{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE:\n", "Wed May 16 15:00:45 PDT 2018\n", "------------\n", "\n", "Distributor ID:\tUbuntu\n", "Description:\tUbuntu 16.04.4 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: 2394.000\n", "CPU max MHz: 2394.0000\n", "CPU min MHz: 1596.0000\n", "BogoMIPS: 4521.81\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 retpoline 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 421M 3.0G 314M 43G 45G\n", "Swap: 47G 281M 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 #Display operating system info\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"HOSTNAME: \"; hostname \n", "echo \"\"\n", "echo \"------------\"\n", "echo \"Computer Specs:\"\n", "echo \"\"\n", "lscpu\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"\"\n", "echo \"Memory Specs\"\n", "echo \"\"\n", "free -mh" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t2476m19.582s\n", "user\t4465m5.380s\n", "sys\t161m8.248s\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs\n", "mkdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc\n", "\n", "cd /home/sam/data/geoduck_EPI\n", "\n", "time \\\n", "/home/shared/TrimGalore-0.4.5/trim_galore \\\n", "--paired \\\n", "--rrbs \\\n", "--output_dir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs \\\n", "--fastqc_args \\\n", "\"--outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc \\\n", "--threads 16\" \\\n", "EPI-103_S27_L005_R1_001.fastq.gz \\\n", "EPI-103_S27_L005_R2_001.fastq.gz \\\n", "EPI-104_S28_L005_R1_001.fastq.gz \\\n", "EPI-104_S28_L005_R2_001.fastq.gz \\\n", "EPI-111_S29_L005_R1_001.fastq.gz \\\n", "EPI-111_S29_L005_R2_001.fastq.gz \\\n", "EPI-113_S30_L005_R1_001.fastq.gz \\\n", "EPI-113_S30_L005_R2_001.fastq.gz \\\n", "EPI-119_S31_L005_R1_001.fastq.gz \\\n", "EPI-119_S31_L005_R2_001.fastq.gz \\\n", "EPI-120_S32_L005_R1_001.fastq.gz \\\n", "EPI-120_S32_L005_R2_001.fastq.gz \\\n", "EPI-127_S33_L005_R1_001.fastq.gz \\\n", "EPI-127_S33_L005_R2_001.fastq.gz \\\n", "EPI-128_S34_L005_R1_001.fastq.gz \\\n", "EPI-128_S34_L005_R2_001.fastq.gz \\\n", "EPI-135_S35_L005_R1_001.fastq.gz \\\n", "EPI-135_S35_L005_R2_001.fastq.gz \\\n", "EPI-136_S36_L005_R1_001.fastq.gz \\\n", "EPI-136_S36_L005_R2_001.fastq.gz \\\n", "EPI-143_S37_L005_R1_001.fastq.gz \\\n", "EPI-143_S37_L005_R2_001.fastq.gz \\\n", "EPI-145_S38_L005_R1_001.fastq.gz \\\n", "EPI-145_S38_L005_R2_001.fastq.gz \\\n", "EPI-151_S2_L002_R1_001.fastq.gz \\\n", "EPI-151_S2_L002_R2_001.fastq.gz \\\n", "EPI-152_S3_L002_R1_001.fastq.gz \\\n", "EPI-152_S3_L002_R2_001.fastq.gz \\\n", "EPI-153_S4_L002_R1_001.fastq.gz \\\n", "EPI-153_S4_L002_R2_001.fastq.gz \\\n", "EPI-154_S5_L002_R1_001.fastq.gz \\\n", "EPI-154_S5_L002_R2_001.fastq.gz \\\n", "EPI-159_S6_L002_R1_001.fastq.gz \\\n", "EPI-159_S6_L002_R2_001.fastq.gz \\\n", "EPI-160_S7_L002_R1_001.fastq.gz \\\n", "EPI-160_S7_L002_R2_001.fastq.gz \\\n", "EPI-161_S8_L002_R1_001.fastq.gz \\\n", "EPI-161_S8_L002_R2_001.fastq.gz \\\n", "EPI-162_S9_L002_R1_001.fastq.gz \\\n", "EPI-162_S9_L002_R2_001.fastq.gz \\\n", "EPI-167_S10_L002_R1_001.fastq.gz \\\n", "EPI-167_S10_L002_R2_001.fastq.gz \\\n", "EPI-168_S11_L002_R1_001.fastq.gz \\\n", "EPI-168_S11_L002_R2_001.fastq.gz \\\n", "EPI-169_S12_L002_R1_001.fastq.gz \\\n", "EPI-169_S12_L002_R2_001.fastq.gz \\\n", "EPI-170_S13_L002_R1_001.fastq.gz \\\n", "EPI-170_S13_L002_R2_001.fastq.gz \\\n", "EPI-175_S14_L003_R1_001.fastq.gz \\\n", "EPI-175_S14_L003_R2_001.fastq.gz \\\n", "EPI-176_S15_L003_R1_001.fastq.gz \\\n", "EPI-176_S15_L003_R2_001.fastq.gz \\\n", "EPI-181_S16_L003_R1_001.fastq.gz \\\n", "EPI-181_S16_L003_R2_001.fastq.gz \\\n", "EPI-182_S17_L003_R1_001.fastq.gz \\\n", "EPI-182_S17_L003_R2_001.fastq.gz \\\n", "EPI-184_S18_L003_R1_001.fastq.gz \\\n", "EPI-184_S18_L003_R2_001.fastq.gz \\\n", "EPI-185_S19_L003_R1_001.fastq.gz \\\n", "EPI-185_S19_L003_R2_001.fastq.gz \\\n", "EPI-187_S20_L003_R1_001.fastq.gz \\\n", "EPI-187_S20_L003_R2_001.fastq.gz \\\n", "EPI-188_S21_L003_R1_001.fastq.gz \\\n", "EPI-188_S21_L003_R2_001.fastq.gz \\\n", "EPI-193_S22_L003_R1_001.fastq.gz \\\n", "EPI-193_S22_L003_R2_001.fastq.gz \\\n", "EPI-194_S23_L003_R1_001.fastq.gz \\\n", "EPI-194_S23_L003_R2_001.fastq.gz \\\n", "EPI-199_S24_L003_R1_001.fastq.gz \\\n", "EPI-199_S24_L003_R2_001.fastq.gz \\\n", "EPI-200_S25_L003_R1_001.fastq.gz \\\n", "EPI-200_S25_L003_R2_001.fastq.gz \\\n", "EPI-205_S26_L004_R1_001.fastq.gz \\\n", "EPI-205_S26_L004_R2_001.fastq.gz \\\n", "EPI-206_S27_L004_R1_001.fastq.gz \\\n", "EPI-206_S27_L004_R2_001.fastq.gz \\\n", "EPI-208_S28_L004_R1_001.fastq.gz \\\n", "EPI-208_S28_L004_R2_001.fastq.gz \\\n", "EPI-209_S29_L004_R1_001.fastq.gz \\\n", "EPI-209_S29_L004_R2_001.fastq.gz \\\n", "EPI-214_S30_L004_R1_001.fastq.gz \\\n", "EPI-214_S30_L004_R2_001.fastq.gz \\\n", "EPI-215_S31_L004_R1_001.fastq.gz \\\n", "EPI-215_S31_L004_R2_001.fastq.gz \\\n", "EPI-220_S32_L004_R1_001.fastq.gz \\\n", "EPI-220_S32_L004_R2_001.fastq.gz \\\n", "EPI-221_S33_L004_R1_001.fastq.gz \\\n", "EPI-221_S33_L004_R2_001.fastq.gz \\\n", "EPI-226_S34_L004_R1_001.fastq.gz \\\n", "EPI-226_S34_L004_R2_001.fastq.gz \\\n", "EPI-227_S35_L004_R1_001.fastq.gz \\\n", "EPI-227_S35_L004_R2_001.fastq.gz \\\n", "EPI-229_S36_L004_R1_001.fastq.gz \\\n", "EPI-229_S36_L004_R2_001.fastq.gz \\\n", "EPI-230_S37_L004_R1_001.fastq.gz \\\n", "EPI-230_S37_L004_R2_001.fastq.gz \\\n", "EPI-41_S38_L005_R1_001.fastq.gz \\\n", "EPI-41_S38_L005_R2_001.fastq.gz \\\n", "EPI-42_S39_L005_R1_001.fastq.gz \\\n", "EPI-42_S39_L005_R2_001.fastq.gz \\\n", "EPI-43_S40_L005_R1_001.fastq.gz \\\n", "EPI-43_S40_L005_R2_001.fastq.gz \\\n", "EPI-44_S41_L005_R1_001.fastq.gz \\\n", "EPI-44_S41_L005_R2_001.fastq.gz \\\n", "> /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_trimgalore.stdout.log \\\n", "2> /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_trimgalore.stderr.log\n", "\n", "sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "85ec9e3b29b275ee66ec3be160bad40c EPI-230_S37_L004_R1_001_val_1.fq.gz\n", "19d0bd60270191591904eb0b3a1f5ccc EPI-230_S37_L004_R2_001_val_2.fq.gz\n", "449084831e4c9ca324d7e956fcd00d55 EPI-41_S38_L005_R1_001_val_1.fq.gz\n", "451ce4da5f41a1fb7a5391d24eb2230a EPI-41_S38_L005_R2_001_val_2.fq.gz\n", "5e1780aff85d128b13f4ed2527a068da EPI-42_S39_L005_R1_001_val_1.fq.gz\n", "5172dc0022030e5e24c2e713d6a21531 EPI-42_S39_L005_R2_001_val_2.fq.gz\n", "d06640779f9ce376084f82cbf2c15a2c EPI-43_S40_L005_R1_001_val_1.fq.gz\n", "d137cbaa90b95334b459e7a6e5e93065 EPI-43_S40_L005_R2_001_val_2.fq.gz\n", "67ce2af15035316ba66b86965d6987e8 EPI-44_S41_L005_R1_001_val_1.fq.gz\n", "81a9286c4fa9b4cbba42ace1118e4dca EPI-44_S41_L005_R2_001_val_2.fq.gz\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t12m26.097s\n", "user\t4m53.484s\n", "sys\t0m49.024s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/\n", "\n", "time \\\n", "for fq in *_val*.gz\n", "do md5sum \"$fq\" >> checksums.md5\n", "done\n", "\n", "tail /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/checksums.md5\n", "\n", "sed '/^Subject:/ s/ / checksums JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Searching 208 files..\n", "total 3820\n", "-rw-rw-r-- 1 sam sam 127519 May 18 08:34 mqc_fastqc_per_base_n_content_plot_1.txt\n", "-rw-rw-r-- 1 sam sam 122609 May 18 08:34 mqc_fastqc_per_base_sequence_quality_plot_1.txt\n", "-rw-rw-r-- 1 sam sam 83123 May 18 08:34 mqc_fastqc_per_sequence_gc_content_plot_Counts.txt\n", "-rw-rw-r-- 1 sam sam 216075 May 18 08:34 mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt\n", "-rw-rw-r-- 1 sam sam 41835 May 18 08:34 mqc_fastqc_per_sequence_quality_scores_plot_1.txt\n", "-rw-rw-r-- 1 sam sam 117874 May 18 08:34 mqc_fastqc_sequence_duplication_levels_plot_1.txt\n", "-rw-rw-r-- 1 sam sam 53330 May 18 08:34 mqc_fastqc_sequence_length_distribution_plot_1.txt\n", "-rw-rw-r-- 1 sam sam 215878 May 18 08:34 multiqc_data.json\n", "-rw-rw-r-- 1 sam sam 24211 May 18 08:34 multiqc_fastqc.txt\n", "-rw-rw-r-- 1 sam sam 10632 May 18 08:34 multiqc_general_stats.txt\n", "-rw-rw-r-- 1 sam sam 30727 May 18 08:34 multiqc.log\n", "-rw-rw-r-- 1 sam sam 2822352 May 18 08:34 multiqc_report.html\n", "-rw-rw-r-- 1 sam sam 19018 May 18 08:34 multiqc_sources.txt\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[INFO ] multiqc : This is MultiQC v1.5.dev0\n", "[INFO ] multiqc : Template : default\n", "[INFO ] multiqc : Searching '.'\n", "[INFO ] fastqc : Found 104 reports\n", "[INFO ] multiqc : Compressing plot data\n", "[INFO ] multiqc : Report : multiqc_report.html\n", "[INFO ] multiqc : Data : multiqc_data\n", "[INFO ] multiqc : MultiQC complete\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc\n", "\n", "/home/shared/anaconda3/bin/multiqc .\n", "\n", "\n", "mv /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_report.html \\\n", "/home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_data/\n", "\n", "ls -l /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_data/" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/\n", "/mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc\n", "/mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc/multiqc_data\n" ] } ], "source": [ "%%bash\n", "find /mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/ \\\n", "-type d" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "EPI-103_S27_L005_R1_001_val_1.fq.gz: OK\n", "EPI-103_S27_L005_R2_001_val_2.fq.gz: OK\n", "EPI-104_S28_L005_R1_001_val_1.fq.gz: OK\n", "EPI-104_S28_L005_R2_001_val_2.fq.gz: OK\n", "EPI-111_S29_L005_R1_001_val_1.fq.gz: OK\n", "EPI-111_S29_L005_R2_001_val_2.fq.gz: OK\n", "EPI-113_S30_L005_R1_001_val_1.fq.gz: OK\n", "EPI-113_S30_L005_R2_001_val_2.fq.gz: OK\n", "EPI-119_S31_L005_R1_001_val_1.fq.gz: OK\n", "EPI-119_S31_L005_R2_001_val_2.fq.gz: OK\n", "EPI-120_S32_L005_R1_001_val_1.fq.gz: OK\n", "EPI-120_S32_L005_R2_001_val_2.fq.gz: OK\n", "EPI-127_S33_L005_R1_001_val_1.fq.gz: OK\n", "EPI-127_S33_L005_R2_001_val_2.fq.gz: OK\n", "EPI-128_S34_L005_R1_001_val_1.fq.gz: OK\n", "EPI-128_S34_L005_R2_001_val_2.fq.gz: OK\n", "EPI-135_S35_L005_R1_001_val_1.fq.gz: OK\n", "EPI-135_S35_L005_R2_001_val_2.fq.gz: OK\n", "EPI-136_S36_L005_R1_001_val_1.fq.gz: OK\n", "EPI-136_S36_L005_R2_001_val_2.fq.gz: OK\n", "EPI-143_S37_L005_R1_001_val_1.fq.gz: OK\n", "EPI-143_S37_L005_R2_001_val_2.fq.gz: OK\n", "EPI-145_S38_L005_R1_001_val_1.fq.gz: OK\n", "EPI-145_S38_L005_R2_001_val_2.fq.gz: OK\n", "EPI-151_S2_L002_R1_001_val_1.fq.gz: OK\n", "EPI-151_S2_L002_R2_001_val_2.fq.gz: OK\n", "EPI-152_S3_L002_R1_001_val_1.fq.gz: OK\n", "EPI-152_S3_L002_R2_001_val_2.fq.gz: OK\n", "EPI-153_S4_L002_R1_001_val_1.fq.gz: OK\n", "EPI-153_S4_L002_R2_001_val_2.fq.gz: OK\n", "EPI-154_S5_L002_R1_001_val_1.fq.gz: OK\n", "EPI-154_S5_L002_R2_001_val_2.fq.gz: OK\n", "EPI-159_S6_L002_R1_001_val_1.fq.gz: OK\n", "EPI-159_S6_L002_R2_001_val_2.fq.gz: OK\n", "EPI-160_S7_L002_R1_001_val_1.fq.gz: OK\n", "EPI-160_S7_L002_R2_001_val_2.fq.gz: OK\n", "EPI-161_S8_L002_R1_001_val_1.fq.gz: OK\n", "EPI-161_S8_L002_R2_001_val_2.fq.gz: OK\n", "EPI-162_S9_L002_R1_001_val_1.fq.gz: OK\n", "EPI-162_S9_L002_R2_001_val_2.fq.gz: OK\n", "EPI-167_S10_L002_R1_001_val_1.fq.gz: OK\n", "EPI-167_S10_L002_R2_001_val_2.fq.gz: OK\n", "EPI-168_S11_L002_R1_001_val_1.fq.gz: OK\n", "EPI-168_S11_L002_R2_001_val_2.fq.gz: OK\n", "EPI-169_S12_L002_R1_001_val_1.fq.gz: OK\n", "EPI-169_S12_L002_R2_001_val_2.fq.gz: OK\n", "EPI-170_S13_L002_R1_001_val_1.fq.gz: OK\n", "EPI-170_S13_L002_R2_001_val_2.fq.gz: OK\n", "EPI-175_S14_L003_R1_001_val_1.fq.gz: OK\n", "EPI-175_S14_L003_R2_001_val_2.fq.gz: OK\n", "EPI-176_S15_L003_R1_001_val_1.fq.gz: OK\n", "EPI-176_S15_L003_R2_001_val_2.fq.gz: OK\n", "EPI-181_S16_L003_R1_001_val_1.fq.gz: OK\n", "EPI-181_S16_L003_R2_001_val_2.fq.gz: OK\n", "EPI-182_S17_L003_R1_001_val_1.fq.gz: OK\n", "EPI-182_S17_L003_R2_001_val_2.fq.gz: OK\n", "EPI-184_S18_L003_R1_001_val_1.fq.gz: OK\n", "EPI-184_S18_L003_R2_001_val_2.fq.gz: OK\n", "EPI-185_S19_L003_R1_001_val_1.fq.gz: OK\n", "EPI-185_S19_L003_R2_001_val_2.fq.gz: OK\n", "EPI-187_S20_L003_R1_001_val_1.fq.gz: OK\n", "EPI-187_S20_L003_R2_001_val_2.fq.gz: OK\n", "EPI-188_S21_L003_R1_001_val_1.fq.gz: OK\n", "EPI-188_S21_L003_R2_001_val_2.fq.gz: OK\n", "EPI-193_S22_L003_R1_001_val_1.fq.gz: OK\n", "EPI-193_S22_L003_R2_001_val_2.fq.gz: OK\n", "EPI-194_S23_L003_R1_001_val_1.fq.gz: OK\n", "EPI-194_S23_L003_R2_001_val_2.fq.gz: OK\n", "EPI-199_S24_L003_R1_001_val_1.fq.gz: OK\n", "EPI-199_S24_L003_R2_001_val_2.fq.gz: OK\n", "EPI-200_S25_L003_R1_001_val_1.fq.gz: OK\n", "EPI-200_S25_L003_R2_001_val_2.fq.gz: OK\n", "EPI-205_S26_L004_R1_001_val_1.fq.gz: OK\n", "EPI-205_S26_L004_R2_001_val_2.fq.gz: OK\n", "EPI-206_S27_L004_R1_001_val_1.fq.gz: OK\n", "EPI-206_S27_L004_R2_001_val_2.fq.gz: OK\n", "EPI-208_S28_L004_R1_001_val_1.fq.gz: OK\n", "EPI-208_S28_L004_R2_001_val_2.fq.gz: OK\n", "EPI-209_S29_L004_R1_001_val_1.fq.gz: OK\n", "EPI-209_S29_L004_R2_001_val_2.fq.gz: OK\n", "EPI-214_S30_L004_R1_001_val_1.fq.gz: OK\n", "EPI-214_S30_L004_R2_001_val_2.fq.gz: OK\n", "EPI-215_S31_L004_R1_001_val_1.fq.gz: OK\n", "EPI-215_S31_L004_R2_001_val_2.fq.gz: OK\n", "EPI-220_S32_L004_R1_001_val_1.fq.gz: OK\n", "EPI-220_S32_L004_R2_001_val_2.fq.gz: OK\n", "EPI-221_S33_L004_R1_001_val_1.fq.gz: OK\n", "EPI-221_S33_L004_R2_001_val_2.fq.gz: OK\n", "EPI-226_S34_L004_R1_001_val_1.fq.gz: OK\n", "EPI-226_S34_L004_R2_001_val_2.fq.gz: OK\n", "EPI-227_S35_L004_R1_001_val_1.fq.gz: OK\n", "EPI-227_S35_L004_R2_001_val_2.fq.gz: OK\n", "EPI-229_S36_L004_R1_001_val_1.fq.gz: OK\n", "EPI-229_S36_L004_R2_001_val_2.fq.gz: OK\n", "EPI-230_S37_L004_R1_001_val_1.fq.gz: OK\n", "EPI-230_S37_L004_R2_001_val_2.fq.gz: OK\n", "EPI-41_S38_L005_R1_001_val_1.fq.gz: OK\n", "EPI-41_S38_L005_R2_001_val_2.fq.gz: OK\n", "EPI-42_S39_L005_R1_001_val_1.fq.gz: OK\n", "EPI-42_S39_L005_R2_001_val_2.fq.gz: OK\n", "EPI-43_S40_L005_R1_001_val_1.fq.gz: OK\n", "EPI-43_S40_L005_R2_001_val_2.fq.gz: OK\n", "EPI-44_S41_L005_R1_001_val_1.fq.gz: OK\n", "EPI-44_S41_L005_R2_001_val_2.fq.gz: OK\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t21m33.769s\n", "user\t4m45.188s\n", "sys\t0m32.968s\n" ] } ], "source": [ "%%bash\n", "\n", "cd /mnt/owl/Athaliana/20180516_geoduck_trimgalore_rrbs/\n", "\n", "time \\\n", "md5sum -c checksums.md5\n", "\n", "sed '/^Subject:/ s/ / checksums JOB COMPLETE/' ~/.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 }