{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE:\n", "Wed May 23 09:58:07 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: 4521.78\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 419M 40G 50M 6.5G 46G\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 #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": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180523_oly_repeatmasker" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "cp: cannot stat '/mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta': No such file or directory\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/data/oly_assemblies\n", "cp /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta /home/sam/data/oly_assemblies" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Forgot that I had restarted roadrunner - need to re-mount owl...\n", "\n", "Needs ```sudo``` so will re-run outside of notebook." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Copy Olympia oyster assembly: [pbjelly_sjw_01](https://github.com/RobertsLab/project-olympia.oyster-genomic/wiki/Genome-Assemblies)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m18.276s\n", "user\t0m0.000s\n", "sys\t0m1.368s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "cp /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta /home/sam/data/oly_assemblies" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 1233740\n", "-rw-rw-r-- 1 sam sam 1263344875 May 23 10:13 jelly.out.fasta\n" ] } ], "source": [ "%%bash\n", "ls -l /home/sam/data/oly_assemblies/" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv /home/sam/analyses/20180523_oly_repeatmasker \\\n", "/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Run RepeatMasker with default setting and following options:\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": 7, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t398m44.441s\n", "user\t4976m30.380s\n", "sys\t1006m29.860s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/jelly.out.fasta \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out \\\n", "2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "------------\n", "STANDARD OUT\n", "------------\n", "cycle 4 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 5 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 6 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 7 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 8 ............................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 9 ............................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 10 ............................................................................................................................................................................................................................................................................................................................................................................................................\n", "Generating output... .........................................................................................................................................................................................................................................................................................................................................................................................................\n", "masking\n", "done\n", "\n", "\n", "------------\n", "STANDARD ERROR\n", "------------\n", "\n", "\n", "------------\n", "REPEATMASKER TABLE\n", "------------\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl: No such file or directory\n" ] } ], "source": [ "%%bash\n", "echo \"------------\"\n", "echo \"STANDARD OUT\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"STANDARD ERROR\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"REPEATMASKER TABLE\"\n", "echo \"------------\"\n", "cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Oof. Ran this in the wrong directory AND started running repeatmasker after this. Can't tell if files are overwritten or what. Need to re-run. Grr." ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t408m50.418s\n", "user\t4841m17.924s\n", "sys\t1297m22.872s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/jelly.out.fasta \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out \\\n", "2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "------------\n", "STANDARD OUT\n", "------------\n", "cycle 4 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 5 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 6 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 7 .......................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 8 ............................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 9 ............................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 10 ............................................................................................................................................................................................................................................................................................................................................................................................................\n", "Generating output... .........................................................................................................................................................................................................................................................................................................................................................................................................\n", "masking\n", "done\n", "\n", "\n", "------------\n", "STANDARD ERROR\n", "------------\n", "\n", "\n", "------------\n", "REPEATMASKER TABLE\n", "------------\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl: No such file or directory\n" ] } ], "source": [ "%%bash\n", "echo \"------------\"\n", "echo \"STANDARD OUT\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stdout.out\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"STANDARD ERROR\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/stderr.err\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"REPEATMASKER TABLE\"\n", "echo \"------------\"\n", "cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Run RepeatMasker with _Crassostrea gigas_ species setting and following options:\n", "\n", "- ```-species \"crassostrea gigas\"``` : Sets species to Crassostrea gigas\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." ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "mkdir: cannot create directory ‘/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02’: File exists\n", "\n", "real\t391m39.372s\n", "user\t4547m11.540s\n", "sys\t1003m40.176s\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02\n", "cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02\n", "\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/jelly.out.fasta \\\n", "-species \"crassostrea gigas\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stdout.out \\\n", "2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stderr.err\n", "\n", "sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "------------\n", "STANDARD OUT\n", "------------\n", "cycle 4 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 5 \n", "cycle 6 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 7 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 8 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 9 .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 10 ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "Generating output... ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "masking\n", "done\n", "\n", "\n", "------------\n", "STANDARD ERROR\n", "------------\n", "\n", "\n", "------------\n", "REPEATMASKER C.GIGAS TABLE\n", "------------\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/jelly.out.fasta.tbl: No such file or directory\n" ] } ], "source": [ "%%bash\n", "echo \"------------\"\n", "echo \"STANDARD OUT\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stdout.out\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"STANDARD ERROR\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/stderr.err\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"REPEATMASKER C.GIGAS TABLE\"\n", "echo \"------------\"\n", "cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Run RepeatMasker with _Crassostrea virginica_ species setting and following options:\n", "\n", "- ```-species \"crassostrea virginica\"``` : Sets species to Crassostrea virginica\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." ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t301m41.551s\n", "user\t3123m55.312s\n", "sys\t1092m28.468s\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03\n", "cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/jelly.out.fasta \\\n", "-species \"crassostrea virginica\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stdout.out \\\n", "2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stderr.err\n", "\n", "sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "------------\n", "STANDARD OUT\n", "------------\n", "cycle 4 ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 5 \n", "cycle 6 ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 7 ....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 8 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 9 ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 10 ...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "Generating output... ...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n", "masking\n", "done\n", "\n", "\n", "------------\n", "STANDARD ERROR\n", "------------\n", "\n", "\n", "------------\n", "REPEATMASKER C.VIRGINICA TABLE\n", "------------\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/jelly.out.fasta.tbl: No such file or directory\n" ] } ], "source": [ "%%bash\n", "echo \"------------\"\n", "echo \"STANDARD OUT\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stdout.out\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"STANDARD ERROR\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/stderr.err\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"REPEATMASKER C.VIRGINICA TABLE\"\n", "echo \"------------\"\n", "cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Run RepeatMasker with _Ostrea lurida_ species setting and following options:\n", "\n", "- ```-species \"ostrea lurida\"``` : Sets species to Ostrea lurida\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." ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t297m9.951s\n", "user\t3102m3.256s\n", "sys\t1096m47.180s\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04\n", "cd /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04\n", "\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/jelly.out.fasta \\\n", "-species \"ostrea lurida\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stdout.out \\\n", "2> /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stderr.err\n", "\n", "sed '/^Subject:/ s/ / repeatmasker JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "------------\n", "STANDARD OUT\n", "------------\n", "cycle 4 ..................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 5 \n", "cycle 6 ..................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 7 ..................................................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 8 ...............................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 9 ...............................................................................................................................................................................................................................................................................................................................................................................\n", "cycle 10 ...............................................................................................................................................................................................................................................................................................................................................................................\n", "Generating output... ...........................................................................................................................................................................................................................................................................................................................................................................\n", "masking\n", "done\n", "\n", "\n", "------------\n", "STANDARD ERROR\n", "------------\n", "\n", "\n", "------------\n", "REPEATMASKER O.LURIDA TABLE\n", "------------\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "cat: /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/jelly.out.fasta.tbl: No such file or directory\n" ] } ], "source": [ "%%bash\n", "echo \"------------\"\n", "echo \"STANDARD OUT\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stdout.out\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"STANDARD ERROR\"\n", "echo \"------------\"\n", "tail /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/stderr.err\n", "\n", "echo \"\"\n", "echo \"\"\n", "\n", "echo \"------------\"\n", "echo \"REPEATMASKER O.LURIDA TABLE\"\n", "echo \"------------\"\n", "cat /home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### It turns out the reason none of the *.tbl files displayed is due to the location from RepeatMasker! It spits some of the output files to the same directory of the genome file and some to a subdirectory that it creates!" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "jelly.out.fasta\n", "jelly.out.fasta.preThuMay240214172018.RMoutput\n", "jelly.out.fasta.preThuMay240845562018.RMoutput\n", "jelly.out.fasta.preThuMay241347382018.RMoutput\n", "jelly.out.fasta.preThuMay241644392018.RMoutput\n" ] } ], "source": [ "%%bash\n", "ls /home/sam/data/oly_assemblies/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### DEFAULT SETTINGS SUMMARY TABLE (_Homo sapiens_)" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: jelly.out.fasta \n", "sequences: 696946\n", "total length: 1253001795 bp (1172226648 bp excl N/X-runs)\n", "GC level: 36.51 %\n", "bases masked: 20002806 bp ( 1.71 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "SINEs: 17794 1061170 bp 0.09 %\n", " ALUs 363 31340 bp 0.00 %\n", " MIRs 1166 92129 bp 0.01 %\n", "\n", "LINEs: 4456 888114 bp 0.08 %\n", " LINE1 976 103929 bp 0.01 %\n", " LINE2 813 82891 bp 0.01 %\n", " L3/CR1 699 63627 bp 0.01 %\n", "\n", "LTR elements: 1187 199118 bp 0.02 %\n", " ERVL 155 15828 bp 0.00 %\n", " ERVL-MaLRs 200 20737 bp 0.00 %\n", " ERV_classI 379 42833 bp 0.00 %\n", " ERV_classII 66 6896 bp 0.00 %\n", "\n", "DNA elements: 2290 196866 bp 0.02 %\n", " hAT-Charlie 190 15468 bp 0.00 %\n", " TcMar-Tigger 732 37473 bp 0.00 %\n", "\n", "Unclassified: 101 12946 bp 0.00 %\n", "\n", "Total interspersed repeats: 2358214 bp 0.20 %\n", "\n", "\n", "Small RNA: 5954 433422 bp 0.04 %\n", "\n", "Satellites: 366 55705 bp 0.00 %\n", "Simple repeats: 310641 14322152 bp 1.22 %\n", "Low complexity: 47381 2844279 bp 0.24 %\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 homo sapiens \n", "RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127\n", " \n", "run with rmblastn version 2.6.0+\n", "\n" ] } ], "source": [ "%%bash\n", "cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### DEFAULT SETTINGS SUMMARY TABLE (_Crassostrea gigas_)" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: jelly.out.fasta \n", "sequences: 696946\n", "total length: 1253001795 bp (1172226648 bp excl N/X-runs)\n", "GC level: 36.51 %\n", "bases masked: 160759267 bp ( 13.71 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "Retroelements 213132 69887654 bp 5.96 %\n", " SINEs: 2374 311974 bp 0.03 %\n", " Penelope 171792 57862186 bp 4.94 %\n", " LINEs: 195605 63430615 bp 5.41 %\n", " CRE/SLACS 0 0 bp 0.00 %\n", " L2/CR1/Rex 731 357995 bp 0.03 %\n", " R1/LOA/Jockey 0 0 bp 0.00 %\n", " R2/R4/NeSL 13 11377 bp 0.00 %\n", " RTE/Bov-B 8085 1948581 bp 0.17 %\n", " L1/CIN4 0 0 bp 0.00 %\n", " LTR elements: 15153 6145065 bp 0.52 %\n", " BEL/Pao 2119 955773 bp 0.08 %\n", " Ty1/Copia 101 75372 bp 0.01 %\n", " Gypsy/DIRS1 11776 4815361 bp 0.41 %\n", " Retroviral 0 0 bp 0.00 %\n", "\n", "DNA transposons 256292 35689117 bp 3.04 %\n", " hobo-Activator 19847 2059651 bp 0.18 %\n", " Tc1-IS630-Pogo 43269 6806311 bp 0.58 %\n", " En-Spm 0 0 bp 0.00 %\n", " MuDR-IS905 0 0 bp 0.00 %\n", " PiggyBac 7935 1060296 bp 0.09 %\n", " Tourist/Harbinger 9503 887332 bp 0.08 %\n", " Other (Mirage, 0 0 bp 0.00 %\n", " P-element, Transib)\n", "\n", "Rolling-circles 0 0 bp 0.00 %\n", "\n", "Unclassified: 174943 38299211 bp 3.27 %\n", "\n", "Total interspersed repeats: 143875982 bp 12.27 %\n", "\n", "\n", "Small RNA: 280 78768 bp 0.01 %\n", "\n", "Satellites: 7383 1362194 bp 0.12 %\n", "Simple repeats: 278809 12982714 bp 1.11 %\n", "Low complexity: 44078 2622506 bp 0.22 %\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 crassostrea gigas\n", "RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127\n", " \n", "run with rmblastn version 2.6.0+\n", "\n" ] } ], "source": [ "%%bash\n", "cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### DEFAULT SETTINGS SUMMARY TABLE (_Crassostrea virginica_)" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: jelly.out.fasta \n", "sequences: 696946\n", "total length: 1253001795 bp (1172226648 bp excl N/X-runs)\n", "GC level: 36.51 %\n", "bases masked: 39598953 bp ( 3.38 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "Retroelements 63882 10327611 bp 0.88 %\n", " SINEs: 63882 10327611 bp 0.88 %\n", " Penelope 0 0 bp 0.00 %\n", " LINEs: 0 0 bp 0.00 %\n", " CRE/SLACS 0 0 bp 0.00 %\n", " L2/CR1/Rex 0 0 bp 0.00 %\n", " R1/LOA/Jockey 0 0 bp 0.00 %\n", " R2/R4/NeSL 0 0 bp 0.00 %\n", " RTE/Bov-B 0 0 bp 0.00 %\n", " L1/CIN4 0 0 bp 0.00 %\n", " LTR elements: 0 0 bp 0.00 %\n", " BEL/Pao 0 0 bp 0.00 %\n", " Ty1/Copia 0 0 bp 0.00 %\n", " Gypsy/DIRS1 0 0 bp 0.00 %\n", " Retroviral 0 0 bp 0.00 %\n", "\n", "DNA transposons 9433 2307292 bp 0.20 %\n", " hobo-Activator 0 0 bp 0.00 %\n", " Tc1-IS630-Pogo 0 0 bp 0.00 %\n", " En-Spm 0 0 bp 0.00 %\n", " MuDR-IS905 0 0 bp 0.00 %\n", " PiggyBac 0 0 bp 0.00 %\n", " Tourist/Harbinger 0 0 bp 0.00 %\n", " Other (Mirage, 0 0 bp 0.00 %\n", " P-element, Transib)\n", "\n", "Rolling-circles 0 0 bp 0.00 %\n", "\n", "Unclassified: 51558 9836468 bp 0.84 %\n", "\n", "Total interspersed repeats: 22471371 bp 1.92 %\n", "\n", "\n", "Small RNA: 64164 10406776 bp 0.89 %\n", "\n", "Satellites: 10 5985 bp 0.00 %\n", "Simple repeats: 298612 14185090 bp 1.21 %\n", "Low complexity: 47510 2866522 bp 0.24 %\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 crassostrea virginica\n", "RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127\n", " \n", "run with rmblastn version 2.6.0+\n", "\n" ] } ], "source": [ "%%bash\n", "cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### DEFAULT SETTINGS SUMMARY TABLE (_Ostrea lurida_)" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: jelly.out.fasta \n", "sequences: 696946\n", "total length: 1253001795 bp (1172226648 bp excl N/X-runs)\n", "GC level: 36.51 %\n", "bases masked: 17617763 bp ( 1.50 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "Retroelements 0 0 bp 0.00 %\n", " SINEs: 0 0 bp 0.00 %\n", " Penelope 0 0 bp 0.00 %\n", " LINEs: 0 0 bp 0.00 %\n", " CRE/SLACS 0 0 bp 0.00 %\n", " L2/CR1/Rex 0 0 bp 0.00 %\n", " R1/LOA/Jockey 0 0 bp 0.00 %\n", " R2/R4/NeSL 0 0 bp 0.00 %\n", " RTE/Bov-B 0 0 bp 0.00 %\n", " L1/CIN4 0 0 bp 0.00 %\n", " LTR elements: 0 0 bp 0.00 %\n", " BEL/Pao 0 0 bp 0.00 %\n", " Ty1/Copia 0 0 bp 0.00 %\n", " Gypsy/DIRS1 0 0 bp 0.00 %\n", " Retroviral 0 0 bp 0.00 %\n", "\n", "DNA transposons 0 0 bp 0.00 %\n", " hobo-Activator 0 0 bp 0.00 %\n", " Tc1-IS630-Pogo 0 0 bp 0.00 %\n", " En-Spm 0 0 bp 0.00 %\n", " MuDR-IS905 0 0 bp 0.00 %\n", " PiggyBac 0 0 bp 0.00 %\n", " Tourist/Harbinger 0 0 bp 0.00 %\n", " Other (Mirage, 0 0 bp 0.00 %\n", " P-element, Transib)\n", "\n", "Rolling-circles 0 0 bp 0.00 %\n", "\n", "Unclassified: 3 189 bp 0.00 %\n", "\n", "Total interspersed repeats: 189 bp 0.00 %\n", "\n", "\n", "Small RNA: 282 79165 bp 0.01 %\n", "\n", "Satellites: 10 5985 bp 0.00 %\n", "Simple repeats: 313082 14662647 bp 1.25 %\n", "Low complexity: 47785 2878201 bp 0.25 %\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 ostrea lurida \n", "RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127\n", " \n", "run with rmblastn version 2.6.0+\n", "\n" ] } ], "source": [ "%%bash\n", "cat /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.tbl" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.masked': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.tbl': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.out': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/readme.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.cat.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput/jelly.out.fasta.out.gff': Permission denied\n", "cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput': Operation not permitted\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.masked': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.out.gff': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.cat.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.tbl': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/jelly.out.fasta.out': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput/readme.txt': Permission denied\n", "cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput': Operation not permitted\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.masked': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.out.gff': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.cat.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.tbl': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/jelly.out.fasta.out': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput/readme.txt': Permission denied\n", "cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput': Operation not permitted\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.masked': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.out.gff': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.cat.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.tbl': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/jelly.out.fasta.out': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput/readme.txt': Permission denied\n", "cp: preserving times for '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput': Operation not permitted\n", "ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput': Permission denied\n", "ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput': Permission denied\n", "ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput': Permission denied\n", "ls: cannot open directory '/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput': Permission denied\n" ] } ], "source": [ "%%bash\n", "cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.* /mnt/owl/Athaliana/\n", "\n", "ls /mnt/owl/Athaliana/jelly.out.fasta.*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Ugh. Ran copy command with ```sudo``` outside of notebok." ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240214172018.RMoutput:\n", "jelly.out.fasta.cat.gz\n", "jelly.out.fasta.masked\n", "jelly.out.fasta.out\n", "jelly.out.fasta.out.gff\n", "jelly.out.fasta.tbl\n", "readme.txt\n", "\n", "/mnt/owl/Athaliana/jelly.out.fasta.preThuMay240845562018.RMoutput:\n", "jelly.out.fasta.cat.gz\n", "jelly.out.fasta.masked\n", "jelly.out.fasta.out\n", "jelly.out.fasta.out.gff\n", "jelly.out.fasta.tbl\n", "readme.txt\n", "\n", "/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241347382018.RMoutput:\n", "jelly.out.fasta.cat.gz\n", "jelly.out.fasta.masked\n", "jelly.out.fasta.out\n", "jelly.out.fasta.out.gff\n", "jelly.out.fasta.tbl\n", "readme.txt\n", "\n", "/mnt/owl/Athaliana/jelly.out.fasta.preThuMay241644392018.RMoutput:\n", "jelly.out.fasta.cat.gz\n", "jelly.out.fasta.masked\n", "jelly.out.fasta.out\n", "jelly.out.fasta.out.gff\n", "jelly.out.fasta.tbl\n", "readme.txt\n" ] } ], "source": [ "%%bash\n", "\n", "ls /mnt/owl/Athaliana/jelly.out.fasta.*" ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "Copied folders to wrong locations. Re-doing. Will need to use sudo outside of notebook." ] }, { "cell_type": "code", "execution_count": 27, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240214172018.RMoutput \\\n", "/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-01/\n", "\n", "cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay240845562018.RMoutput \\\n", "/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-02/\n", "\n", "cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241347382018.RMoutput \\\n", "/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-03/\n", "\n", "cp -pR /home/sam/data/oly_assemblies/jelly.out.fasta.preThuMay241644392018.RMoutput \\\n", "/home/sam/analyses/20180523_oly_repeatmasker_pbjelly_sjw_01-04/" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-01:\n", "jelly.out.fasta.preThuMay240214172018.RMoutput\n", "readme.txt\n", "stderr.err\n", "stdout.out\n", "\n", "/mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-02:\n", "jelly.out.fasta.preThuMay240845562018.RMoutput\n", "stderr.err\n", "stdout.out\n", "\n", "/mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-03:\n", "jelly.out.fasta.preThuMay241347382018.RMoutput\n", "stderr.err\n", "stdout.out\n", "\n", "/mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-04:\n", "jelly.out.fasta.preThuMay241644392018.RMoutput\n", "stderr.err\n", "stdout.out\n" ] } ], "source": [ "%%bash\n", "ls /mnt/owl/Athaliana/20180523_oly_repeatmasker_pbjelly_sjw_01-0*" ] }, { "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 }