{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE:\n", "Mon Aug 5 15:01:13 PDT 2019\n", "------------\n", "\n", "Distributor ID:\tUbuntu\n", "Description:\tUbuntu 16.04.6 LTS\n", "Release:\t16.04\n", "Codename:\txenial\n", "\n", "------------\n", "HOSTNAME: \n", "swoose\n", "\n", "------------\n", "Computer Specs:\n", "\n", "Architecture: x86_64\n", "CPU op-mode(s): 32-bit, 64-bit\n", "Byte Order: Little Endian\n", "CPU(s): 24\n", "On-line CPU(s) list: 0-23\n", "Thread(s) per core: 2\n", "Core(s) per socket: 6\n", "Socket(s): 2\n", "NUMA node(s): 1\n", "Vendor ID: GenuineIntel\n", "CPU family: 6\n", "Model: 44\n", "Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz\n", "Stepping: 2\n", "CPU MHz: 2925.984\n", "BogoMIPS: 5851.89\n", "Virtualization: VT-x\n", "L1d cache: 32K\n", "L1i cache: 32K\n", "L2 cache: 256K\n", "L3 cache: 12288K\n", "NUMA node0 CPU(s): 0-23\n", "Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb ssbd ibrs ibpb stibp kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_l1d\n", "\n", "------------\n", "\n", "Memory Specs\n", "\n", " total used free shared buff/cache available\n", "Mem: 70G 9.5G 48G 593M 12G 60G\n", "Swap: 4.7G 0B 4.7G\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": [ "env: wd=/home/sam/analyses/20190805_Pgenerosa_v070_repeatmasker_all\n", "env: fasta_url=https://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.fa\n", "env: fasta=Pgenerosa_v070.fa\n", "env: repeat_masker=/home/shared/RepeatMasker-4.0.7/RepeatMasker\n", "env: cpus=23\n", "env: checksum=de0958fec4b9f8845babf3717ce7168c\n" ] } ], "source": [ "%env wd=/home/sam/analyses/20190805_Pgenerosa_v070_repeatmasker_all\n", "%env fasta_url=https://owl.fish.washington.edu/halfshell/genomic-databank/Pgenerosa_v070.fa\n", "%env fasta=Pgenerosa_v070.fa\n", "%env repeat_masker=/home/shared/RepeatMasker-4.0.7/RepeatMasker\n", "%env cpus=23\n", "# Checksum taken from https://github.com/RobertsLab/resources/wiki/Genomic-Resources\n", "%env checksum=de0958fec4b9f8845babf3717ce7168c" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Create necessary directories" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir --parents ${wd}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Download _Crassostrea gigas genome FastA file\n", "\n", "Info on FastA file is here: [https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome](https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome)" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "receiving incremental file list\n", "Pgenerosa_v070.fa\n", " 2,247,117,885 100% 22.06MB/s 0:01:37 (xfr#1, to-chk=0/1)\n", "\n", "sent 30 bytes received 2,247,392,295 bytes 22,586,857.54 bytes/sec\n", "total size is 2,247,117,885 speedup is 1.00\n", "\n", "\n", "----------------------------------------------------------\n", "total 2.1G\n", "-rw-r--r-- 1 sam users 2.1G Feb 11 12:13 Pgenerosa_v070.fa\n" ] } ], "source": [ "%%bash\n", "cd ${wd}\n", "\n", "rsync \\\n", "--archive \\\n", "--verbose \\\n", "--progress \\\n", "owl:/volume1/web/halfshell/genomic-databank/${fasta} .\n", "\n", "echo \"\"\n", "echo \"\"\n", "echo \"----------------------------------------------------------\"\n", "\n", "ls -lh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### If need to download via wget, change cell below to code, instead of markdown\n", "\n", "#### Also, change cell with md5 checksum comparisons to code, instead of markdown" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "%%bash\n", "time \\\n", "wget ${fasta_url} \\\n", "--quiet \\\n", "--directory-prefix=${wd}\n", "\n", "ls -lh ${wd}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Verify MD5 checksum\n", "\n", "Original MD5 checksum taken from GitHub Genomic Resource linked above.\n", "\n", "Use ```md5sum``` to generate checksum from downloaded FastA file and ```awk``` to print the first field (i.e. the checksum value). This is saved to the variable: ```dl_md5```\n", "\n", "Then, check for differences between the two variables. \n", "\n", "No output confirms no difference." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "%%bash\n", "md5=${checksum}\n", "dl_md5=$(md5sum ${wd}/${fasta} | awk '{ print $1 }')\n", "diff <(echo \"$md5\") <(echo \"$dl_md5\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Trim FastA header length to avoid RepeatMasker error of length >50 characters" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 2.1G\n", "-rw-rw-r-- 1 sam sam 2.1G Aug 5 15:41 Pgenerosa_v070.fa\n" ] } ], "source": [ "%%bash\n", "cd ${wd}\n", "cut -f 1-2 -d \"_\" \"${fasta}\" > Pgenerosa_v070.fa.tmp\n", "mv Pgenerosa_v070.fa.tmp \"${fasta}\"\n", "\n", "ls -ltrh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Run RepeatMasker with _all_ species setting and following options:\n", "\n", "```-species \"all\"``` : Sets species to all\n", "\n", "```-par ${cpus}``` : Use n CPU threads\n", "\n", "```-gff``` : Create GFF output file (in addition to default files)\n", "\n", "```-excln``` : Adjusts output table calculations to exclude sequence runs of >=25Ns. Useful for draft genome assemblies.\n", "\n", "```-1>``` : Send stdout to file instead of printing to notebook.\n", "\n", "```-2>``` : Send stderr to file instead of printing to notebook.\n" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m0.001s\n", "user\t0m0.000s\n", "sys\t0m0.000s\n" ] }, { "ename": "CalledProcessError", "evalue": "Command 'b'\\ncd ${wd}\\ntime \\\\\\n${repeat_masker} \\\\\\n${fasta} \\\\\\n-species \"all\" \\\\\\n-par ${cpus} \\\\\\n-gff \\\\\\n-excln \\\\\\n1> stdout.out \\\\\\n2> stderr.err\\n'' returned non-zero exit status 127.", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)", "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mget_ipython\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrun_cell_magic\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'bash'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m''\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'\\ncd ${wd}\\ntime \\\\\\n${repeat_masker} \\\\\\n${fasta} \\\\\\n-species \"all\" \\\\\\n-par ${cpus} \\\\\\n-gff \\\\\\n-excln \\\\\\n1> stdout.out \\\\\\n2> stderr.err\\n'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", "\u001b[0;32m~/programs/minicocnda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py\u001b[0m in \u001b[0;36mrun_cell_magic\u001b[0;34m(self, magic_name, line, cell)\u001b[0m\n\u001b[1;32m 2350\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuiltin_trap\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2351\u001b[0m \u001b[0margs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mmagic_arg_s\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2352\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2353\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2354\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m~/programs/minicocnda3/lib/python3.6/site-packages/IPython/core/magics/script.py\u001b[0m in \u001b[0;36mnamed_script_magic\u001b[0;34m(line, cell)\u001b[0m\n\u001b[1;32m 140\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 141\u001b[0m \u001b[0mline\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mscript\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 142\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mshebang\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mline\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 143\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 144\u001b[0m \u001b[0;31m# write a basic docstring:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m\u001b[0m in \u001b[0;36mshebang\u001b[0;34m(self, line, cell)\u001b[0m\n", "\u001b[0;32m~/programs/minicocnda3/lib/python3.6/site-packages/IPython/core/magic.py\u001b[0m in \u001b[0;36m\u001b[0;34m(f, *a, **k)\u001b[0m\n\u001b[1;32m 185\u001b[0m \u001b[0;31m# but it's overkill for just that one bit of state.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 186\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mmagic_deco\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 187\u001b[0;31m \u001b[0mcall\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mlambda\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 188\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 189\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mcallable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;32m~/programs/minicocnda3/lib/python3.6/site-packages/IPython/core/magics/script.py\u001b[0m in \u001b[0;36mshebang\u001b[0;34m(self, line, cell)\u001b[0m\n\u001b[1;32m 243\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstderr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mflush\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 244\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_error\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m!=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 245\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mCalledProcessError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreturncode\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mout\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstderr\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 246\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 247\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_run_script\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcell\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mto_close\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", "\u001b[0;31mCalledProcessError\u001b[0m: Command 'b'\\ncd ${wd}\\ntime \\\\\\n${repeat_masker} \\\\\\n${fasta} \\\\\\n-species \"all\" \\\\\\n-par ${cpus} \\\\\\n-gff \\\\\\n-excln \\\\\\n1> stdout.out \\\\\\n2> stderr.err\\n'' returned non-zero exit status 127." ] } ], "source": [ "%%bash\n", "\n", "cd ${wd}\n", "time \\\n", "${repeat_masker} \\\n", "${fasta} \\\n", "-species \"all\" \\\n", "-par ${cpus} \\\n", "-gff \\\n", "-excln \\\n", "1> stdout.out \\\n", "2> stderr.err\n", "\n", "sed '/^Subject:/ s/ / repeatmasker_pgenv070_all JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 2.2G\n", "-rw-rw-r-- 1 sam sam 914M Jun 26 14:43 Pgenerosa_v074.fa\n", "-rw-rw-r-- 1 sam sam 170M Jun 28 00:27 Pgenerosa_v074.fa.cat.gz\n", "-rw-rw-r-- 1 sam sam 917M Jun 28 00:27 Pgenerosa_v074.fa.masked\n", "-rw-rw-r-- 1 sam sam 91M Jun 28 00:27 Pgenerosa_v074.fa.out\n", "-rw-rw-r-- 1 sam sam 60M Jun 28 00:27 Pgenerosa_v074.fa.out.gff\n", "-rw-rw-r-- 1 sam sam 2.4K Jun 28 00:27 Pgenerosa_v074.fa.tbl\n", "-rw-rw-r-- 1 sam sam 0 Jun 26 14:43 stderr.err\n", "-rw-rw-r-- 1 sam sam 3.2M Jun 28 00:27 stdout.out\n" ] } ], "source": [ "%%bash\n", "ls -lh ${wd}" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### SUMMARY TABLE" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: Pgenerosa_v074.fa \n", "sequences: 18\n", "total length: 942353201 bp (784808881 bp excl N/X-runs)\n", "GC level: 33.78 %\n", "bases masked: 65221692 bp ( 8.31 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "Retroelements 204336 32863590 bp 4.19 %\n", " SINEs: 127691 15752737 bp 2.01 %\n", " Penelope 2382 279223 bp 0.04 %\n", " LINEs: 49426 11965761 bp 1.52 %\n", " CRE/SLACS 453 37114 bp 0.00 %\n", " L2/CR1/Rex 13913 2779414 bp 0.35 %\n", " R1/LOA/Jockey 3341 1189171 bp 0.15 %\n", " R2/R4/NeSL 1211 165338 bp 0.02 %\n", " RTE/Bov-B 9983 2559753 bp 0.33 %\n", " L1/CIN4 6194 1146568 bp 0.15 %\n", " LTR elements: 27219 5145092 bp 0.66 %\n", " BEL/Pao 1918 317492 bp 0.04 %\n", " Ty1/Copia 4335 355225 bp 0.05 %\n", " Gypsy/DIRS1 16012 3831098 bp 0.49 %\n", " Retroviral 2945 204333 bp 0.03 %\n", "\n", "DNA transposons 89437 12061369 bp 1.54 %\n", " hobo-Activator 10103 1142451 bp 0.15 %\n", " Tc1-IS630-Pogo 24664 3657788 bp 0.47 %\n", " En-Spm 0 0 bp 0.00 %\n", " MuDR-IS905 0 0 bp 0.00 %\n", " PiggyBac 472 38428 bp 0.00 %\n", " Tourist/Harbinger 2582 369771 bp 0.05 %\n", " Other (Mirage, 628 39925 bp 0.01 %\n", " P-element, Transib)\n", "\n", "Rolling-circles 0 0 bp 0.00 %\n", "\n", "Unclassified: 38482 5369675 bp 0.68 %\n", "\n", "Total interspersed repeats: 50294634 bp 6.41 %\n", "\n", "\n", "Small RNA: 16303 859653 bp 0.11 %\n", "\n", "Satellites: 10312 1878369 bp 0.24 %\n", "Simple repeats: 239752 12742842 bp 1.62 %\n", "Low complexity: 31725 1550615 bp 0.20 %\n", "==================================================\n", "\n", "* most repeats fragmented by insertions or deletions\n", " have been counted as one element\n", " Runs of >=20 X/Ns in query were excluded in % calcs\n", "\n", "\n", "The query species was assumed to be root \n", "RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127\n", " \n", "run with rmblastn version 2.6.0+\n", "\n" ] } ], "source": [ "%%bash\n", "cat ${wd}/${fasta}.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Delete FastA (not needed) and `rsync` to my folder on Gannet" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "sending incremental file list\n", "\n", "sent 288 bytes received 16 bytes 608.00 bytes/sec\n", "total size is 2,258,210,520 speedup is 7,428,324.08\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/\n", "\n", "rsync \\\n", "--archive \\\n", "--verbose \\\n", "--progress \\\n", "--relative \\\n", "./20190805_Pgenerosa_v070_repeatmasker_all \\\n", "gannet:/volume2/web/Atumefaciens" ] }, { "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": "3.6.8" } }, "nbformat": 4, "nbformat_minor": 2 }