{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE:\n", "Tue Sep 11 12:47:33 PDT 2018\n", "------------\n", "\n", "Distributor ID:\tUbuntu\n", "Description:\tUbuntu 16.04.5 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: 4521.80\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 eagerfpu 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 2.1G 9.8G 559M 35G 43G\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", "#Display operating system info\n", "lsb_release -a\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"HOSTNAME: \"; hostname \n", "echo \"\"\n", "echo \"------------\"\n", "echo \"Computer Specs:\"\n", "echo \"\"\n", "lscpu\n", "echo \"\"\n", "echo \"------------\"\n", "echo \"\"\n", "echo \"Memory Specs\"\n", "echo \"\"\n", "free -mh" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "20180910_Cvirginica_oil_fastqc\n", "2112_lane1_ACAGTG.fastq.gz\n", "2112_lane1_ATCACG.fastq.gz\n", "2112_lane1_CAGATC.fastq.gz\n", "2112_lane1_GCCAAT.fastq.gz\n", "2112_lane1_TGACCA.fastq.gz\n", "2112_lane1_TTAGGC.fastq.gz\n" ] } ], "source": [ "%%bash\n", "ls /home/sam/data/Cvirginica/concatenated/" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m0.091s\n", "user\t0m0.044s\n", "sys\t0m0.004s\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01\n", "mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc\n", "cd /home/sam/data/Cvirginica/concatenated/\n", "\n", "time \\\n", "/home/shared/TrimGalore-0.4.5/trim_galore \\\n", "--ouput_dir /home/sam/analyses/20180911_virginica_oil_trimgalore_01 \\\n", "--fastqc_args \\\n", "\"--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc \\\n", "--threads 16\" \\\n", "2112_lane1_ACAGTG.fastq.gz \\\n", "2112_lane1_ATCACG.fastq.gz \\\n", "2112_lane1_CAGATC.fastq.gz \\\n", "2112_lane1_GCCAAT.fastq.gz \\\n", "2112_lane1_TGACCA.fastq.gz \\\n", "2112_lane1_TTAGGC.fastq.gz \\\n", "> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stdout.log \\\n", "2> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stderr.log\n", "\n", "sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "tail /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stdout.log" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Unknown option: ouput_dir\n", "Please respecify command line options\n" ] } ], "source": [ "%%bash\n", "tail /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stderr.log" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Fix typo" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "mkdir: cannot create directory ‘/home/sam/analyses/20180911_virginica_oil_trimgalore_01’: File exists\n", "mkdir: cannot create directory ‘/home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc’: File exists\n", "\n", "real\t78m53.332s\n", "user\t144m38.712s\n", "sys\t3m52.692s\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01\n", "mkdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc\n", "cd /home/sam/data/Cvirginica/concatenated/\n", "\n", "time \\\n", "/home/shared/TrimGalore-0.4.5/trim_galore \\\n", "--output_dir /home/sam/analyses/20180911_virginica_oil_trimgalore_01 \\\n", "--fastqc_args \\\n", "\"--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc \\\n", "--threads 16\" \\\n", "2112_lane1_ACAGTG.fastq.gz \\\n", "2112_lane1_ATCACG.fastq.gz \\\n", "2112_lane1_CAGATC.fastq.gz \\\n", "2112_lane1_GCCAAT.fastq.gz \\\n", "2112_lane1_TGACCA.fastq.gz \\\n", "2112_lane1_TTAGGC.fastq.gz \\\n", "> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stdout.log \\\n", "2> /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_trimgalore.stderr.log\n", "\n", "sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "20180911_trimgalore.stderr.log\n", "20180911_trimgalore.stdout.log\n", "20180911_virginica_oil_trimmed_fastqc\n", "2112_lane1_ACAGTG.fastq.gz_trimming_report.txt\n", "2112_lane1_ACAGTG_trimmed.fq.gz\n", "2112_lane1_ATCACG.fastq.gz_trimming_report.txt\n", "2112_lane1_ATCACG_trimmed.fq.gz\n", "2112_lane1_CAGATC.fastq.gz_trimming_report.txt\n", "2112_lane1_CAGATC_trimmed.fq.gz\n", "2112_lane1_GCCAAT.fastq.gz_trimming_report.txt\n", "2112_lane1_GCCAAT_trimmed.fq.gz\n", "2112_lane1_TGACCA.fastq.gz_trimming_report.txt\n", "2112_lane1_TGACCA_trimmed.fq.gz\n", "2112_lane1_TTAGGC.fastq.gz_trimming_report.txt\n", "2112_lane1_TTAGGC_trimmed.fq.gz\n" ] } ], "source": [ "%%bash\n", "ls /home/sam/analyses/20180911_virginica_oil_trimgalore_01" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "2112_lane1_ACAGTG_trimmed_fastqc.html\n", "2112_lane1_ACAGTG_trimmed_fastqc.zip\n", "2112_lane1_ATCACG_trimmed_fastqc.html\n", "2112_lane1_ATCACG_trimmed_fastqc.zip\n", "2112_lane1_CAGATC_trimmed_fastqc.html\n", "2112_lane1_CAGATC_trimmed_fastqc.zip\n", "2112_lane1_GCCAAT_trimmed_fastqc.html\n", "2112_lane1_GCCAAT_trimmed_fastqc.zip\n", "2112_lane1_TGACCA_trimmed_fastqc.html\n", "2112_lane1_TGACCA_trimmed_fastqc.zip\n", "2112_lane1_TTAGGC_trimmed_fastqc.html\n", "2112_lane1_TTAGGC_trimmed_fastqc.zip\n" ] } ], "source": [ "%%bash\n", "ls /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Searching 26 files..\n", "Searching 12 files..\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[WARNING] multiqc : MultiQC Version v1.6 now available!\n", "[INFO ] multiqc : This is MultiQC v1.5.dev0\n", "[INFO ] multiqc : Template : default\n", "[INFO ] multiqc : Searching '.'\n", "[INFO ] cutadapt : Found 6 reports\n", "[INFO ] fastqc : Found 6 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", "[WARNING] multiqc : MultiQC Version v1.6 now available!\n", "[INFO ] multiqc : This is MultiQC v1.5.dev0\n", "[INFO ] multiqc : Template : default\n", "[INFO ] multiqc : Searching '.'\n", "[INFO ] fastqc : Found 6 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/analyses/20180911_virginica_oil_trimgalore_01\n", "multiqc .\n", "cd /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc\n", "multiqc .\n", "\n", "sed '/^Subject:/ s/ / multiqc JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Used ```sudo``` to copy to Owl outside of notebook" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/mnt/owl/Athaliana/20180911_virginica_oil_trimgalore_01/\n", "├── 20180911_trimgalore.stderr.log\n", "├── 20180911_trimgalore.stdout.log\n", "├── 20180911_virginica_oil_trimmed_fastqc\n", "│   ├── 2112_lane1_ACAGTG_trimmed_fastqc.html\n", "│   ├── 2112_lane1_ACAGTG_trimmed_fastqc.zip\n", "│   ├── 2112_lane1_ATCACG_trimmed_fastqc.html\n", "│   ├── 2112_lane1_ATCACG_trimmed_fastqc.zip\n", "│   ├── 2112_lane1_CAGATC_trimmed_fastqc.html\n", "│   ├── 2112_lane1_CAGATC_trimmed_fastqc.zip\n", "│   ├── 2112_lane1_GCCAAT_trimmed_fastqc.html\n", "│   ├── 2112_lane1_GCCAAT_trimmed_fastqc.zip\n", "│   ├── 2112_lane1_TGACCA_trimmed_fastqc.html\n", "│   ├── 2112_lane1_TGACCA_trimmed_fastqc.zip\n", "│   ├── 2112_lane1_TTAGGC_trimmed_fastqc.html\n", "│   ├── 2112_lane1_TTAGGC_trimmed_fastqc.zip\n", "│   ├── multiqc_data\n", "│   │   ├── multiqc_data.json\n", "│   │   ├── multiqc_fastqc.txt\n", "│   │   ├── multiqc_general_stats.txt\n", "│   │   ├── multiqc.log\n", "│   │   └── multiqc_sources.txt\n", "│   └── multiqc_report.html\n", "├── 2112_lane1_ACAGTG.fastq.gz_trimming_report.txt\n", "├── 2112_lane1_ACAGTG_trimmed.fq.gz\n", "├── 2112_lane1_ATCACG.fastq.gz_trimming_report.txt\n", "├── 2112_lane1_ATCACG_trimmed.fq.gz\n", "├── 2112_lane1_CAGATC.fastq.gz_trimming_report.txt\n", "├── 2112_lane1_CAGATC_trimmed.fq.gz\n", "├── 2112_lane1_GCCAAT.fastq.gz_trimming_report.txt\n", "├── 2112_lane1_GCCAAT_trimmed.fq.gz\n", "├── 2112_lane1_TGACCA.fastq.gz_trimming_report.txt\n", "├── 2112_lane1_TGACCA_trimmed.fq.gz\n", "├── 2112_lane1_TTAGGC.fastq.gz_trimming_report.txt\n", "├── 2112_lane1_TTAGGC_trimmed.fq.gz\n", "├── multiqc_data\n", "│   ├── multiqc_cutadapt.txt\n", "│   ├── multiqc_data.json\n", "│   ├── multiqc_fastqc.txt\n", "│   ├── multiqc_general_stats.txt\n", "│   ├── multiqc.log\n", "│   └── multiqc_sources.txt\n", "└── multiqc_report.html\n", "\n", "3 directories, 39 files\n" ] } ], "source": [ "%%bash\n", "tree /mnt/owl/Athaliana/20180911_virginica_oil_trimgalore_01/" ] }, { "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 }