{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "ename": "SyntaxError", "evalue": "invalid syntax (, line 1)", "output_type": "error", "traceback": [ "\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m echo \"TODAY'S DATE:\"\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n" ] } ], "source": [ "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": [ "TODAY'S DATE:\n", "Mon Jul 2 08:32:22 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: 1596.000\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 518M 14G 509M 31G 45G\n", "Swap: 47G 4.8M 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": "markdown", "metadata": {}, "source": [ "#### Assembly ```Olurida_v081.fa``` details are here: https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome-1" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Make output directories" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/analyses/20180702_oly_repeatmasker_defaults\n", "mkdir /home/sam/analyses/20180702_oly_repeatmasker_Cgigas\n", "mkdir /home/sam/analyses/20180702_oly_repeatmasker_Cvirginica\n", "mkdir /home/sam/analyses/20180702_oly_repeatmasker_Olurida" ] }, { "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." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t252m34.218s\n", "user\t3228m1.044s\n", "sys\t539m4.084s\n" ] } ], "source": [ "%%bash\n", "wd=\"/home/sam/analyses/20180702_oly_repeatmasker_defaults\"\n", "cd \"$wd\"\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/Olurida_v081.fa \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> \"$wd\"/stdout.out \\\n", "2> \"$wd\"/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker defaults JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "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": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t248m53.801s\n", "user\t3021m41.000s\n", "sys\t399m32.716s\n" ] } ], "source": [ "%%bash\n", "wd=\"/home/sam/analyses/20180702_oly_repeatmasker_Cgigas\"\n", "cd \"$wd\"\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/Olurida_v081.fa \\\n", "-species \"crassostrea gigas\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> \"$wd\"/stdout.out \\\n", "2> \"$wd\"/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker gigas JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "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": 6, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t151m26.032s\n", "user\t1605m31.120s\n", "sys\t426m29.152s\n" ] } ], "source": [ "%%bash\n", "wd=\"/home/sam/analyses/20180702_oly_repeatmasker_Cvirginica\"\n", "cd \"$wd\"\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/Olurida_v081.fa \\\n", "-species \"crassostrea virginica\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> \"$wd\"/stdout.out \\\n", "2> \"$wd\"/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker virginica JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "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.\n" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t146m27.018s\n", "user\t1575m41.164s\n", "sys\t428m13.936s\n" ] } ], "source": [ "%%bash\n", "wd=\"/home/sam/analyses/20180702_oly_repeatmasker_Olurida\"\n", "cd \"$wd\"\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/Olurida_v081.fa \\\n", "-species \"ostrea lurida\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> \"$wd\"/stdout.out \\\n", "2> \"$wd\"/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker lurida JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Re-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.\n", "\n", "Re-ran this due to problems with output files being ovewritten by subsequent job(s). This is an irritating aspect of RepeatMasker..." ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t247m19.775s\n", "user\t3003m2.852s\n", "sys\t397m16.468s\n" ] } ], "source": [ "%%bash\n", "wd=\"/home/sam/analyses/20180702_oly_repeatmasker_Cgigas\"\n", "cd \"$wd\"\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/Olurida_v081.fa \\\n", "-species \"crassostrea gigas\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> \"$wd\"/stdout.out \\\n", "2> \"$wd\"/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker gigas JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Re-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.\n", "\n", "Re-ran this due to problems with output files being ovewritten by subsequent job(s). This is an irritating aspect of RepeatMasker...\n" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t147m27.320s\n", "user\t1578m28.308s\n", "sys\t437m29.592s\n" ] } ], "source": [ "%%bash\n", "wd=\"/home/sam/analyses/20180702_oly_repeatmasker_Olurida\"\n", "cd \"$wd\"\n", "time \\\n", "/home/shared/RepeatMasker-4.0.7/RepeatMasker \\\n", "/home/sam/data/oly_assemblies/Olurida_v081.fa \\\n", "-species \"ostrea lurida\" \\\n", "-par 15 \\\n", "-gff \\\n", "-excln \\\n", "1> \"$wd\"/stdout.out \\\n", "2> \"$wd\"/stderr.err\n", "sed '/^Subject:/ s/ / repeatmasker lurida JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### SUMMARY TABLE (default settings)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: Olurida_v081.fa \n", "sequences: 159429\n", "total length: 1140787867 bp (1077373535 bp excl N/X-runs)\n", "GC level: 36.58 %\n", "bases masked: 17954347 bp ( 1.67 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "SINEs: 16599 978030 bp 0.09 %\n", " ALUs 1 292 bp 0.00 %\n", " MIRs 937 72873 bp 0.01 %\n", "\n", "LINEs: 3279 752631 bp 0.07 %\n", " LINE1 172 10882 bp 0.00 %\n", " LINE2 646 67827 bp 0.01 %\n", " L3/CR1 659 60327 bp 0.01 %\n", "\n", "LTR elements: 569 127808 bp 0.01 %\n", " ERVL 32 1949 bp 0.00 %\n", " ERVL-MaLRs 10 490 bp 0.00 %\n", " ERV_classI 165 17699 bp 0.00 %\n", " ERV_classII 26 1590 bp 0.00 %\n", "\n", "DNA elements: 1911 161957 bp 0.02 %\n", " hAT-Charlie 74 4216 bp 0.00 %\n", " TcMar-Tigger 584 24985 bp 0.00 %\n", "\n", "Unclassified: 78 9834 bp 0.00 %\n", "\n", "Total interspersed repeats: 2030260 bp 0.19 %\n", "\n", "\n", "Small RNA: 5592 409456 bp 0.04 %\n", "\n", "Satellites: 117 21278 bp 0.00 %\n", "Simple repeats: 270784 12935570 bp 1.20 %\n", "Low complexity: 42130 2568284 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/analyses/20180702_oly_repeatmasker_defaults/Olurida_v081.fa.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### SUMMARY TABLE (_Crassostrea gigas_)" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: Olurida_v081.fa \n", "sequences: 159429\n", "total length: 1140787867 bp (1077373535 bp excl N/X-runs)\n", "GC level: 36.58 %\n", "bases masked: 152816516 bp ( 14.18 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "Retroelements 193250 67253771 bp 6.24 %\n", " SINEs: 2087 284274 bp 0.03 %\n", " Penelope 158576 56080082 bp 5.21 %\n", " LINEs: 179430 61300904 bp 5.69 %\n", " CRE/SLACS 0 0 bp 0.00 %\n", " L2/CR1/Rex 675 348273 bp 0.03 %\n", " R1/LOA/Jockey 0 0 bp 0.00 %\n", " R2/R4/NeSL 7 10781 bp 0.00 %\n", " RTE/Bov-B 7051 1827344 bp 0.17 %\n", " L1/CIN4 0 0 bp 0.00 %\n", " LTR elements: 11733 5668593 bp 0.53 %\n", " BEL/Pao 1517 871288 bp 0.08 %\n", " Ty1/Copia 78 72481 bp 0.01 %\n", " Gypsy/DIRS1 9151 4445789 bp 0.41 %\n", " Retroviral 0 0 bp 0.00 %\n", "\n", "DNA transposons 233691 33727339 bp 3.13 %\n", " hobo-Activator 17578 1886743 bp 0.18 %\n", " Tc1-IS630-Pogo 39184 6403235 bp 0.59 %\n", " En-Spm 0 0 bp 0.00 %\n", " MuDR-IS905 0 0 bp 0.00 %\n", " PiggyBac 7261 1003937 bp 0.09 %\n", " Tourist/Harbinger 8635 823434 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: 157855 36675484 bp 3.40 %\n", "\n", "Total interspersed repeats: 137656594 bp 12.78 %\n", "\n", "\n", "Small RNA: 222 72690 bp 0.01 %\n", "\n", "Satellites: 6260 1238331 bp 0.11 %\n", "Simple repeats: 241081 11662466 bp 1.08 %\n", "Low complexity: 38915 2347827 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/analyses/20180702_oly_repeatmasker_Cgigas/Olurida_v081.fa.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### SUMMARY TABLE (_Crassostrea virginica_)" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: Olurida_v081.fa \n", "sequences: 159429\n", "total length: 1140787867 bp (1077373535 bp excl N/X-runs)\n", "GC level: 36.58 %\n", "bases masked: 36996910 bp ( 3.43 %)\n", "==================================================\n", " number of length percentage\n", " elements* occupied of sequence\n", "--------------------------------------------------\n", "Retroelements 59806 9886111 bp 0.92 %\n", " SINEs: 59806 9886111 bp 0.92 %\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 8720 2230426 bp 0.21 %\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: 47005 9434652 bp 0.88 %\n", "\n", "Total interspersed repeats: 21551189 bp 2.00 %\n", "\n", "\n", "Small RNA: 60030 9959172 bp 0.92 %\n", "\n", "Satellites: 8 5100 bp 0.00 %\n", "Simple repeats: 259134 12795379 bp 1.19 %\n", "Low complexity: 42184 2581162 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/analyses/20180702_oly_repeatmasker_Cvirginica/Olurida_v081.fa.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### SUMMARY TABLE (_Ostrea lurida_)" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "cat: /home/sam/analyses/20180702_oly_repeatmasker_Olurida/Olurida_v081.fa.tbl: No such file or directory\n" ] } ], "source": [ "%%bash\n", "cat /home/sam/analyses/20180702_oly_repeatmasker_Olurida/Olurida_v081.fa.tbl" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "==================================================\n", "file name: Olurida_v081.fa \n", "sequences: 159429\n", "total length: 1140787867 bp (1077373535 bp excl N/X-runs)\n", "GC level: 36.58 %\n", "bases masked: 15918797 bp ( 1.48 %)\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: 224 73061 bp 0.01 %\n", "\n", "Satellites: 8 5100 bp 0.00 %\n", "Simple repeats: 273098 13256460 bp 1.23 %\n", "Low complexity: 42443 2592212 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 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/analyses/20180702_oly_repeatmasker_Olurida/Olurida_v081.fa.tbl" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Had to use sudo to copy files to Owl." ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/mnt/owl/Athaliana/20180702_oly_repeatmasker_Cgigas:\n", "Olurida_v081.fa.cat.gz\n", "Olurida_v081.fa.masked\n", "Olurida_v081.fa.out\n", "Olurida_v081.fa.out.gff\n", "Olurida_v081.fa.tbl\n", "readme.txt\n", "stderr.err\n", "stdout.out\n", "\n", "/mnt/owl/Athaliana/20180702_oly_repeatmasker_Cvirginica:\n", "Olurida_v081.fa.cat.gz\n", "Olurida_v081.fa.masked\n", "Olurida_v081.fa.out\n", "Olurida_v081.fa.out.gff\n", "Olurida_v081.fa.tbl\n", "readme.txt\n", "stderr.err\n", "stdout.out\n", "\n", "/mnt/owl/Athaliana/20180702_oly_repeatmasker_defaults:\n", "Olurida_v081.fa.cat.gz\n", "Olurida_v081.fa.masked\n", "Olurida_v081.fa.out\n", "Olurida_v081.fa.out.gff\n", "Olurida_v081.fa.tbl\n", "readme.txt\n", "stderr.err\n", "stdout.out\n", "\n", "/mnt/owl/Athaliana/20180702_oly_repeatmasker_Olurida:\n", "Olurida_v081.fa.cat.gz\n", "Olurida_v081.fa.masked\n", "Olurida_v081.fa.out\n", "Olurida_v081.fa.out.gff\n", "Olurida_v081.fa.tbl\n", "readme.txt\n", "stderr.err\n", "stdout.out\n" ] } ], "source": [ "%%bash\n", "ls /mnt/owl/Athaliana/20180702_oly_repeatmasker*" ] }, { "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 }