "\n", "no_read_validation 1\n", "\n", "use_cluster 0\n", "\n", "local_num_procs 16\n", "\n", "local_max_retries 0\n", "\n" ] } ], "source": [ "%%bash\n", "cat /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Process is terminated.\n" ] } ], "source": [ "%%bash\n", "cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh \\\n", "-dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ \\\n", "-cleanup_level 2 \\\n", "-c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Filesystem Size Used Avail Use% Mounted on\n", "udev 24G 0 24G 0% /dev\n", "tmpfs 4.8G 522M 4.3G 11% /run\n", "/dev/sdb2 1.8T 493G 1.2T 30% /\n", "tmpfs 24G 308K 24G 1% /dev/shm\n", "tmpfs 5.0M 0 5.0M 0% /run/lock\n", "tmpfs 24G 0 24G 0% /sys/fs/cgroup\n", "/dev/sdb1 511M 3.5M 508M 1% /boot/efi\n", "tmpfs 4.8G 112K 4.8G 1% /run/user/1001\n", "//owl.fish.washington.edu/web 51T 41T 11T 80% /home/sam/owl\n", "/dev/sda1 1.9T 1.8T 44G 98% /media/sam/toaster\n" ] } ], "source": [ "%%bash\n", "df -h" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Filesystem Size Used Avail Use% Mounted on\n", "udev 24G 0 24G 0% /dev\n", "tmpfs 4.8G 522M 4.3G 11% /run\n", "/dev/sdb2 1.8T 493G 1.2T 30% /\n", "tmpfs 24G 308K 24G 1% /dev/shm\n", "tmpfs 5.0M 0 5.0M 0% /run/lock\n", "tmpfs 24G 0 24G 0% /sys/fs/cgroup\n", "/dev/sdb1 511M 3.5M 508M 1% /boot/efi\n", "tmpfs 4.8G 112K 4.8G 1% /run/user/1001\n", "//owl.fish.washington.edu/web 51T 41T 11T 80% /home/sam/owl\n", "/dev/sda1 1.9T 125M 1.9T 1% /media/sam/toaster\n" ] } ], "source": [ "%%bash\n", "rm -rf /media/sam/toaster/geoduck_novaseq_meraculous_assembly/run*\n", "df -h" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "cd /media/sam/toaster/geoduck_novaseq_meraculous_assembly/\n", "time /home/shared/meraculous-2.2.5/bin/run_meraculous.sh \\\n", "-dir /media/sam/toaster/geoduck_novaseq_meraculous_assembly/ \\\n", "-cleanup_level 2 \\\n", "-c /media/sam/toaster/geoduck_novaseq_meraculous_assembly/meraculous.config\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "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": "3.6.3" } }, "nbformat": 4, "nbformat_minor": 2 }