{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "TODAY'S DATE:\n",
      "Wed Mar 27 08:34:53 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",
      "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:              4521.81\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 ssbd ibrs ibpb stibp kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida flush_l1d\n",
      "\n",
      "------------\n",
      "\n",
      "Memory Specs\n",
      "\n",
      "              total        used        free      shared  buff/cache   available\n",
      "Mem:            47G        1.3G         38G        584M        7.0G         44G\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": [
      "env: wd=/home/sam/analyses/20190327_cgig_repeatmasker_all\n",
      "env: fasta_url=http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n",
      "env: fasta=Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n",
      "env: repeat_masker=/home/shared/RepeatMasker-4.0.7/RepeatMasker\n",
      "env: cpus=16\n",
      "env: checksum=6de9d1239eb10ea0545bed6c4e746d6c\n"
     ]
    }
   ],
   "source": [
    "%env wd=/home/sam/analyses/20190327_cgig_repeatmasker_all\n",
    "%env fasta_url=http://owl.fish.washington.edu/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n",
    "%env fasta=Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n",
    "%env repeat_masker=/home/shared/RepeatMasker-4.0.7/RepeatMasker\n",
    "%env cpus=16\n",
    "%env checksum=6de9d1239eb10ea0545bed6c4e746d6c"
   ]
  },
  {
   "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": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "receiving incremental file list\n",
      "Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n",
      "\r",
      "              0   0%    0.00kB/s    0:00:00  \r",
      "        491,520   0%   14.11kB/s   11:09:48  \r",
      "     22,478,848   3%  626.91kB/s    0:14:29  \r",
      "     49,020,928   8%    1.30MB/s    0:06:30  \r",
      "     65,732,608  11%    1.69MB/s    0:04:49  \r",
      "     92,078,080  16%   21.84MB/s    0:00:21  \r",
      "    119,209,984  21%   23.07MB/s    0:00:18  \r",
      "    143,982,592  25%   22.65MB/s    0:00:18  \r",
      "    173,506,560  30%   25.64MB/s    0:00:15  \r",
      "    204,505,088  36%   26.75MB/s    0:00:13  \r",
      "    233,537,536  41%   27.20MB/s    0:00:11  \r",
      "    263,651,328  46%   28.47MB/s    0:00:10  \r",
      "    280,494,080  49%   25.42MB/s    0:00:11  \r",
      "    284,655,616  50%   15.82MB/s    0:00:17  \r",
      "    285,114,368  50%    8.01MB/s    0:00:34  \r",
      "    288,849,920  50%    2.51MB/s    0:01:48  \r",
      "    308,314,112  54%    2.78MB/s    0:01:31  \r",
      "    334,888,960  59%    5.15MB/s    0:00:44  \r",
      "    334,987,264  59%    4.40MB/s    0:00:51  \r",
      "    336,494,592  59%    6.05MB/s    0:00:37  \r",
      "    338,362,368  59%    3.47MB/s    0:01:04  \r",
      "    339,181,568  59%  532.11kB/s    0:07:09  \r",
      "    339,279,872  59%  816.52kB/s    0:04:39  \r",
      "    341,278,720  60%  829.99kB/s    0:04:32  \r",
      "    347,471,872  61%    1.68MB/s    0:02:07  \r",
      "    350,027,776  61%    1.99MB/s    0:01:46  \r",
      "    355,958,784  62%    2.86MB/s    0:01:12  \r",
      "    364,347,392  64%    4.41MB/s    0:00:45  \r",
      "    366,444,544  64%    3.76MB/s    0:00:52  \r",
      "    367,099,904  64%    3.29MB/s    0:00:59  \r",
      "    372,736,000  65%    3.44MB/s    0:00:55  \r",
      "    374,833,152  66%    2.16MB/s    0:01:27  \r",
      "    382,140,416  67%    3.07MB/s    0:00:58  \r",
      "    391,610,368  68%    5.06MB/s    0:00:33  \r",
      "    398,131,200  70%    5.25MB/s    0:00:31  \r",
      "    404,160,512  71%    2.59MB/s    0:01:01  \r",
      "    424,935,424  74%    3.90MB/s    0:00:35  \r",
      "    447,021,056  78%    5.10MB/s    0:00:23  \r",
      "    476,053,504  83%    7.27MB/s    0:00:12  \r",
      "    504,856,576  88%   23.27MB/s    0:00:02  \r",
      "    523,665,408  92%   22.81MB/s    0:00:01  \r",
      "    538,411,008  94%   19.61MB/s    0:00:01  \r",
      "    540,508,160  95%   12.62MB/s    0:00:02  \r",
      "    542,605,312  95%    7.49MB/s    0:00:03  \r",
      "    544,669,696  95%    1.72MB/s    0:00:13  \r",
      "    567,574,528  99%    2.41MB/s    0:00:00  \r",
      "    567,592,991 100%    5.15MB/s    0:01:45 (xfr#1, to-chk=0/1)\n",
      "\n",
      "sent 30 bytes  received 567,662,409 bytes  5,137,216.64 bytes/sec\n",
      "total size is 567,592,991  speedup is 1.00\n",
      "total 542M\n",
      "-rw-rw-rw- 1 sam users 542M Aug 24  2018 Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "# Using rsync\n",
    "cd ${wd}\n",
    "\n",
    "rsync \\\n",
    "--archive \\\n",
    "--verbose \\\n",
    "--progress \\\n",
    "owl:/volume1/web/halfshell/genomic-databank/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa .\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 ${wd}"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Verify MD5 checksum\n",
    "\n",
    "Original MD5 checksum taken from GitHub Genomic Resource linked above.\n",
    "\n",
    "Use ```md5sum``` to generate checksum from downloaded FastA file and ```awk``` to print the first field (i.e. the checksum value). This is saved to the variable: ```dl_md5```\n",
    "\n",
    "Then, check for differences between the two variables. \n",
    "\n",
    "No output confirms no difference."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "%%bash\n",
    "md5=${checksum}\n",
    "dl_md5=$(md5sum ${wd}/${fasta} | awk '{ print $1 }')\n",
    "diff <(echo \"$md5\") <(echo \"$dl_md5\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Run RepeatMasker with _all_ species setting and following options:\n",
    "\n",
    "```-species \"all\"``` : Sets species to all\n",
    "\n",
    "```-par 15``` : Use 15 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": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "\n",
      "real\t1419m34.303s\n",
      "user\t21339m49.472s\n",
      "sys\t111m2.000s\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "\n",
    "cd ${wd}\n",
    "time \\\n",
    "${repeat_masker} \\\n",
    "${fasta} \\\n",
    "-species \"all\" \\\n",
    "-par ${cpus} \\\n",
    "-gff \\\n",
    "-excln \\\n",
    "1> stdout.out \\\n",
    "2> stderr.err\n",
    "\n",
    "sed '/^Subject:/ s/ / repeatmasker_gigas_all JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total 1.5G\n",
      "-rw-rw-rw- 1 sam users 542M Aug 24  2018 Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n",
      "-rw-rw-r-- 1 sam sam   244M Mar 28 08:43 Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.cat.gz\n",
      "-rw-rw-r-- 1 sam sam   544M Mar 28 08:43 Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.masked\n",
      "-rw-rw-r-- 1 sam sam    90M Mar 28 08:43 Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out\n",
      "-rw-rw-r-- 1 sam sam    58M Mar 28 08:43 Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out.gff\n",
      "-rw-rw-r-- 1 sam sam   2.4K Mar 28 08:43 Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.tbl\n",
      "-rw-rw-r-- 1 sam sam      0 Mar 27 09:04 stderr.err\n",
      "-rw-rw-r-- 1 sam sam   2.1M Mar 28 08:43 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: Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa\n",
      "sequences:          7658\n",
      "total length:  557717710 bp  (491860439 bp excl N/X-runs)\n",
      "GC level:         33.42 %\n",
      "bases masked:  160369613 bp ( 32.60 %)\n",
      "==================================================\n",
      "               number of      length   percentage\n",
      "               elements*    occupied  of sequence\n",
      "--------------------------------------------------\n",
      "Retroelements        48481     19773596 bp    4.02 %\n",
      "   SINEs:             2498       317084 bp    0.06 %\n",
      "   Penelope           5749      1808270 bp    0.37 %\n",
      "   LINEs:            26463     10472676 bp    2.13 %\n",
      "    CRE/SLACS           15         1289 bp    0.00 %\n",
      "     L2/CR1/Rex       1712       307207 bp    0.06 %\n",
      "     R1/LOA/Jockey     299        21470 bp    0.00 %\n",
      "     R2/R4/NeSL        218        69735 bp    0.01 %\n",
      "     RTE/Bov-B        8417      3631379 bp    0.74 %\n",
      "     L1/CIN4           983        64189 bp    0.01 %\n",
      "   LTR elements:     19520      8983836 bp    1.83 %\n",
      "     BEL/Pao          2050      1349545 bp    0.27 %\n",
      "     Ty1/Copia        2139       189535 bp    0.04 %\n",
      "     Gypsy/DIRS1     11971      6501545 bp    1.32 %\n",
      "       Retroviral     1263        69288 bp    0.01 %\n",
      "\n",
      "DNA transposons     299050     85782505 bp   17.44 %\n",
      "   hobo-Activator     9348      2278556 bp    0.46 %\n",
      "   Tc1-IS630-Pogo    32515      8695261 bp    1.77 %\n",
      "   En-Spm                0            0 bp    0.00 %\n",
      "   MuDR-IS905            0            0 bp    0.00 %\n",
      "   PiggyBac           4136       747000 bp    0.15 %\n",
      "   Tourist/Harbinger 11590      2828277 bp    0.58 %\n",
      "   Other (Mirage,      232        14514 bp    0.00 %\n",
      "    P-element, Transib)\n",
      "\n",
      "Rolling-circles          0            0 bp    0.00 %\n",
      "\n",
      "Unclassified:       109149     49075277 bp    9.98 %\n",
      "\n",
      "Total interspersed repeats:   154631378 bp   31.44 %\n",
      "\n",
      "\n",
      "Small RNA:             830        93282 bp    0.02 %\n",
      "\n",
      "Satellites:           2087       401812 bp    0.08 %\n",
      "Simple repeats:     110847      4687373 bp    0.95 %\n",
      "Low complexity:      16716       787611 bp    0.16 %\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": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sending incremental file list\n",
      "drwxrwxr-x          4,096 2019/03/27 08:45:17 .\n",
      "\n",
      "sent 49 bytes  received 64 bytes  226.00 bytes/sec\n",
      "total size is 0  speedup is 0.00\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "rsync: link_stat \"/home/sam/analyses/home/sam/analyses/20190327_cgig_repeatmasker_all\" failed: No such file or directory (2)\n",
      "rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1183) [sender=3.1.1]\n",
      "bash: line 10: gannet:/volume2/web/Atumefaciens: No such file or directory\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cd ${wd}\n",
    "rm ${fasta}\n",
    "cd ..\n",
    "rsync \\\n",
    "--archive \\\n",
    "--verbose \\\n",
    "--progress \\\n",
    "--relative \\\n",
    "./home/sam/analyses/20190327_cgig_repeatmasker_all \n",
    "gannet:/volume2/web/Atumefaciens"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sending incremental file list\n",
      "drwxrwxr-x          4,096 2019/03/27 08:45:17 .\n",
      "drwxrwxr-x          4,096 2019/03/28 11:54:45 20190327_cgig_repeatmasker_all\n",
      "-rw-rw-r--    255,343,202 2019/03/28 08:43:43 20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.cat.gz\n",
      "-rw-rw-r--    569,452,085 2019/03/28 08:43:44 20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.masked\n",
      "-rw-rw-r--     93,415,468 2019/03/28 08:43:44 20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out\n",
      "-rw-rw-r--     59,778,663 2019/03/28 08:43:43 20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out.gff\n",
      "-rw-rw-r--          2,444 2019/03/28 08:43:43 20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.tbl\n",
      "-rw-rw-r--              0 2019/03/27 09:04:11 20190327_cgig_repeatmasker_all/stderr.err\n",
      "-rw-rw-r--      2,119,050 2019/03/28 08:43:41 20190327_cgig_repeatmasker_all/stdout.out\n",
      "\n",
      "sent 353 bytes  received 1,000 bytes  2,706.00 bytes/sec\n",
      "total size is 980,110,912  speedup is 724,398.31\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "rm: cannot remove 'Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa': No such file or directory\n",
      "bash: line 10: gannet:/volume2/web/Atumefaciens: No such file or directory\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cd ${wd}\n",
    "rm ${fasta}\n",
    "cd ..\n",
    "rsync \\\n",
    "--archive \\\n",
    "--verbose \\\n",
    "--progress \\\n",
    "--relative \\\n",
    "./20190327_cgig_repeatmasker_all \n",
    "gannet:/volume2/web/Atumefaciens"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Restarted notbook in case `gannet` shortuct wasn't loaded. However, problem was most likely due to missing continuatino slash after repeatmasker directory..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "sending incremental file list\n",
      "./\n",
      "20190327_cgig_repeatmasker_all/\n",
      "20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.cat.gz\n",
      "\r",
      "         32,768   0%    0.00kB/s    0:00:00  \r",
      "    118,947,840  46%  113.41MB/s    0:00:01  \r",
      "    236,191,744  92%  112.67MB/s    0:00:00  \r",
      "    255,343,202 100%  112.72MB/s    0:00:02 (xfr#1, to-chk=6/9)\n",
      "20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.masked\n",
      "\r",
      "         32,768   0%  197.53kB/s    0:48:02  \r",
      "     98,205,696  17%   93.66MB/s    0:00:04  \r",
      "    215,515,136  37%  102.82MB/s    0:00:03  \r",
      "    332,693,504  58%  105.83MB/s    0:00:02  \r",
      "    449,871,872  79%  107.34MB/s    0:00:01  \r",
      "    567,017,472  99%  111.86MB/s    0:00:00  \r",
      "    569,452,085 100%  108.29MB/s    0:00:05 (xfr#2, to-chk=5/9)\n",
      "20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out\n",
      "\r",
      "         32,768   0%    1.56MB/s    0:00:58  \r",
      "     93,415,468 100%  109.04MB/s    0:00:00 (xfr#3, to-chk=4/9)\n",
      "20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.out.gff\n",
      "\r",
      "         32,768   0%   39.12kB/s    0:25:27  \r",
      "     21,397,504  35%   20.41MB/s    0:00:01  \r",
      "     59,778,663 100%   42.96MB/s    0:00:01 (xfr#4, to-chk=3/9)\n",
      "20190327_cgig_repeatmasker_all/Crassostrea_gigas.oyster_v9.dna_sm.toplevel.fa.tbl\n",
      "\r",
      "          2,444 100%    7.28kB/s    0:00:00  \r",
      "          2,444 100%    7.28kB/s    0:00:00 (xfr#5, to-chk=2/9)\n",
      "20190327_cgig_repeatmasker_all/stderr.err\n",
      "\r",
      "              0 100%    0.00kB/s    0:00:00 (xfr#6, to-chk=1/9)\n",
      "20190327_cgig_repeatmasker_all/stdout.out\n",
      "\r",
      "         32,768   1%   97.56kB/s    0:00:21  \r",
      "      2,119,050 100%    5.82MB/s    0:00:00 (xfr#7, to-chk=0/9)\n",
      "\n",
      "sent 980,350,785 bytes  received 163 bytes  103,194,836.63 bytes/sec\n",
      "total size is 980,110,912  speedup is 1.00\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "cd /home/sam/analyses/\n",
    "\n",
    "rsync \\\n",
    "--archive \\\n",
    "--verbose \\\n",
    "--progress \\\n",
    "--relative \\\n",
    "./20190327_cgig_repeatmasker_all \\\n",
    "gannet:/volume2/web/Atumefaciens"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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