{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "TODAY'S DATE:\n", "Mon May 14 13:10:58 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: 4521.81\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 retpoline 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 428M 1.5G 500M 45G 45G\n", "Swap: 47G 524K 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": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "cp: target 'home/sam/data/geoduck_EPI' is not a directory\n", "\n", "real\t0m0.614s\n", "user\t0m0.004s\n", "sys\t0m0.004s\n" ] } ], "source": [ "%%bash\n", "mkdir /home/sam/data/geoduck_EPI\n", "\n", "time \\\n", "cp -p /mnt/owl/nightingales/P_generosa/EPI* home/sam/data/geoduck_EPI\n", "\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "cp: target 'home/sam/data/geoduck_EPI' is not a directory\n", "\n", "real\t0m0.035s\n", "user\t0m0.000s\n", "sys\t0m0.004s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "cp -p /mnt/owl/nightingales/P_generosa/EPI* home/sam/data/geoduck_EPI\n", "\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t38m10.131s\n", "user\t0m1.864s\n", "sys\t3m15.448s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "cp -p /mnt/owl/nightingales/P_generosa/EPI* /home/sam/data/geoduck_EPI\n", "\n", "cat ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t13m44.510s\n", "user\t7m24.524s\n", "sys\t1m14.624s\n", "sed: can't read .default-subject.mail: No such file or directory\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/data/geoduck_EPI\n", "\n", "time \\\n", "for file in *.gz\n", "do md5sum \"$file\" >> 20180514_checksums.md5\n", "done\n", "\n", "sed '/^Subject:/ s/ / md5 JOB COMPLETE/' .default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m1.554s\n", "user\t0m0.008s\n", "sys\t0m0.024s\n", "sed: can't read .default-subject.mail: No such file or directory\n" ] } ], "source": [ "%%bash\n", "time \\\n", "for file in /home/sam/data/geoduck_EPI/*.gz\n", "do grep \"$file\" /mnt/owl/nightingales/P_generosa/checksums.md5 >> \\\n", "/home/sam/data/geoduck_EPI/owl_checksums.md5\n", "done\n", "\n", "sed '/^Subject:/ s/ / grep JOB COMPLETE/' .default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0a1,106\n", "> 0008a46af2c71ecf3bca81c91fd1256c EPI-214_S30_L004_R2_001.fastq.gz\n", "> 01442d00a6aa4fb2bb83d1822124ee0d EPI-143_S37_L005_R2_001.fastq.gz\n", "> 01622ddd42536f2e4402a886cc238452 EPI-151_S2_L002_R2_001.fastq.gz\n", "> 06639a0de7dbbdaf172078a71b477505 EPI-167_S10_L002_R2_001.fastq.gz\n", "> 0778c863bd849c9f03a2ce414b77c3c0 EPI-221_S33_L004_R2_001.fastq.gz\n", "> 093663928a827da87055024e851cf7c9 EPI-151_S2_L002_R1_001.fastq.gz\n", "> 0b62c98e81b23dee9cad6b12fe16f6e2 EPI-227_S35_L004_R2_001.fastq.gz\n", "> 1203bdd2c90ba1a3ee3c448d85d0ded5 EPI-185_S19_L003_R1_001.fastq.gz\n", "> 12c44de55c548c3f460ef7c71e3ae993 EPI-170_S13_L002_R1_001.fastq.gz\n", "> 1329cfe4f0aca9401f52de0a381c34dd EPI-193_S22_L003_R1_001.fastq.gz\n", "> 14201cba377cb89d97f567680a8adffd EPI-209_S29_L004_R2_001.fastq.gz\n", "> 14f1692de83305a2ac31556916aba832 EPI-181_S16_L003_R2_001.fastq.gz\n", "> 16d30e78a0f3553e291c234e0cde707d EPI-169_S12_L002_R1_001.fastq.gz\n", "> 17dbac3c0a80c19b7cf9c65840188dc0 EPI-103_S27_L005_R1_001.fastq.gz\n", "> 1849c59c8f788a87ce038b684b7f50b0 EPI-127_S33_L005_R1_001.fastq.gz\n", "> 19d9af2a034dc0d2f6108cd12c51d5e1 EPI-184_S18_L003_R1_001.fastq.gz\n", "> 1a33a67e19868ee205ef987b45d86ba3 EPI-162_S9_L002_R1_001.fastq.gz\n", "> 1cae2a72398e94e68947eca56f875d97 EPI-119_S31_L005_R1_001.fastq.gz\n", "> 1d4fb44a60cb4b50367f35751d71b040 EPI-104_S28_L005_R1_001.fastq.gz\n", "> 2030d48b44ab6ceb02ee17ae184d514b EPI-161_S8_L002_R2_001.fastq.gz\n", "> 2256a06956601d00e8126f78c1ebd671 EPI-128_S34_L005_R2_001.fastq.gz\n", "> 2c046be5e0edf358c129ed04be7b160d EPI-220_S32_L004_R2_001.fastq.gz\n", "> 2dfe384eed4440559bcb93dc74a20c76 EPI-199_S24_L003_R1_001.fastq.gz\n", "> 32d3d12940ad2b2aeb76ce5438070e6e EPI-200_S25_L003_R2_001.fastq.gz\n", "> 340dfe49b0eed4a2d113286ee6f4e157 EPI-226_S34_L004_R2_001.fastq.gz\n", "> 3491813841279cc6b63971ab5bad9972 EPI-42_S39_L005_R1_001.fastq.gz\n", "> 3a3da121e8871e57d7a09180831d2ffd EPI-135_S35_L005_R2_001.fastq.gz\n", "> 3b2c02d050a9fc60a5b3894dcd8e5fd6 EPI-120_S32_L005_R2_001.fastq.gz\n", "> 3f4cdb3f2f22ce0d00e8b4bb836e622b EPI-159_S6_L002_R2_001.fastq.gz\n", "> 44ab652e5b37a558ddac9717b9546c2a EPI-135WG_S42_L005_R2_001.fastq.gz\n", "> 4a5fbb9b56d219e25091aadea8ca8a71 EPI-154_S5_L002_R2_001.fastq.gz\n", "> 4b8fedbcfa36146f0a1fc27ea66d3fef EPI-205_S26_L004_R2_001.fastq.gz\n", "> 4ec237a381460fd7635b77b84bc530f1 EPI-103_S27_L005_R2_001.fastq.gz\n", "> 4f40f1e20fae9cae68aaefd35fd6281a EPI-205_S26_L004_R1_001.fastq.gz\n", "> 5211ee55bda2d9fc104cd3fd862b4e5a EPI-111_S29_L005_R1_001.fastq.gz\n", "> 526340cec71d1919e011f003c0c4635b EPI-135WG_S42_L005_R1_001.fastq.gz\n", "> 560c5d40f5827b4c11a278381b68346b EPI-215_S31_L004_R2_001.fastq.gz\n", "> 5676c6f6d3b4194c5f2ded8f18181a22 EPI-184_S18_L003_R2_001.fastq.gz\n", "> 593534642c0871499e807dcfeb29e440 EPI-153_S4_L002_R2_001.fastq.gz\n", "> 5e48888ca407559f4da4c8cfea47f604 EPI-230_S37_L004_R1_001.fastq.gz\n", "> 61030272675714e68daa27406e10d625 EPI-44_S41_L005_R1_001.fastq.gz\n", "> 6220c5904edd95a5abb0786750775ae4 EPI-194_S23_L003_R1_001.fastq.gz\n", "> 624ce2bdf92a3799be54f7fd3ab19e10 EPI-194_S23_L003_R2_001.fastq.gz\n", "> 6bf50011fe4dacad4379828897d3b99b EPI-111_S29_L005_R2_001.fastq.gz\n", "> 6d8058be169234534288abbd36066dee EPI-120_S32_L005_R1_001.fastq.gz\n", "> 70033052415b60895658c86f88f0c609 EPI-200_S25_L003_R1_001.fastq.gz\n", "> 73e042e44f8072574fe3cf2eb62e71ef EPI-215_S31_L004_R1_001.fastq.gz\n", "> 74461e7cfc369eef5f3350e033de8544 EPI-145_S38_L005_R1_001.fastq.gz\n", "> 76dfc6efe90d3dd2d5317abea31f3bb4 EPI-154_S5_L002_R1_001.fastq.gz\n", "> 785578fe3b427896e40c5b82aca28d6b EPI-188_S21_L003_R2_001.fastq.gz\n", "> 7ca64d5b500f0768b3ce697c21614948 EPI-113_S30_L005_R1_001.fastq.gz\n", "> 85a3d2237c14fdb474fee3fa959bca26 EPI-175_S14_L003_R2_001.fastq.gz\n", "> 85b48a03757fbd3ae6738dce05cc62b8 EPI-127_S33_L005_R2_001.fastq.gz\n", "> 8d15f59c59cf89091cef520b36aabad8 EPI-41_S38_L005_R2_001.fastq.gz\n", "> 8f3ab566a1e10c978a4ed6a90ecfcda2 EPI-119_S31_L005_R2_001.fastq.gz\n", "> 917c4a9196ee7a075c7c825629586f4d EPI-160_S7_L002_R2_001.fastq.gz\n", "> 94a157b11c9c65e6994a9ab1bda31a4c EPI-230_S37_L004_R2_001.fastq.gz\n", "> 9513868093be2c85a24e73baff7a808f EPI-44_S41_L005_R2_001.fastq.gz\n", "> 9a91bef27bccedc315844bf9f60d4b85 EPI-220_S32_L004_R1_001.fastq.gz\n", "> 9b53ef4c4fbfe65939418ec1ffe379f9 EPI-209_S29_L004_R1_001.fastq.gz\n", "> 9c46b153ad0d6cdfd7a053921f428a5f EPI-41_S38_L005_R1_001.fastq.gz\n", "> 9c7aa85749188759920f8f17aec8093f EPI-152_S3_L002_R2_001.fastq.gz\n", "> 9dd4c79a0a29a34da420ffd8ec656d8d EPI-161_S8_L002_R1_001.fastq.gz\n", "> a197591179b5d889f7a2f3c4e7cb457a EPI-43_S40_L005_R1_001.fastq.gz\n", "> a3a4a4c46537d24d7897aafe94136f35 EPI-227_S35_L004_R1_001.fastq.gz\n", "> a42c8589d85b0524509ec3069b613dd8 EPI-206_S27_L004_R2_001.fastq.gz\n", "> a59b275111575bcf5907561dabf3872a EPI-136_S36_L005_R1_001.fastq.gz\n", "> a889f064932f77407ae3df107e79bc22 EPI-160_S7_L002_R1_001.fastq.gz\n", "> a9e0d97b58d81c50955be3f7e617b854 EPI-168_S11_L002_R2_001.fastq.gz\n", "> aae2b1afec70b43a58c9700b5e81f91a EPI-187_S20_L003_R1_001.fastq.gz\n", "> ac932672c331c31867d37889bd0d9a47 EPI-152_S3_L002_R1_001.fastq.gz\n", "> b0a219abf08a30710c0741259b663e44 EPI-167_S10_L002_R1_001.fastq.gz\n", "> b717944572b5f631c2e9f372ecde0e8a EPI-43_S40_L005_R2_001.fastq.gz\n", "> b73945c56c67f79fb92c1e9283d90bdf EPI-136_S36_L005_R2_001.fastq.gz\n", "> b8772ae3cfef50928fdc8551bba3da39 EPI-135_S35_L005_R1_001.fastq.gz\n", "> c89f049090efd2a6825cedee82f0c643 EPI-143_S37_L005_R1_001.fastq.gz\n", "> cadb57598aa13d60ae77782b28b5d585 EPI-214_S30_L004_R1_001.fastq.gz\n", "> cb8e11eef79768ec57c3d24a33f17256 EPI-176_S15_L003_R2_001.fastq.gz\n", "> d0e9d98bdf0452e4dea8dbdd39feb5cc EPI-176_S15_L003_R1_001.fastq.gz\n", "> d2bb5864f9cec7c8b079eb703a11d37a EPI-221_S33_L004_R1_001.fastq.gz\n", "> d43bd849a566ac88fd6703e542825650 EPI-162_S9_L002_R2_001.fastq.gz\n", "> d7b97aab1f950c0dfb6114b530be68e6 EPI-188_S21_L003_R1_001.fastq.gz\n", "> d7ec7b3c0766ea6bd16a992f275595cb EPI-145_S38_L005_R2_001.fastq.gz\n", "> d7f0b916c4c4b2720cbb755e14658a46 EPI-182_S17_L003_R2_001.fastq.gz\n", "> dc50b4be71239948a45d74ecbe54ef03 EPI-42_S39_L005_R2_001.fastq.gz\n", "> dc5896535011bf55ea6a38915800e755 EPI-153_S4_L002_R1_001.fastq.gz\n", "> ddc2988966835ea69cfd0f4a94d65cba EPI-113_S30_L005_R2_001.fastq.gz\n", "> e022a618beeb319e91cf19481994acfb EPI-226_S34_L004_R1_001.fastq.gz\n", "> e140c7aa45be0b43c92bf50c5a345999 EPI-208_S28_L004_R1_001.fastq.gz\n", "> e2988b4b413031f4ed38c6a655cab7d7 EPI-170_S13_L002_R2_001.fastq.gz\n", "> e616855d5270077a04205b9407dff0a4 EPI-159_S6_L002_R1_001.fastq.gz\n", "> e63add6d56842254ea351fa59b890027 EPI-185_S19_L003_R2_001.fastq.gz\n", "> e6d9650884923f3a57af77b462c28ff2 EPI-229_S36_L004_R2_001.fastq.gz\n", "> e7f70fa0e712eaffabcc20ac5992b0c1 EPI-168_S11_L002_R1_001.fastq.gz\n", "> e84cc23a8bb4686a96b4857469861280 EPI-199_S24_L003_R2_001.fastq.gz\n", "> e84ecd41bb4254fd6d0307b39c662c79 EPI-128_S34_L005_R1_001.fastq.gz\n", "> ec15ac15be944eab383a0926895b7f93 EPI-187_S20_L003_R2_001.fastq.gz\n", "> ef7a9faf25ba9dc8e330d318c198589a EPI-208_S28_L004_R2_001.fastq.gz\n", "> f09534df38e3ccbad4852cdcafc913ee EPI-182_S17_L003_R1_001.fastq.gz\n", "> f534dea1569d9c3a7345fe0e6230f10d EPI-104_S28_L005_R2_001.fastq.gz\n", "> f62e3995dc29b53c819aa9bec85f8e6a EPI-193_S22_L003_R2_001.fastq.gz\n", "> f7faa1213dfbc90ce1a0afe3c44a92f4 EPI-206_S27_L004_R1_001.fastq.gz\n", "> f8aac98f67d3842c6f377fdf1cde3426 EPI-229_S36_L004_R1_001.fastq.gz\n", "> fc70f1334f6deea225ba2372383d9352 EPI-169_S12_L002_R2_001.fastq.gz\n", "> ff4c1893adf7764a63755731704331b5 EPI-181_S16_L003_R1_001.fastq.gz\n", "> ff9f985b3d6e6d434ec2aa745d1286b6 EPI-175_S14_L003_R1_001.fastq.gz\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "sed: can't read .default-subject.mail: No such file or directory\n" ] } ], "source": [ "%%bash\n", "\n", "diff <(sort /home/sam/data/geoduck_EPI/owl_checksums.md5) <(sort /home/sam/data/geoduck_EPI/20180514_checksums.md5)\n", "\n", "sed '/^Subject:/ s/ / diff JOB COMPLETE/' .default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "head <(sort /home/sam/data/geoduck_EPI/owl_checksums.md5)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0008a46af2c71ecf3bca81c91fd1256c EPI-214_S30_L004_R2_001.fastq.gz\n", "01442d00a6aa4fb2bb83d1822124ee0d EPI-143_S37_L005_R2_001.fastq.gz\n", "01622ddd42536f2e4402a886cc238452 EPI-151_S2_L002_R2_001.fastq.gz\n", "06639a0de7dbbdaf172078a71b477505 EPI-167_S10_L002_R2_001.fastq.gz\n", "0778c863bd849c9f03a2ce414b77c3c0 EPI-221_S33_L004_R2_001.fastq.gz\n", "093663928a827da87055024e851cf7c9 EPI-151_S2_L002_R1_001.fastq.gz\n", "0b62c98e81b23dee9cad6b12fe16f6e2 EPI-227_S35_L004_R2_001.fastq.gz\n", "1203bdd2c90ba1a3ee3c448d85d0ded5 EPI-185_S19_L003_R1_001.fastq.gz\n", "12c44de55c548c3f460ef7c71e3ae993 EPI-170_S13_L002_R1_001.fastq.gz\n", "1329cfe4f0aca9401f52de0a381c34dd EPI-193_S22_L003_R1_001.fastq.gz\n" ] } ], "source": [ "%%bash\n", "head <(sort /home/sam/data/geoduck_EPI/20180514_checksums.md5)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m0.884s\n", "user\t0m0.012s\n", "sys\t0m0.020s\n", "sed: can't read ~.default-subject.mail: No such file or directory\n" ] } ], "source": [ "%%bash\n", "time \\\n", "for file in /home/sam/data/geoduck_EPI/*.gz\n", "do grep \"$file\" /mnt/owl/nightingales/P_generosa/checksums.md5 >> /home/sam/data/geoduck_EPI/owl_checksums.md5\n", "done\n", "\n", "sed '/^Subject:/ s/ / grep JOB COMPLETE/' ~.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "head /home/sam/data/geoduck_EPI/owl_checksums.md5" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0a1,106\n", "> 0008a46af2c71ecf3bca81c91fd1256c EPI-214_S30_L004_R2_001.fastq.gz\n", "> 01442d00a6aa4fb2bb83d1822124ee0d EPI-143_S37_L005_R2_001.fastq.gz\n", "> 01622ddd42536f2e4402a886cc238452 EPI-151_S2_L002_R2_001.fastq.gz\n", "> 06639a0de7dbbdaf172078a71b477505 EPI-167_S10_L002_R2_001.fastq.gz\n", "> 0778c863bd849c9f03a2ce414b77c3c0 EPI-221_S33_L004_R2_001.fastq.gz\n", "> 093663928a827da87055024e851cf7c9 EPI-151_S2_L002_R1_001.fastq.gz\n", "> 0b62c98e81b23dee9cad6b12fe16f6e2 EPI-227_S35_L004_R2_001.fastq.gz\n", "> 1203bdd2c90ba1a3ee3c448d85d0ded5 EPI-185_S19_L003_R1_001.fastq.gz\n", "> 12c44de55c548c3f460ef7c71e3ae993 EPI-170_S13_L002_R1_001.fastq.gz\n", "> 1329cfe4f0aca9401f52de0a381c34dd EPI-193_S22_L003_R1_001.fastq.gz\n", "> 14201cba377cb89d97f567680a8adffd EPI-209_S29_L004_R2_001.fastq.gz\n", "> 14f1692de83305a2ac31556916aba832 EPI-181_S16_L003_R2_001.fastq.gz\n", "> 16d30e78a0f3553e291c234e0cde707d EPI-169_S12_L002_R1_001.fastq.gz\n", "> 17dbac3c0a80c19b7cf9c65840188dc0 EPI-103_S27_L005_R1_001.fastq.gz\n", "> 1849c59c8f788a87ce038b684b7f50b0 EPI-127_S33_L005_R1_001.fastq.gz\n", "> 19d9af2a034dc0d2f6108cd12c51d5e1 EPI-184_S18_L003_R1_001.fastq.gz\n", "> 1a33a67e19868ee205ef987b45d86ba3 EPI-162_S9_L002_R1_001.fastq.gz\n", "> 1cae2a72398e94e68947eca56f875d97 EPI-119_S31_L005_R1_001.fastq.gz\n", "> 1d4fb44a60cb4b50367f35751d71b040 EPI-104_S28_L005_R1_001.fastq.gz\n", "> 2030d48b44ab6ceb02ee17ae184d514b EPI-161_S8_L002_R2_001.fastq.gz\n", "> 2256a06956601d00e8126f78c1ebd671 EPI-128_S34_L005_R2_001.fastq.gz\n", "> 2c046be5e0edf358c129ed04be7b160d EPI-220_S32_L004_R2_001.fastq.gz\n", "> 2dfe384eed4440559bcb93dc74a20c76 EPI-199_S24_L003_R1_001.fastq.gz\n", "> 32d3d12940ad2b2aeb76ce5438070e6e EPI-200_S25_L003_R2_001.fastq.gz\n", "> 340dfe49b0eed4a2d113286ee6f4e157 EPI-226_S34_L004_R2_001.fastq.gz\n", "> 3491813841279cc6b63971ab5bad9972 EPI-42_S39_L005_R1_001.fastq.gz\n", "> 3a3da121e8871e57d7a09180831d2ffd EPI-135_S35_L005_R2_001.fastq.gz\n", "> 3b2c02d050a9fc60a5b3894dcd8e5fd6 EPI-120_S32_L005_R2_001.fastq.gz\n", "> 3f4cdb3f2f22ce0d00e8b4bb836e622b EPI-159_S6_L002_R2_001.fastq.gz\n", "> 44ab652e5b37a558ddac9717b9546c2a EPI-135WG_S42_L005_R2_001.fastq.gz\n", "> 4a5fbb9b56d219e25091aadea8ca8a71 EPI-154_S5_L002_R2_001.fastq.gz\n", "> 4b8fedbcfa36146f0a1fc27ea66d3fef EPI-205_S26_L004_R2_001.fastq.gz\n", "> 4ec237a381460fd7635b77b84bc530f1 EPI-103_S27_L005_R2_001.fastq.gz\n", "> 4f40f1e20fae9cae68aaefd35fd6281a EPI-205_S26_L004_R1_001.fastq.gz\n", "> 5211ee55bda2d9fc104cd3fd862b4e5a EPI-111_S29_L005_R1_001.fastq.gz\n", "> 526340cec71d1919e011f003c0c4635b EPI-135WG_S42_L005_R1_001.fastq.gz\n", "> 560c5d40f5827b4c11a278381b68346b EPI-215_S31_L004_R2_001.fastq.gz\n", "> 5676c6f6d3b4194c5f2ded8f18181a22 EPI-184_S18_L003_R2_001.fastq.gz\n", "> 593534642c0871499e807dcfeb29e440 EPI-153_S4_L002_R2_001.fastq.gz\n", "> 5e48888ca407559f4da4c8cfea47f604 EPI-230_S37_L004_R1_001.fastq.gz\n", "> 61030272675714e68daa27406e10d625 EPI-44_S41_L005_R1_001.fastq.gz\n", "> 6220c5904edd95a5abb0786750775ae4 EPI-194_S23_L003_R1_001.fastq.gz\n", "> 624ce2bdf92a3799be54f7fd3ab19e10 EPI-194_S23_L003_R2_001.fastq.gz\n", "> 6bf50011fe4dacad4379828897d3b99b EPI-111_S29_L005_R2_001.fastq.gz\n", "> 6d8058be169234534288abbd36066dee EPI-120_S32_L005_R1_001.fastq.gz\n", "> 70033052415b60895658c86f88f0c609 EPI-200_S25_L003_R1_001.fastq.gz\n", "> 73e042e44f8072574fe3cf2eb62e71ef EPI-215_S31_L004_R1_001.fastq.gz\n", "> 74461e7cfc369eef5f3350e033de8544 EPI-145_S38_L005_R1_001.fastq.gz\n", "> 76dfc6efe90d3dd2d5317abea31f3bb4 EPI-154_S5_L002_R1_001.fastq.gz\n", "> 785578fe3b427896e40c5b82aca28d6b EPI-188_S21_L003_R2_001.fastq.gz\n", "> 7ca64d5b500f0768b3ce697c21614948 EPI-113_S30_L005_R1_001.fastq.gz\n", "> 85a3d2237c14fdb474fee3fa959bca26 EPI-175_S14_L003_R2_001.fastq.gz\n", "> 85b48a03757fbd3ae6738dce05cc62b8 EPI-127_S33_L005_R2_001.fastq.gz\n", "> 8d15f59c59cf89091cef520b36aabad8 EPI-41_S38_L005_R2_001.fastq.gz\n", "> 8f3ab566a1e10c978a4ed6a90ecfcda2 EPI-119_S31_L005_R2_001.fastq.gz\n", "> 917c4a9196ee7a075c7c825629586f4d EPI-160_S7_L002_R2_001.fastq.gz\n", "> 94a157b11c9c65e6994a9ab1bda31a4c EPI-230_S37_L004_R2_001.fastq.gz\n", "> 9513868093be2c85a24e73baff7a808f EPI-44_S41_L005_R2_001.fastq.gz\n", "> 9a91bef27bccedc315844bf9f60d4b85 EPI-220_S32_L004_R1_001.fastq.gz\n", "> 9b53ef4c4fbfe65939418ec1ffe379f9 EPI-209_S29_L004_R1_001.fastq.gz\n", "> 9c46b153ad0d6cdfd7a053921f428a5f EPI-41_S38_L005_R1_001.fastq.gz\n", "> 9c7aa85749188759920f8f17aec8093f EPI-152_S3_L002_R2_001.fastq.gz\n", "> 9dd4c79a0a29a34da420ffd8ec656d8d EPI-161_S8_L002_R1_001.fastq.gz\n", "> a197591179b5d889f7a2f3c4e7cb457a EPI-43_S40_L005_R1_001.fastq.gz\n", "> a3a4a4c46537d24d7897aafe94136f35 EPI-227_S35_L004_R1_001.fastq.gz\n", "> a42c8589d85b0524509ec3069b613dd8 EPI-206_S27_L004_R2_001.fastq.gz\n", "> a59b275111575bcf5907561dabf3872a EPI-136_S36_L005_R1_001.fastq.gz\n", "> a889f064932f77407ae3df107e79bc22 EPI-160_S7_L002_R1_001.fastq.gz\n", "> a9e0d97b58d81c50955be3f7e617b854 EPI-168_S11_L002_R2_001.fastq.gz\n", "> aae2b1afec70b43a58c9700b5e81f91a EPI-187_S20_L003_R1_001.fastq.gz\n", "> ac932672c331c31867d37889bd0d9a47 EPI-152_S3_L002_R1_001.fastq.gz\n", "> b0a219abf08a30710c0741259b663e44 EPI-167_S10_L002_R1_001.fastq.gz\n", "> b717944572b5f631c2e9f372ecde0e8a EPI-43_S40_L005_R2_001.fastq.gz\n", "> b73945c56c67f79fb92c1e9283d90bdf EPI-136_S36_L005_R2_001.fastq.gz\n", "> b8772ae3cfef50928fdc8551bba3da39 EPI-135_S35_L005_R1_001.fastq.gz\n", "> c89f049090efd2a6825cedee82f0c643 EPI-143_S37_L005_R1_001.fastq.gz\n", "> cadb57598aa13d60ae77782b28b5d585 EPI-214_S30_L004_R1_001.fastq.gz\n", "> cb8e11eef79768ec57c3d24a33f17256 EPI-176_S15_L003_R2_001.fastq.gz\n", "> d0e9d98bdf0452e4dea8dbdd39feb5cc EPI-176_S15_L003_R1_001.fastq.gz\n", "> d2bb5864f9cec7c8b079eb703a11d37a EPI-221_S33_L004_R1_001.fastq.gz\n", "> d43bd849a566ac88fd6703e542825650 EPI-162_S9_L002_R2_001.fastq.gz\n", "> d7b97aab1f950c0dfb6114b530be68e6 EPI-188_S21_L003_R1_001.fastq.gz\n", "> d7ec7b3c0766ea6bd16a992f275595cb EPI-145_S38_L005_R2_001.fastq.gz\n", "> d7f0b916c4c4b2720cbb755e14658a46 EPI-182_S17_L003_R2_001.fastq.gz\n", "> dc50b4be71239948a45d74ecbe54ef03 EPI-42_S39_L005_R2_001.fastq.gz\n", "> dc5896535011bf55ea6a38915800e755 EPI-153_S4_L002_R1_001.fastq.gz\n", "> ddc2988966835ea69cfd0f4a94d65cba EPI-113_S30_L005_R2_001.fastq.gz\n", "> e022a618beeb319e91cf19481994acfb EPI-226_S34_L004_R1_001.fastq.gz\n", "> e140c7aa45be0b43c92bf50c5a345999 EPI-208_S28_L004_R1_001.fastq.gz\n", "> e2988b4b413031f4ed38c6a655cab7d7 EPI-170_S13_L002_R2_001.fastq.gz\n", "> e616855d5270077a04205b9407dff0a4 EPI-159_S6_L002_R1_001.fastq.gz\n", "> e63add6d56842254ea351fa59b890027 EPI-185_S19_L003_R2_001.fastq.gz\n", "> e6d9650884923f3a57af77b462c28ff2 EPI-229_S36_L004_R2_001.fastq.gz\n", "> e7f70fa0e712eaffabcc20ac5992b0c1 EPI-168_S11_L002_R1_001.fastq.gz\n", "> e84cc23a8bb4686a96b4857469861280 EPI-199_S24_L003_R2_001.fastq.gz\n", "> e84ecd41bb4254fd6d0307b39c662c79 EPI-128_S34_L005_R1_001.fastq.gz\n", "> ec15ac15be944eab383a0926895b7f93 EPI-187_S20_L003_R2_001.fastq.gz\n", "> ef7a9faf25ba9dc8e330d318c198589a EPI-208_S28_L004_R2_001.fastq.gz\n", "> f09534df38e3ccbad4852cdcafc913ee EPI-182_S17_L003_R1_001.fastq.gz\n", "> f534dea1569d9c3a7345fe0e6230f10d EPI-104_S28_L005_R2_001.fastq.gz\n", "> f62e3995dc29b53c819aa9bec85f8e6a EPI-193_S22_L003_R2_001.fastq.gz\n", "> f7faa1213dfbc90ce1a0afe3c44a92f4 EPI-206_S27_L004_R1_001.fastq.gz\n", "> f8aac98f67d3842c6f377fdf1cde3426 EPI-229_S36_L004_R1_001.fastq.gz\n", "> fc70f1334f6deea225ba2372383d9352 EPI-169_S12_L002_R2_001.fastq.gz\n", "> ff4c1893adf7764a63755731704331b5 EPI-181_S16_L003_R1_001.fastq.gz\n", "> ff9f985b3d6e6d434ec2aa745d1286b6 EPI-175_S14_L003_R1_001.fastq.gz\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m0.959s\n", "user\t0m0.008s\n", "sys\t0m0.020s\n" ] } ], "source": [ "%%bash\n", "cd /mnt/owl/nightingales/P_generosa/\n", "time \\\n", "for file in /home/sam/data/geoduck_EPI/*.gz\n", "do grep \"$file\" /mnt/owl/nightingales/P_generosa/checksums.md5 >> \\\n", "/home/sam/data/geoduck_EPI/owl_checksums.md5\n", "done\n", "\n", "diff <(sort /home/sam/data/geoduck_EPI/owl_checksums.md5) <(sort /home/sam/data/geoduck_EPI/20180514_checksums.md5)\n", "\n", "sed '/^Subject:/ s/ / grep JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "2d1\n", "< 0062c59dc8fcda8fcfa452ebb717419c JD002B_S132_L005_R2_001.fastq.gz\n", "5,8d3\n", "< 019e96cd8171f3464484dabd62923a21 Geoduck-2_S2_L008_R1_001.fastq.gz\n", "< 02db37aebfc0cd0f8e1184e9d444bb2d JD002K_S141_L005_R2_001.fastq.gz\n", "< 03b66907d4349d7e965bf8f3fa848406 Geoduck-NMP-gDNA-2_S5_L002_R2_001.fastq.gz\n", "< 063ac217889a5b56ad438fc60bc26cc6 Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001.fastq.gz\n", "11d5\n", "< 0803bcdb947c15ee4635497fcea8c288 Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001.fastq.gz\n", "13,15d6\n", "< 0958b79f9c7eef5193a09fa39a508d79 Geoduck-1_S1_L004_I1_001.fastq.gz\n", "< 09e54284660986b049c9cf07dc0ef35e JD002L_S142_L005_R2_001.fastq.gz\n", "< 0ac1c27b01c699af5e20b827f657b2f9 Geoduck-NMP-gDNA-2_S5_L002_R1_001.fastq.gz\n", "17,25d7\n", "< 0b8f9bb7401336c5f4509916d54ccedc Geoduck-6_S2_L007_R2_001.fastq.gz\n", "< 0c2f1b9a951b54694e1b8f287ac82793 JD002H_S138_L005_R2_001.fastq.gz\n", "< 0c6c80505c9c8889804c3732e7f7cd78 Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001.fastq.gz\n", "< 0d44e44352dfb11eac8a7d3d1e155d7f Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001.fastq.gz\n", "< 0d4e953296924154d616c1143f9c4ad8 JD002E_S135_L005_R1_001.fastq.gz\n", "< 0d9876ec17cf6728b5364235fcc4829d Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001.fastq.gz\n", "< 0fdf2a546eccbbcd32a5b17499051b53 Geoduck-NMP-gDNA-1_S1_L001_R1_001.fastq.gz\n", "< 0fdf2a546eccbbcd32a5b17499051b53 Geoduck-NMP-gDNA-1_S1_L001_R1_001.fastq.gz\n", "< 103ca692e4d824eebc907495f6f288d7 JD002L_S142_L005_R1_001.fastq.gz\n", "29d10\n", "< 1403cafaa172d2b009404e98ef6503ae JD002H_S138_L005_R1_001.fastq.gz\n", "31d11\n", "< 149a662ba729b16956fea39e2fa319a4 Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001.fastq.gz\n", "33d12\n", "< 168c2dbf1a7585d2a2a1b13a56e2f4e6 JD002G_S137_L005_R2_001.fastq.gz\n", "35d13\n", "< 17b0a7c63b01524ee771f4cf8ed474e8 Geoduck-6_S2_L007_I1_001.fastq.gz\n", "38d15\n", "< 19089f2e76fdec6970d8210c76c1bf57 Geoduck-6_S2_L008_R2_001.fastq.gz\n", "41,42d17\n", "< 1aa29d8c6d9d55ca2bdcfd2b0668a568 Geoduck-1_S1_L003_R2_001.fastq.gz\n", "< 1abea619075366f23f4510ffb1d9ad26 JD002I_S139_L005_R1_001.fastq.gz\n", "45,47d19\n", "< 1de0477e750461fae078b669a53d9722 Geoduck-NMP-gDNA-4_S13_L004_R2_001.fastq.gz\n", "< 1e85254bbb5d547de848e99f3099f697 Geoduck-2_S2_L007_I1_001.fastq.gz\n", "< 1f7fd70bea1d4b07dbfdebfb10499eb6 Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001.fastq.gz\n", "49d20\n", "< 2140bf177dc95f4218c66ff5eae5608d Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001.fastq.gz\n", "51,54d21\n", "< 26ccc350bef37e367d76f45d06d732ad Geoduck-5_S1_L002_R2_001.fastq.gz\n", "< 27770739f84a5ffe64947120e0c9d7b1 Geoduck-2_S2_L006_R1_001.fastq.gz\n", "< 27a4bed7f18e5f71372f4676e0369a6e JD002D_S134_L005_R1_001.fastq.gz\n", "< 2b218367191075b9e4fcb0bf148c715a Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001.fastq.gz\n", "57,58d23\n", "< 302431eccd6c0303d2246f30acda22e6 Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001.fastq.gz\n", "< 329e3d0eb21aa91da08555a915d1c87c Geoduck-NMP-gDNA-5_S17_L005_R1_001.fastq.gz\n", "61d25\n", "< 347753c1589d76319c8f4ac16ed77830 Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001.fastq.gz\n", "63,66d26\n", "< 35cd7cf06da1c115b2d7c81de850bc6d Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001.fastq.gz\n", "< 37db1019efea8f887d349facb62aeb70 Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001.fastq.gz\n", "< 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Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001.fastq.gz\n", "213d81\n", "< d4f66f34c10ba1f58704b089016a3a6b Geoduck-6_S2_L006_I1_001.fastq.gz\n", "217,218d84\n", "< d8968dc209461435a66af6382f049a19 JD002F_S136_L005_R2_001.fastq.gz\n", "< d958e5585e6caf615ff613bfe17555bd Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001.fastq.gz\n", "222d87\n", "< dfb4cfada176b4991f246b0a298ebf98 Geoduck-6_S2_L008_R1_001.fastq.gz\n", "224,226d88\n", "< e05eea61dbd405c890f241f824b2012b JD002_S0_L005_R1_001.fastq.gz\n", "< e05eea61dbd405c890f241f824b2012b JD002_S0_L005_R1_001.fastq.gz\n", "< e10365fe45b890c880c2d5a0eeefe03a Geoduck_HiC_S2_L002_R1_001.fastq.gz\n", "229d90\n", "< e5da7e7ce6492940461d5dbd50f832c6 JD002J_S140_L005_R2_001.fastq.gz\n", "233,234d93\n", "< e75ac059e78aeb6511a428d8c25855d1 Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001.fastq.gz\n", "< e784b8312ae39d25613988a9af88a157 Geoduck-2_S2_L007_R2_001.fastq.gz\n", "239d97\n", "< ee23c59a4f0d9efe702d5538418972d9 Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001.fastq.gz\n", "242,243d99\n", "< f30ee929433f4e94d7773c76431f38e4 Geoduck-6_S2_L006_R2_001.fastq.gz\n", "< f3761df2b6bce9f4a086242b5b54f3e2 Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001.fastq.gz\n", "248,254d103\n", "< f8faf66e711bb7a65241a659567be36c Geoduck-5_S1_L004_R1_001.fastq.gz\n", "< f9b1624bdbb4bcb262d0e5bbdd2a456c Geoduck-1_S1_L001_R2_001.fastq.gz\n", "< f9b1624bdbb4bcb262d0e5bbdd2a456c Geoduck-1_S1_L001_R2_001.fastq.gz\n", "< f9f7116b03eb204d9010a65801c4b4e8 Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001.fastq.gz\n", "< fafaa0e08c0aa4cdc347a882e5fa0690 Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001.fastq.gz\n", "< fb885eaaf603a605b44531e9e1bdf867 Geoduck-NMP-gDNA-1_S1_L001_R2_001.fastq.gz\n", "< fb885eaaf603a605b44531e9e1bdf867 Geoduck-NMP-gDNA-1_S1_L001_R2_001.fastq.gz\n", "256d104\n", "< fd52300fe95525328239ea412e79fbe4 Geoduck-5_S1_L001_R1_001.fastq.gz\n", "259,280d106\n", "< MD5 (151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_1.fq.gz) = 4e95a487fd10e60ea5af7b62287f88a0\n", "< MD5 (151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_2.fq.gz) = ce78b1856aa612473de14a9599d0c4ff\n", "< MD5 (151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_1.fq.gz) = a21f45349c1ebae6f8723d07613189cb\n", "< MD5 (151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_2.fq.gz) = 23fcb4cda2aba74e97644a8cfac46a59\n", "< MD5 (151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_1.fq.gz) = 4b6225d3d0280fc9bf4161c6f86b5586\n", "< MD5 (151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_2.fq.gz) = b9f80f96fda43362da9ee08aced56bef\n", "< MD5 (160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_1.fq.gz) = b0dfe5ea6ded0272024d97bdc387f0d0\n", "< MD5 (160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_2.fq.gz) = 4d6dcf410e7a110d94fca646dff07ea7\n", "< MD5 (160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_1.fq.gz) = 146fcf32aac04eecc41671389e37ae61\n", "< MD5 (160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_2.fq.gz) = 62017aeb0276b3da77a4b014255a1bf8\n", "< MD5 (160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_1.fq.gz) = efcefa598dfc9230aa2f5b4d787388ee\n", "< MD5 (160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_2.fq.gz) = 0d3fabf04fc56e6249378fcddc286f06\n", "< MD5 (160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_1.fq.gz) = c2f4fa5c539cc028e4afdfd7765416ca\n", "< MD5 (160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_2.fq.gz) = 4a8fa8aee94bccf81e6f600b63935242\n", "< MD5 (160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_1.fq.gz) = 666f18e9cf0ba248e41bc089736932bb\n", "< MD5 (160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_2.fq.gz) = e73619c9bff1dbc816b6b17ca16518b1\n", "< MD5 (160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_1.fq.gz) = 46f6762bafdeec810c12496c43f0c85c\n", "< MD5 (160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_2.fq.gz) = 1da60e5843632956234b0a4cf10427f5\n", "< MD5 (Geo_Pool_F_GGCTAC_L006_R1_001.fastq.gz) = 67a8ec79f655b903b7afa32e4dc3727d\n", "< MD5 (Geo_Pool_F_GGCTAC_L006_R2_001.fastq.gz) = f51d8644ba9280cb6f005b96e080666a\n", "< MD5 (Geo_Pool_M_CTTGTA_L006_R1_001.fastq.gz) = ae44d4dc794b8cd20ba90d7426ef9123\n", "< MD5 (Geo_Pool_M_CTTGTA_L006_R2_001.fastq.gz) = 03fcf100e0e59cb6f36f50aaec1407b6\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m4.416s\n", "user\t0m0.060s\n", "sys\t0m0.068s\n" ] } ], "source": [ "%%bash\n", "cd /mnt/owl/nightingales/P_generosa/\n", "time \\\n", "for file in *.gz\n", "do grep \"$file\" /mnt/owl/nightingales/P_generosa/checksums.md5 >> \\\n", "/home/sam/data/geoduck_EPI/owl_checksums.md5\n", "done\n", "\n", "diff <(sort /home/sam/data/geoduck_EPI/owl_checksums.md5) <(sort /home/sam/data/geoduck_EPI/20180514_checksums.md5)\n", "\n", "sed '/^Subject:/ s/ / grep JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m2.988s\n", "user\t0m0.000s\n", "sys\t0m0.028s\n" ] } ], "source": [ "%%bash\n", "rm /home/sam/data/geoduck_EPI/owl_checksums.md5\n", "cd /mnt/owl/nightingales/P_generosa/\n", "time \\\n", "for file in EPI*.gz\n", "do grep \"$file\" /mnt/owl/nightingales/P_generosa/checksums.md5 >> \\\n", "/home/sam/data/geoduck_EPI/owl_checksums.md5\n", "done\n", "\n", "diff <(sort /home/sam/data/geoduck_EPI/owl_checksums.md5) <(sort /home/sam/data/geoduck_EPI/20180514_checksums.md5)\n", "\n", "sed '/^Subject:/ s/ / grep JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mkdir /home/sam/data/geoduck_EPI/20180514_trimgalore_rrbs" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv /home/sam/data/geoduck_EPI/20180514_trimgalore_rrbs /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs\n", "mkdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "EPI-103_S27_L005_R1_001.fastq.gz \\\n", "EPI-103_S27_L005_R2_001.fastq.gz \\\n", "EPI-104_S28_L005_R1_001.fastq.gz \\\n", "EPI-104_S28_L005_R2_001.fastq.gz \\\n", "EPI-111_S29_L005_R1_001.fastq.gz \\\n", "EPI-111_S29_L005_R2_001.fastq.gz \\\n", "EPI-113_S30_L005_R1_001.fastq.gz \\\n", "EPI-113_S30_L005_R2_001.fastq.gz \\\n", "EPI-119_S31_L005_R1_001.fastq.gz \\\n", "EPI-119_S31_L005_R2_001.fastq.gz \\\n", "EPI-120_S32_L005_R1_001.fastq.gz \\\n", "EPI-120_S32_L005_R2_001.fastq.gz \\\n", "EPI-127_S33_L005_R1_001.fastq.gz \\\n", "EPI-127_S33_L005_R2_001.fastq.gz \\\n", "EPI-128_S34_L005_R1_001.fastq.gz \\\n", "EPI-128_S34_L005_R2_001.fastq.gz \\\n", "EPI-135_S35_L005_R1_001.fastq.gz \\\n", "EPI-135_S35_L005_R2_001.fastq.gz \\\n", "EPI-135WG_S42_L005_R1_001.fastq.gz \\\n", "EPI-135WG_S42_L005_R2_001.fastq.gz \\\n", "EPI-136_S36_L005_R1_001.fastq.gz \\\n", "EPI-136_S36_L005_R2_001.fastq.gz \\\n", "EPI-143_S37_L005_R1_001.fastq.gz \\\n", "EPI-143_S37_L005_R2_001.fastq.gz \\\n", "EPI-145_S38_L005_R1_001.fastq.gz \\\n", "EPI-145_S38_L005_R2_001.fastq.gz \\\n", "EPI-151_S2_L002_R1_001.fastq.gz \\\n", "EPI-151_S2_L002_R2_001.fastq.gz \\\n", "EPI-152_S3_L002_R1_001.fastq.gz \\\n", "EPI-152_S3_L002_R2_001.fastq.gz \\\n", "EPI-153_S4_L002_R1_001.fastq.gz \\\n", "EPI-153_S4_L002_R2_001.fastq.gz \\\n", "EPI-154_S5_L002_R1_001.fastq.gz \\\n", "EPI-154_S5_L002_R2_001.fastq.gz \\\n", "EPI-159_S6_L002_R1_001.fastq.gz \\\n", "EPI-159_S6_L002_R2_001.fastq.gz \\\n", "EPI-160_S7_L002_R1_001.fastq.gz \\\n", "EPI-160_S7_L002_R2_001.fastq.gz \\\n", "EPI-161_S8_L002_R1_001.fastq.gz \\\n", "EPI-161_S8_L002_R2_001.fastq.gz \\\n", "EPI-162_S9_L002_R1_001.fastq.gz \\\n", "EPI-162_S9_L002_R2_001.fastq.gz \\\n", "EPI-167_S10_L002_R1_001.fastq.gz \\\n", "EPI-167_S10_L002_R2_001.fastq.gz \\\n", "EPI-168_S11_L002_R1_001.fastq.gz \\\n", "EPI-168_S11_L002_R2_001.fastq.gz \\\n", "EPI-169_S12_L002_R1_001.fastq.gz \\\n", "EPI-169_S12_L002_R2_001.fastq.gz \\\n", "EPI-170_S13_L002_R1_001.fastq.gz \\\n", "EPI-170_S13_L002_R2_001.fastq.gz \\\n", "EPI-175_S14_L003_R1_001.fastq.gz \\\n", "EPI-175_S14_L003_R2_001.fastq.gz \\\n", "EPI-176_S15_L003_R1_001.fastq.gz \\\n", "EPI-176_S15_L003_R2_001.fastq.gz \\\n", "EPI-181_S16_L003_R1_001.fastq.gz \\\n", "EPI-181_S16_L003_R2_001.fastq.gz \\\n", "EPI-182_S17_L003_R1_001.fastq.gz \\\n", "EPI-182_S17_L003_R2_001.fastq.gz \\\n", "EPI-184_S18_L003_R1_001.fastq.gz \\\n", "EPI-184_S18_L003_R2_001.fastq.gz \\\n", "EPI-185_S19_L003_R1_001.fastq.gz \\\n", "EPI-185_S19_L003_R2_001.fastq.gz \\\n", "EPI-187_S20_L003_R1_001.fastq.gz \\\n", "EPI-187_S20_L003_R2_001.fastq.gz \\\n", "EPI-188_S21_L003_R1_001.fastq.gz \\\n", "EPI-188_S21_L003_R2_001.fastq.gz \\\n", "EPI-193_S22_L003_R1_001.fastq.gz \\\n", "EPI-193_S22_L003_R2_001.fastq.gz \\\n", "EPI-194_S23_L003_R1_001.fastq.gz \\\n", "EPI-194_S23_L003_R2_001.fastq.gz \\\n", "EPI-199_S24_L003_R1_001.fastq.gz \\\n", "EPI-199_S24_L003_R2_001.fastq.gz \\\n", "EPI-200_S25_L003_R1_001.fastq.gz \\\n", "EPI-200_S25_L003_R2_001.fastq.gz \\\n", "EPI-205_S26_L004_R1_001.fastq.gz \\\n", "EPI-205_S26_L004_R2_001.fastq.gz \\\n", "EPI-206_S27_L004_R1_001.fastq.gz \\\n", "EPI-206_S27_L004_R2_001.fastq.gz \\\n", "EPI-208_S28_L004_R1_001.fastq.gz \\\n", "EPI-208_S28_L004_R2_001.fastq.gz \\\n", "EPI-209_S29_L004_R1_001.fastq.gz \\\n", "EPI-209_S29_L004_R2_001.fastq.gz \\\n", "EPI-214_S30_L004_R1_001.fastq.gz \\\n", "EPI-214_S30_L004_R2_001.fastq.gz \\\n", "EPI-215_S31_L004_R1_001.fastq.gz \\\n", "EPI-215_S31_L004_R2_001.fastq.gz \\\n", "EPI-220_S32_L004_R1_001.fastq.gz \\\n", "EPI-220_S32_L004_R2_001.fastq.gz \\\n", "EPI-221_S33_L004_R1_001.fastq.gz \\\n", "EPI-221_S33_L004_R2_001.fastq.gz \\\n", "EPI-226_S34_L004_R1_001.fastq.gz \\\n", "EPI-226_S34_L004_R2_001.fastq.gz \\\n", "EPI-227_S35_L004_R1_001.fastq.gz \\\n", "EPI-227_S35_L004_R2_001.fastq.gz \\\n", "EPI-229_S36_L004_R1_001.fastq.gz \\\n", "EPI-229_S36_L004_R2_001.fastq.gz \\\n", "EPI-230_S37_L004_R1_001.fastq.gz \\\n", "EPI-230_S37_L004_R2_001.fastq.gz \\\n", "EPI-41_S38_L005_R1_001.fastq.gz \\\n", "EPI-41_S38_L005_R2_001.fastq.gz \\\n", "EPI-42_S39_L005_R1_001.fastq.gz \\\n", "EPI-42_S39_L005_R2_001.fastq.gz \\\n", "EPI-43_S40_L005_R1_001.fastq.gz \\\n", "EPI-43_S40_L005_R2_001.fastq.gz \\\n", "EPI-44_S41_L005_R1_001.fastq.gz \\\n", "EPI-44_S41_L005_R2_001.fastq.gz \\\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/data/geoduck_EPI/\n", "\n", "for file in *.gz\n", "do printf \"%s \\\\\\\\\\\\n\" \"$file\"\n", "done" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m1.667s\n", "user\t0m0.092s\n", "sys\t0m0.040s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "/home/shared/TrimGalore-0.4.5/trim_galore \\\n", "--paired \\\n", "--rrbs \\\n", "--non_directional \\\n", "--output_dir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/ \\\n", "--fastqc_args \\\n", "\"--outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc \\\n", "--threads 16\" \\\n", "EPI-103_S27_L005_R1_001.fastq.gz \\\n", "EPI-103_S27_L005_R2_001.fastq.gz \\\n", "EPI-104_S28_L005_R1_001.fastq.gz \\\n", "EPI-104_S28_L005_R2_001.fastq.gz \\\n", "EPI-111_S29_L005_R1_001.fastq.gz \\\n", "EPI-111_S29_L005_R2_001.fastq.gz \\\n", "EPI-113_S30_L005_R1_001.fastq.gz \\\n", "EPI-113_S30_L005_R2_001.fastq.gz \\\n", "EPI-119_S31_L005_R1_001.fastq.gz \\\n", "EPI-119_S31_L005_R2_001.fastq.gz \\\n", "EPI-120_S32_L005_R1_001.fastq.gz \\\n", "EPI-120_S32_L005_R2_001.fastq.gz \\\n", "EPI-127_S33_L005_R1_001.fastq.gz \\\n", "EPI-127_S33_L005_R2_001.fastq.gz \\\n", "EPI-128_S34_L005_R1_001.fastq.gz \\\n", "EPI-128_S34_L005_R2_001.fastq.gz \\\n", "EPI-135_S35_L005_R1_001.fastq.gz \\\n", "EPI-135_S35_L005_R2_001.fastq.gz \\\n", "EPI-136_S36_L005_R1_001.fastq.gz \\\n", "EPI-136_S36_L005_R2_001.fastq.gz \\\n", "EPI-143_S37_L005_R1_001.fastq.gz \\\n", "EPI-143_S37_L005_R2_001.fastq.gz \\\n", "EPI-145_S38_L005_R1_001.fastq.gz \\\n", "EPI-145_S38_L005_R2_001.fastq.gz \\\n", "EPI-151_S2_L002_R1_001.fastq.gz \\\n", "EPI-151_S2_L002_R2_001.fastq.gz \\\n", "EPI-152_S3_L002_R1_001.fastq.gz \\\n", "EPI-152_S3_L002_R2_001.fastq.gz \\\n", "EPI-153_S4_L002_R1_001.fastq.gz \\\n", "EPI-153_S4_L002_R2_001.fastq.gz \\\n", "EPI-154_S5_L002_R1_001.fastq.gz \\\n", "EPI-154_S5_L002_R2_001.fastq.gz \\\n", "EPI-159_S6_L002_R1_001.fastq.gz \\\n", "EPI-159_S6_L002_R2_001.fastq.gz \\\n", "EPI-160_S7_L002_R1_001.fastq.gz \\\n", "EPI-160_S7_L002_R2_001.fastq.gz \\\n", "EPI-161_S8_L002_R1_001.fastq.gz \\\n", "EPI-161_S8_L002_R2_001.fastq.gz \\\n", "EPI-162_S9_L002_R1_001.fastq.gz \\\n", "EPI-162_S9_L002_R2_001.fastq.gz \\\n", "EPI-167_S10_L002_R1_001.fastq.gz \\\n", "EPI-167_S10_L002_R2_001.fastq.gz \\\n", "EPI-168_S11_L002_R1_001.fastq.gz \\\n", "EPI-168_S11_L002_R2_001.fastq.gz \\\n", "EPI-169_S12_L002_R1_001.fastq.gz \\\n", "EPI-169_S12_L002_R2_001.fastq.gz \\\n", "EPI-170_S13_L002_R1_001.fastq.gz \\\n", "EPI-170_S13_L002_R2_001.fastq.gz \\\n", "EPI-175_S14_L003_R1_001.fastq.gz \\\n", "EPI-175_S14_L003_R2_001.fastq.gz \\\n", "EPI-176_S15_L003_R1_001.fastq.gz \\\n", "EPI-176_S15_L003_R2_001.fastq.gz \\\n", "EPI-181_S16_L003_R1_001.fastq.gz \\\n", "EPI-181_S16_L003_R2_001.fastq.gz \\\n", "EPI-182_S17_L003_R1_001.fastq.gz \\\n", "EPI-182_S17_L003_R2_001.fastq.gz \\\n", "EPI-184_S18_L003_R1_001.fastq.gz \\\n", "EPI-184_S18_L003_R2_001.fastq.gz \\\n", "EPI-185_S19_L003_R1_001.fastq.gz \\\n", "EPI-185_S19_L003_R2_001.fastq.gz \\\n", "EPI-187_S20_L003_R1_001.fastq.gz \\\n", "EPI-187_S20_L003_R2_001.fastq.gz \\\n", "EPI-188_S21_L003_R1_001.fastq.gz \\\n", "EPI-188_S21_L003_R2_001.fastq.gz \\\n", "EPI-193_S22_L003_R1_001.fastq.gz \\\n", "EPI-193_S22_L003_R2_001.fastq.gz \\\n", "EPI-194_S23_L003_R1_001.fastq.gz \\\n", "EPI-194_S23_L003_R2_001.fastq.gz \\\n", "EPI-199_S24_L003_R1_001.fastq.gz \\\n", "EPI-199_S24_L003_R2_001.fastq.gz \\\n", "EPI-200_S25_L003_R1_001.fastq.gz \\\n", "EPI-200_S25_L003_R2_001.fastq.gz \\\n", "EPI-205_S26_L004_R1_001.fastq.gz \\\n", "EPI-205_S26_L004_R2_001.fastq.gz \\\n", "EPI-206_S27_L004_R1_001.fastq.gz \\\n", "EPI-206_S27_L004_R2_001.fastq.gz \\\n", "EPI-208_S28_L004_R1_001.fastq.gz \\\n", "EPI-208_S28_L004_R2_001.fastq.gz \\\n", "EPI-209_S29_L004_R1_001.fastq.gz \\\n", "EPI-209_S29_L004_R2_001.fastq.gz \\\n", "EPI-214_S30_L004_R1_001.fastq.gz \\\n", "EPI-214_S30_L004_R2_001.fastq.gz \\\n", "EPI-215_S31_L004_R1_001.fastq.gz \\\n", "EPI-215_S31_L004_R2_001.fastq.gz \\\n", "EPI-220_S32_L004_R1_001.fastq.gz \\\n", "EPI-220_S32_L004_R2_001.fastq.gz \\\n", "EPI-221_S33_L004_R1_001.fastq.gz \\\n", "EPI-221_S33_L004_R2_001.fastq.gz \\\n", "EPI-226_S34_L004_R1_001.fastq.gz \\\n", "EPI-226_S34_L004_R2_001.fastq.gz \\\n", "EPI-227_S35_L004_R1_001.fastq.gz \\\n", "EPI-227_S35_L004_R2_001.fastq.gz \\\n", "EPI-229_S36_L004_R1_001.fastq.gz \\\n", "EPI-229_S36_L004_R2_001.fastq.gz \\\n", "EPI-230_S37_L004_R1_001.fastq.gz \\\n", "EPI-230_S37_L004_R2_001.fastq.gz \\\n", "EPI-41_S38_L005_R1_001.fastq.gz \\\n", "EPI-41_S38_L005_R2_001.fastq.gz \\\n", "EPI-42_S39_L005_R1_001.fastq.gz \\\n", "EPI-42_S39_L005_R2_001.fastq.gz \\\n", "EPI-43_S40_L005_R1_001.fastq.gz \\\n", "EPI-43_S40_L005_R2_001.fastq.gz \\\n", "EPI-44_S41_L005_R1_001.fastq.gz \\\n", "EPI-44_S41_L005_R2_001.fastq.gz \\\n", "> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stdout.log \\\n", "2> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log\n", "\n", "sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1.9.1\n", "-------------------\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "bash: line 5: /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log: Permission denied\n" ] } ], "source": [ "%%bash\n", "cat /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stdout.log\n", "\n", "echo \"-------------------\"\n", "\n", "/home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-rwxr-xr-x 1 sam sam 68054 Nov 13 02:43 /home/shared/TrimGalore-0.4.5/trim_galore\n" ] } ], "source": [ "%%bash\n", "ls -l /home/shared/TrimGalore-0.4.5/trim_galore" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-rwxr-xr-x 1 root root 134 Jan 19 2016 /usr/bin/cutadapt\n" ] } ], "source": [ "%%bash\n", "ls -l /usr/bin/cutadapt" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-rwxr-xr-x 1 root adm 134 Jan 19 2016 /usr/bin/cutadapt\n" ] } ], "source": [ "%%bash\n", "ls -l /usr/bin/cutadapt" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t0m1.137s\n", "user\t0m0.112s\n", "sys\t0m0.012s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "/home/shared/TrimGalore-0.4.5/trim_galore \\\n", "--paired \\\n", "--rrbs \\\n", "--non_directional \\\n", "--output_dir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/ \\\n", "--fastqc_args \\\n", "\"--outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc \\\n", "--threads 16\" \\\n", "EPI-103_S27_L005_R1_001.fastq.gz \\\n", "EPI-103_S27_L005_R2_001.fastq.gz \\\n", "EPI-104_S28_L005_R1_001.fastq.gz \\\n", "EPI-104_S28_L005_R2_001.fastq.gz \\\n", "EPI-111_S29_L005_R1_001.fastq.gz \\\n", "EPI-111_S29_L005_R2_001.fastq.gz \\\n", "EPI-113_S30_L005_R1_001.fastq.gz \\\n", "EPI-113_S30_L005_R2_001.fastq.gz \\\n", "EPI-119_S31_L005_R1_001.fastq.gz \\\n", "EPI-119_S31_L005_R2_001.fastq.gz \\\n", "EPI-120_S32_L005_R1_001.fastq.gz \\\n", "EPI-120_S32_L005_R2_001.fastq.gz \\\n", "EPI-127_S33_L005_R1_001.fastq.gz \\\n", "EPI-127_S33_L005_R2_001.fastq.gz \\\n", "EPI-128_S34_L005_R1_001.fastq.gz \\\n", "EPI-128_S34_L005_R2_001.fastq.gz \\\n", "EPI-135_S35_L005_R1_001.fastq.gz \\\n", "EPI-135_S35_L005_R2_001.fastq.gz \\\n", "EPI-136_S36_L005_R1_001.fastq.gz \\\n", "EPI-136_S36_L005_R2_001.fastq.gz \\\n", "EPI-143_S37_L005_R1_001.fastq.gz \\\n", "EPI-143_S37_L005_R2_001.fastq.gz \\\n", "EPI-145_S38_L005_R1_001.fastq.gz \\\n", "EPI-145_S38_L005_R2_001.fastq.gz \\\n", "EPI-151_S2_L002_R1_001.fastq.gz \\\n", "EPI-151_S2_L002_R2_001.fastq.gz \\\n", "EPI-152_S3_L002_R1_001.fastq.gz \\\n", "EPI-152_S3_L002_R2_001.fastq.gz \\\n", "EPI-153_S4_L002_R1_001.fastq.gz \\\n", "EPI-153_S4_L002_R2_001.fastq.gz \\\n", "EPI-154_S5_L002_R1_001.fastq.gz \\\n", "EPI-154_S5_L002_R2_001.fastq.gz \\\n", "EPI-159_S6_L002_R1_001.fastq.gz \\\n", "EPI-159_S6_L002_R2_001.fastq.gz \\\n", "EPI-160_S7_L002_R1_001.fastq.gz \\\n", "EPI-160_S7_L002_R2_001.fastq.gz \\\n", "EPI-161_S8_L002_R1_001.fastq.gz \\\n", "EPI-161_S8_L002_R2_001.fastq.gz \\\n", "EPI-162_S9_L002_R1_001.fastq.gz \\\n", "EPI-162_S9_L002_R2_001.fastq.gz \\\n", "EPI-167_S10_L002_R1_001.fastq.gz \\\n", "EPI-167_S10_L002_R2_001.fastq.gz \\\n", "EPI-168_S11_L002_R1_001.fastq.gz \\\n", "EPI-168_S11_L002_R2_001.fastq.gz \\\n", "EPI-169_S12_L002_R1_001.fastq.gz \\\n", "EPI-169_S12_L002_R2_001.fastq.gz \\\n", "EPI-170_S13_L002_R1_001.fastq.gz \\\n", "EPI-170_S13_L002_R2_001.fastq.gz \\\n", "EPI-175_S14_L003_R1_001.fastq.gz \\\n", "EPI-175_S14_L003_R2_001.fastq.gz \\\n", "EPI-176_S15_L003_R1_001.fastq.gz \\\n", "EPI-176_S15_L003_R2_001.fastq.gz \\\n", "EPI-181_S16_L003_R1_001.fastq.gz \\\n", "EPI-181_S16_L003_R2_001.fastq.gz \\\n", "EPI-182_S17_L003_R1_001.fastq.gz \\\n", "EPI-182_S17_L003_R2_001.fastq.gz \\\n", "EPI-184_S18_L003_R1_001.fastq.gz \\\n", "EPI-184_S18_L003_R2_001.fastq.gz \\\n", "EPI-185_S19_L003_R1_001.fastq.gz \\\n", "EPI-185_S19_L003_R2_001.fastq.gz \\\n", "EPI-187_S20_L003_R1_001.fastq.gz \\\n", "EPI-187_S20_L003_R2_001.fastq.gz \\\n", "EPI-188_S21_L003_R1_001.fastq.gz \\\n", "EPI-188_S21_L003_R2_001.fastq.gz \\\n", "EPI-193_S22_L003_R1_001.fastq.gz \\\n", "EPI-193_S22_L003_R2_001.fastq.gz \\\n", "EPI-194_S23_L003_R1_001.fastq.gz \\\n", "EPI-194_S23_L003_R2_001.fastq.gz \\\n", "EPI-199_S24_L003_R1_001.fastq.gz \\\n", "EPI-199_S24_L003_R2_001.fastq.gz \\\n", "EPI-200_S25_L003_R1_001.fastq.gz \\\n", "EPI-200_S25_L003_R2_001.fastq.gz \\\n", "EPI-205_S26_L004_R1_001.fastq.gz \\\n", "EPI-205_S26_L004_R2_001.fastq.gz \\\n", "EPI-206_S27_L004_R1_001.fastq.gz \\\n", "EPI-206_S27_L004_R2_001.fastq.gz \\\n", "EPI-208_S28_L004_R1_001.fastq.gz \\\n", "EPI-208_S28_L004_R2_001.fastq.gz \\\n", "EPI-209_S29_L004_R1_001.fastq.gz \\\n", "EPI-209_S29_L004_R2_001.fastq.gz \\\n", "EPI-214_S30_L004_R1_001.fastq.gz \\\n", "EPI-214_S30_L004_R2_001.fastq.gz \\\n", "EPI-215_S31_L004_R1_001.fastq.gz \\\n", "EPI-215_S31_L004_R2_001.fastq.gz \\\n", "EPI-220_S32_L004_R1_001.fastq.gz \\\n", "EPI-220_S32_L004_R2_001.fastq.gz \\\n", "EPI-221_S33_L004_R1_001.fastq.gz \\\n", "EPI-221_S33_L004_R2_001.fastq.gz \\\n", "EPI-226_S34_L004_R1_001.fastq.gz \\\n", "EPI-226_S34_L004_R2_001.fastq.gz \\\n", "EPI-227_S35_L004_R1_001.fastq.gz \\\n", "EPI-227_S35_L004_R2_001.fastq.gz \\\n", "EPI-229_S36_L004_R1_001.fastq.gz \\\n", "EPI-229_S36_L004_R2_001.fastq.gz \\\n", "EPI-230_S37_L004_R1_001.fastq.gz \\\n", "EPI-230_S37_L004_R2_001.fastq.gz \\\n", "EPI-41_S38_L005_R1_001.fastq.gz \\\n", "EPI-41_S38_L005_R2_001.fastq.gz \\\n", "EPI-42_S39_L005_R1_001.fastq.gz \\\n", "EPI-42_S39_L005_R2_001.fastq.gz \\\n", "EPI-43_S40_L005_R1_001.fastq.gz \\\n", "EPI-43_S40_L005_R2_001.fastq.gz \\\n", "EPI-44_S41_L005_R1_001.fastq.gz \\\n", "EPI-44_S41_L005_R2_001.fastq.gz \\\n", "> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stdout.log \\\n", "2> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log\n", "\n", "sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "STDOUT LOG\n", "1.9.1\n", "-------------------------------------------\n", "STDERR LOG\n", "No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)\n", "\n", "gzip: EPI-103_S27_L005_R1_001.fastq.gz: No such file or directory\n", "Input file 'EPI-103_S27_L005_R1_001.fastq.gz' seems to be completely empty. Consider respecifying!\n", "\n", "Path to Cutadapt set as: 'cutadapt' (default)\n", "Cutadapt seems to be working fine (tested command 'cutadapt --version')\n", "\n", "\n", "AUTO-DETECTING ADAPTER TYPE\n", "===========================\n", "Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> EPI-103_S27_L005_R1_001.fastq.gz <<)\n", "\n", "gzip: EPI-103_S27_L005_R1_001.fastq.gz: No such file or directory\n", "Found perfect matches for the following adapter sequences:\n", "Adapter type\tCount\tSequence\tSequences analysed\tPercentage\n", "Illegal division by zero at /home/shared/TrimGalore-0.4.5/trim_galore line 1240.\n" ] } ], "source": [ "%%bash\n", "\n", "echo \"STDOUT LOG\"\n", "cat /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stdout.log\n", "\n", "echo \"-------------------------------------------\"\n", "\n", "echo \"STDERR LOG\"\n", "cat /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Process is interrupted.\n" ] } ], "source": [ "%%bash\n", "\n", "cd /home/sam/data/geoduck_EPI\n", "\n", "time \\\n", "/home/shared/TrimGalore-0.4.5/trim_galore \\\n", "--paired \\\n", "--rrbs \\\n", "--non_directional \\\n", "--output_dir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/ \\\n", "--fastqc_args \\\n", "\"--outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc \\\n", "--threads 16\" \\\n", "EPI-103_S27_L005_R1_001.fastq.gz \\\n", "EPI-103_S27_L005_R2_001.fastq.gz \\\n", "EPI-104_S28_L005_R1_001.fastq.gz \\\n", "EPI-104_S28_L005_R2_001.fastq.gz \\\n", "EPI-111_S29_L005_R1_001.fastq.gz \\\n", "EPI-111_S29_L005_R2_001.fastq.gz \\\n", "EPI-113_S30_L005_R1_001.fastq.gz \\\n", "EPI-113_S30_L005_R2_001.fastq.gz \\\n", "EPI-119_S31_L005_R1_001.fastq.gz \\\n", "EPI-119_S31_L005_R2_001.fastq.gz \\\n", "EPI-120_S32_L005_R1_001.fastq.gz \\\n", "EPI-120_S32_L005_R2_001.fastq.gz \\\n", "EPI-127_S33_L005_R1_001.fastq.gz \\\n", "EPI-127_S33_L005_R2_001.fastq.gz \\\n", "EPI-128_S34_L005_R1_001.fastq.gz \\\n", "EPI-128_S34_L005_R2_001.fastq.gz \\\n", "EPI-135_S35_L005_R1_001.fastq.gz \\\n", "EPI-135_S35_L005_R2_001.fastq.gz \\\n", "EPI-136_S36_L005_R1_001.fastq.gz \\\n", "EPI-136_S36_L005_R2_001.fastq.gz \\\n", "EPI-143_S37_L005_R1_001.fastq.gz \\\n", "EPI-143_S37_L005_R2_001.fastq.gz \\\n", "EPI-145_S38_L005_R1_001.fastq.gz \\\n", "EPI-145_S38_L005_R2_001.fastq.gz \\\n", "EPI-151_S2_L002_R1_001.fastq.gz \\\n", "EPI-151_S2_L002_R2_001.fastq.gz \\\n", "EPI-152_S3_L002_R1_001.fastq.gz \\\n", "EPI-152_S3_L002_R2_001.fastq.gz \\\n", "EPI-153_S4_L002_R1_001.fastq.gz \\\n", "EPI-153_S4_L002_R2_001.fastq.gz \\\n", "EPI-154_S5_L002_R1_001.fastq.gz \\\n", "EPI-154_S5_L002_R2_001.fastq.gz \\\n", "EPI-159_S6_L002_R1_001.fastq.gz \\\n", "EPI-159_S6_L002_R2_001.fastq.gz \\\n", "EPI-160_S7_L002_R1_001.fastq.gz \\\n", "EPI-160_S7_L002_R2_001.fastq.gz \\\n", "EPI-161_S8_L002_R1_001.fastq.gz \\\n", "EPI-161_S8_L002_R2_001.fastq.gz \\\n", "EPI-162_S9_L002_R1_001.fastq.gz \\\n", "EPI-162_S9_L002_R2_001.fastq.gz \\\n", "EPI-167_S10_L002_R1_001.fastq.gz \\\n", "EPI-167_S10_L002_R2_001.fastq.gz \\\n", "EPI-168_S11_L002_R1_001.fastq.gz \\\n", "EPI-168_S11_L002_R2_001.fastq.gz \\\n", "EPI-169_S12_L002_R1_001.fastq.gz \\\n", "EPI-169_S12_L002_R2_001.fastq.gz \\\n", "EPI-170_S13_L002_R1_001.fastq.gz \\\n", "EPI-170_S13_L002_R2_001.fastq.gz \\\n", "EPI-175_S14_L003_R1_001.fastq.gz \\\n", "EPI-175_S14_L003_R2_001.fastq.gz \\\n", "EPI-176_S15_L003_R1_001.fastq.gz \\\n", "EPI-176_S15_L003_R2_001.fastq.gz \\\n", "EPI-181_S16_L003_R1_001.fastq.gz \\\n", "EPI-181_S16_L003_R2_001.fastq.gz \\\n", "EPI-182_S17_L003_R1_001.fastq.gz \\\n", "EPI-182_S17_L003_R2_001.fastq.gz \\\n", "EPI-184_S18_L003_R1_001.fastq.gz \\\n", "EPI-184_S18_L003_R2_001.fastq.gz \\\n", "EPI-185_S19_L003_R1_001.fastq.gz \\\n", "EPI-185_S19_L003_R2_001.fastq.gz \\\n", "EPI-187_S20_L003_R1_001.fastq.gz \\\n", "EPI-187_S20_L003_R2_001.fastq.gz \\\n", "EPI-188_S21_L003_R1_001.fastq.gz \\\n", "EPI-188_S21_L003_R2_001.fastq.gz \\\n", "EPI-193_S22_L003_R1_001.fastq.gz \\\n", "EPI-193_S22_L003_R2_001.fastq.gz \\\n", "EPI-194_S23_L003_R1_001.fastq.gz \\\n", "EPI-194_S23_L003_R2_001.fastq.gz \\\n", "EPI-199_S24_L003_R1_001.fastq.gz \\\n", "EPI-199_S24_L003_R2_001.fastq.gz \\\n", "EPI-200_S25_L003_R1_001.fastq.gz \\\n", "EPI-200_S25_L003_R2_001.fastq.gz \\\n", "EPI-205_S26_L004_R1_001.fastq.gz \\\n", "EPI-205_S26_L004_R2_001.fastq.gz \\\n", "EPI-206_S27_L004_R1_001.fastq.gz \\\n", "EPI-206_S27_L004_R2_001.fastq.gz \\\n", "EPI-208_S28_L004_R1_001.fastq.gz \\\n", "EPI-208_S28_L004_R2_001.fastq.gz \\\n", "EPI-209_S29_L004_R1_001.fastq.gz \\\n", "EPI-209_S29_L004_R2_001.fastq.gz \\\n", "EPI-214_S30_L004_R1_001.fastq.gz \\\n", "EPI-214_S30_L004_R2_001.fastq.gz \\\n", "EPI-215_S31_L004_R1_001.fastq.gz \\\n", "EPI-215_S31_L004_R2_001.fastq.gz \\\n", "EPI-220_S32_L004_R1_001.fastq.gz \\\n", "EPI-220_S32_L004_R2_001.fastq.gz \\\n", "EPI-221_S33_L004_R1_001.fastq.gz \\\n", "EPI-221_S33_L004_R2_001.fastq.gz \\\n", "EPI-226_S34_L004_R1_001.fastq.gz \\\n", "EPI-226_S34_L004_R2_001.fastq.gz \\\n", "EPI-227_S35_L004_R1_001.fastq.gz \\\n", "EPI-227_S35_L004_R2_001.fastq.gz \\\n", "EPI-229_S36_L004_R1_001.fastq.gz \\\n", "EPI-229_S36_L004_R2_001.fastq.gz \\\n", "EPI-230_S37_L004_R1_001.fastq.gz \\\n", "EPI-230_S37_L004_R2_001.fastq.gz \\\n", "EPI-41_S38_L005_R1_001.fastq.gz \\\n", "EPI-41_S38_L005_R2_001.fastq.gz \\\n", "EPI-42_S39_L005_R1_001.fastq.gz \\\n", "EPI-42_S39_L005_R2_001.fastq.gz \\\n", "EPI-43_S40_L005_R1_001.fastq.gz \\\n", "EPI-43_S40_L005_R2_001.fastq.gz \\\n", "EPI-44_S41_L005_R1_001.fastq.gz \\\n", "EPI-44_S41_L005_R2_001.fastq.gz \\\n", "> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stdout.log \\\n", "2> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log\n", "\n", "sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Killed the job in order to remove \"--non-directional\" argument.\n", "\n", "[Looking through Hollie's info](https://github.com/hputnam/project_juvenile_geoduck_OA/blob/master/Sample_Processing/Sample.Info_Pool1.csv), she used the TruSeq DNA Methylation Kit (Illumina) for library prep, which is directional. Can read this [Qiagen protocl (PDF)](http://resources.qiagenbioinformatics.com/manuals/bisulfite-sequencing/current/BisulfiteSequencing_Plugin_User_Manual.pdf) for reference." ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "rm: cannot remove '*trim*.*': No such file or directory\n", "\n", "real\t2476m0.854s\n", "user\t4487m4.188s\n", "sys\t160m40.412s\n" ] } ], "source": [ "%%bash\n", "\n", "cd /home/sam/data/geoduck_EPI\n", "\n", "rm *trim*.*\n", "\n", "time \\\n", "/home/shared/TrimGalore-0.4.5/trim_galore \\\n", "--paired \\\n", "--rrbs \\\n", "--non_directional \\\n", "--output_dir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/ \\\n", "--fastqc_args \\\n", "\"--outdir /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc \\\n", "--threads 16\" \\\n", "EPI-103_S27_L005_R1_001.fastq.gz \\\n", "EPI-103_S27_L005_R2_001.fastq.gz \\\n", "EPI-104_S28_L005_R1_001.fastq.gz \\\n", "EPI-104_S28_L005_R2_001.fastq.gz \\\n", "EPI-111_S29_L005_R1_001.fastq.gz \\\n", "EPI-111_S29_L005_R2_001.fastq.gz \\\n", "EPI-113_S30_L005_R1_001.fastq.gz \\\n", "EPI-113_S30_L005_R2_001.fastq.gz \\\n", "EPI-119_S31_L005_R1_001.fastq.gz \\\n", "EPI-119_S31_L005_R2_001.fastq.gz \\\n", "EPI-120_S32_L005_R1_001.fastq.gz \\\n", "EPI-120_S32_L005_R2_001.fastq.gz \\\n", "EPI-127_S33_L005_R1_001.fastq.gz \\\n", "EPI-127_S33_L005_R2_001.fastq.gz \\\n", "EPI-128_S34_L005_R1_001.fastq.gz \\\n", "EPI-128_S34_L005_R2_001.fastq.gz \\\n", "EPI-135_S35_L005_R1_001.fastq.gz \\\n", "EPI-135_S35_L005_R2_001.fastq.gz \\\n", "EPI-136_S36_L005_R1_001.fastq.gz \\\n", "EPI-136_S36_L005_R2_001.fastq.gz \\\n", "EPI-143_S37_L005_R1_001.fastq.gz \\\n", "EPI-143_S37_L005_R2_001.fastq.gz \\\n", "EPI-145_S38_L005_R1_001.fastq.gz \\\n", "EPI-145_S38_L005_R2_001.fastq.gz \\\n", "EPI-151_S2_L002_R1_001.fastq.gz \\\n", "EPI-151_S2_L002_R2_001.fastq.gz \\\n", "EPI-152_S3_L002_R1_001.fastq.gz \\\n", "EPI-152_S3_L002_R2_001.fastq.gz \\\n", "EPI-153_S4_L002_R1_001.fastq.gz \\\n", "EPI-153_S4_L002_R2_001.fastq.gz \\\n", "EPI-154_S5_L002_R1_001.fastq.gz \\\n", "EPI-154_S5_L002_R2_001.fastq.gz \\\n", "EPI-159_S6_L002_R1_001.fastq.gz \\\n", "EPI-159_S6_L002_R2_001.fastq.gz \\\n", "EPI-160_S7_L002_R1_001.fastq.gz \\\n", "EPI-160_S7_L002_R2_001.fastq.gz \\\n", "EPI-161_S8_L002_R1_001.fastq.gz \\\n", "EPI-161_S8_L002_R2_001.fastq.gz \\\n", "EPI-162_S9_L002_R1_001.fastq.gz \\\n", "EPI-162_S9_L002_R2_001.fastq.gz \\\n", "EPI-167_S10_L002_R1_001.fastq.gz \\\n", "EPI-167_S10_L002_R2_001.fastq.gz \\\n", "EPI-168_S11_L002_R1_001.fastq.gz \\\n", "EPI-168_S11_L002_R2_001.fastq.gz \\\n", "EPI-169_S12_L002_R1_001.fastq.gz \\\n", "EPI-169_S12_L002_R2_001.fastq.gz \\\n", "EPI-170_S13_L002_R1_001.fastq.gz \\\n", "EPI-170_S13_L002_R2_001.fastq.gz \\\n", "EPI-175_S14_L003_R1_001.fastq.gz \\\n", "EPI-175_S14_L003_R2_001.fastq.gz \\\n", "EPI-176_S15_L003_R1_001.fastq.gz \\\n", "EPI-176_S15_L003_R2_001.fastq.gz \\\n", "EPI-181_S16_L003_R1_001.fastq.gz \\\n", "EPI-181_S16_L003_R2_001.fastq.gz \\\n", "EPI-182_S17_L003_R1_001.fastq.gz \\\n", "EPI-182_S17_L003_R2_001.fastq.gz \\\n", "EPI-184_S18_L003_R1_001.fastq.gz \\\n", "EPI-184_S18_L003_R2_001.fastq.gz \\\n", "EPI-185_S19_L003_R1_001.fastq.gz \\\n", "EPI-185_S19_L003_R2_001.fastq.gz \\\n", "EPI-187_S20_L003_R1_001.fastq.gz \\\n", "EPI-187_S20_L003_R2_001.fastq.gz \\\n", "EPI-188_S21_L003_R1_001.fastq.gz \\\n", "EPI-188_S21_L003_R2_001.fastq.gz \\\n", "EPI-193_S22_L003_R1_001.fastq.gz \\\n", "EPI-193_S22_L003_R2_001.fastq.gz \\\n", "EPI-194_S23_L003_R1_001.fastq.gz \\\n", "EPI-194_S23_L003_R2_001.fastq.gz \\\n", "EPI-199_S24_L003_R1_001.fastq.gz \\\n", "EPI-199_S24_L003_R2_001.fastq.gz \\\n", "EPI-200_S25_L003_R1_001.fastq.gz \\\n", "EPI-200_S25_L003_R2_001.fastq.gz \\\n", "EPI-205_S26_L004_R1_001.fastq.gz \\\n", "EPI-205_S26_L004_R2_001.fastq.gz \\\n", "EPI-206_S27_L004_R1_001.fastq.gz \\\n", "EPI-206_S27_L004_R2_001.fastq.gz \\\n", "EPI-208_S28_L004_R1_001.fastq.gz \\\n", "EPI-208_S28_L004_R2_001.fastq.gz \\\n", "EPI-209_S29_L004_R1_001.fastq.gz \\\n", "EPI-209_S29_L004_R2_001.fastq.gz \\\n", "EPI-214_S30_L004_R1_001.fastq.gz \\\n", "EPI-214_S30_L004_R2_001.fastq.gz \\\n", "EPI-215_S31_L004_R1_001.fastq.gz \\\n", "EPI-215_S31_L004_R2_001.fastq.gz \\\n", "EPI-220_S32_L004_R1_001.fastq.gz \\\n", "EPI-220_S32_L004_R2_001.fastq.gz \\\n", "EPI-221_S33_L004_R1_001.fastq.gz \\\n", "EPI-221_S33_L004_R2_001.fastq.gz \\\n", "EPI-226_S34_L004_R1_001.fastq.gz \\\n", "EPI-226_S34_L004_R2_001.fastq.gz \\\n", "EPI-227_S35_L004_R1_001.fastq.gz \\\n", "EPI-227_S35_L004_R2_001.fastq.gz \\\n", "EPI-229_S36_L004_R1_001.fastq.gz \\\n", "EPI-229_S36_L004_R2_001.fastq.gz \\\n", "EPI-230_S37_L004_R1_001.fastq.gz \\\n", "EPI-230_S37_L004_R2_001.fastq.gz \\\n", "EPI-41_S38_L005_R1_001.fastq.gz \\\n", "EPI-41_S38_L005_R2_001.fastq.gz \\\n", "EPI-42_S39_L005_R1_001.fastq.gz \\\n", "EPI-42_S39_L005_R2_001.fastq.gz \\\n", "EPI-43_S40_L005_R1_001.fastq.gz \\\n", "EPI-43_S40_L005_R2_001.fastq.gz \\\n", "EPI-44_S41_L005_R1_001.fastq.gz \\\n", "EPI-44_S41_L005_R2_001.fastq.gz \\\n", "> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stdout.log \\\n", "2> /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log\n", "\n", "sed '/^Subject:/ s/ / trimgalore JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t11m54.256s\n", "user\t4m55.168s\n", "sys\t0m48.880s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/\n", "\n", "time \\\n", "for fq in *_val*.gz\n", "do md5sum \"$fq\" >> checksums.md5\n", "done\n", "\n", "sed '/^Subject:/ s/ / checksums JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "23ba9a3282d5d7d982837aaa7e55e526 EPI-230_S37_L004_R1_001_val_1.fq.gz\n", "f2d3b92853a1b9f08686652cde404605 EPI-230_S37_L004_R2_001_val_2.fq.gz\n", "6f25df4c25588258bc6cc233b0e095f5 EPI-41_S38_L005_R1_001_val_1.fq.gz\n", "7fd7eb223a32396672c5a899beefeb1f EPI-41_S38_L005_R2_001_val_2.fq.gz\n", "015e566c9f429ac1adfdf416da8fb7be EPI-42_S39_L005_R1_001_val_1.fq.gz\n", "2dac11e3fbe945df8a99af3d1646c690 EPI-42_S39_L005_R2_001_val_2.fq.gz\n", "55eed9fd7ae731214226bd397da94e57 EPI-43_S40_L005_R1_001_val_1.fq.gz\n", "44e69924356495047aa1ab782c83627d EPI-43_S40_L005_R2_001_val_2.fq.gz\n", "daeb67f7ec0306743775bb50722bb630 EPI-44_S41_L005_R1_001_val_1.fq.gz\n", "1faf07f26e227e9ce9a6702e7f579bec EPI-44_S41_L005_R2_001_val_2.fq.gz\n" ] } ], "source": [ "%%bash\n", "tail /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/checksums.md5" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Searching 208 files..\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "[INFO ] multiqc : This is MultiQC v1.5.dev0\n", "[INFO ] multiqc : Template : default\n", "[INFO ] multiqc : Searching '.'\n", "[INFO ] fastqc : Found 104 reports\n", "[INFO ] multiqc : Compressing plot data\n", "[INFO ] multiqc : Report : multiqc_report.html\n", "[INFO ] multiqc : Data : multiqc_data\n", "[INFO ] multiqc : MultiQC complete\n", "\n", "real\t0m25.745s\n", "user\t0m13.696s\n", "sys\t0m0.476s\n" ] } ], "source": [ "%%bash\n", "cd /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc\n", "\n", "time \\\n", "/home/shared/anaconda3/bin/multiqc ." ] }, { "cell_type": "code", "execution_count": 30, "metadata": { "collapsed": true }, "outputs": [], "source": [ "%%bash\n", "mv /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc/multiqc_report.html \\\n", "/home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc/multiqc_data/" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "cp: cannot create directory '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stdout.log': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/20180514_trimgalore.stderr.log': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-103_S27_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/checksums.md5': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-104_S28_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-103_S27_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-111_S29_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-103_S27_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-103_S27_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-104_S28_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-113_S30_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-104_S28_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-104_S28_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-111_S29_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-119_S31_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-111_S29_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-111_S29_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-113_S30_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-120_S32_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-113_S30_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-113_S30_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-119_S31_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-127_S33_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-119_S31_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-119_S31_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-120_S32_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-128_S34_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-120_S32_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-120_S32_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-127_S33_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-135_S35_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-127_S33_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-127_S33_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-128_S34_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-136_S36_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-128_S34_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-128_S34_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-135_S35_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-143_S37_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-135_S35_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-135_S35_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-136_S36_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-145_S38_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-136_S36_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-136_S36_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-143_S37_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-151_S2_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-143_S37_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-143_S37_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-145_S38_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-152_S3_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-145_S38_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-145_S38_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-151_S2_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-153_S4_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-151_S2_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-151_S2_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-152_S3_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-154_S5_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-152_S3_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-152_S3_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-153_S4_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-159_S6_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-153_S4_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-153_S4_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-154_S5_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-160_S7_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-154_S5_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-154_S5_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-159_S6_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-161_S8_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-159_S6_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-159_S6_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-160_S7_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-162_S9_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-160_S7_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-160_S7_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-161_S8_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-167_S10_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-161_S8_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-161_S8_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-162_S9_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-168_S11_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-162_S9_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-162_S9_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-167_S10_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-169_S12_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-167_S10_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-167_S10_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-168_S11_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-170_S13_L002_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-168_S11_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-168_S11_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-169_S12_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-175_S14_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-169_S12_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-169_S12_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-170_S13_L002_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-176_S15_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-170_S13_L002_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-170_S13_L002_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-175_S14_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-181_S16_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-175_S14_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-175_S14_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-176_S15_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-182_S17_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-176_S15_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-176_S15_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-181_S16_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-184_S18_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-181_S16_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-181_S16_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-182_S17_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-185_S19_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-182_S17_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-182_S17_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-184_S18_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-187_S20_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-184_S18_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-184_S18_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-185_S19_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-188_S21_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-185_S19_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-185_S19_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-187_S20_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-193_S22_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-187_S20_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-187_S20_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-188_S21_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-194_S23_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-188_S21_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-188_S21_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-193_S22_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-199_S24_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-193_S22_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-193_S22_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-194_S23_L003_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-200_S25_L003_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-194_S23_L003_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-194_S23_L003_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file 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'/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-206_S27_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-209_S29_L004_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-206_S27_L004_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-206_S27_L004_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-208_S28_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-214_S30_L004_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file 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'/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-214_S30_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-220_S32_L004_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-214_S30_L004_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-214_S30_L004_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-215_S31_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-221_S33_L004_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file 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'/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-221_S33_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-227_S35_L004_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-221_S33_L004_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-221_S33_L004_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-226_S34_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-229_S36_L004_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file 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'/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-229_S36_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-41_S38_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-229_S36_L004_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-229_S36_L004_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-230_S37_L004_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-42_S39_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file 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'/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-42_S39_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-44_S41_L005_R1_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-42_S39_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-42_S39_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-43_S40_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-43_S40_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-43_S40_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-44_S41_L005_R2_001.fastq.gz_trimming_report.txt': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-44_S41_L005_R1_001_val_1.fq.gz': Permission denied\n", "cp: cannot create regular file '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-44_S41_L005_R2_001_val_2.fq.gz': Permission denied\n", "cp: preserving times for '/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs': Operation not permitted\n", "\n", "real\t0m0.544s\n", "user\t0m0.004s\n", "sys\t0m0.004s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "cp -pR /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/ \\\n", "/mnt/owl/Athaliana/" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", 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"drwxr-xr-x 2 276601 20746 0 Mar 26 01:56 20180322_SparseAssembler_novaseq_geoduck\n", "drwxr-xr-x 3 root users 0 Mar 28 08:13 20180327_bgi_fastqc\n", "-rw-r--r-- 1 1027 users 1641206 Apr 4 12:14 20180327_bottles.jpg\n", "drwxr-xr-x 3 root users 0 Mar 28 10:19 20180328_illumina_hiseq_geoduck_fastqc\n", "drwxr-xr-x 4 root users 0 Apr 4 13:58 20180328_trim_galore_illumina_hiseq_geoduck\n", "drwxr-xr-x 2 sean sean 0 Apr 15 11:32 20180405_sparseassembler_kmer101_geoduck\n", "drwxrwxr-x 3 sean sean 0 Apr 9 15:14 20180409_fastqc_Cvirginica_MBD\n", "drwxrwxr-x 3 sean sean 0 Apr 10 06:58 20180409_trimgalore_autotrim_Cvirginica_MBD\n", "drwxrwxr-x 3 sean sean 0 Apr 11 06:54 20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD\n", "drwxrwxr-x 3 sean sean 0 Apr 10 13:11 20180410_trimgalore_trim14bp_Cvirginica_MBD\n", "-rw-r--r-- 1 1027 users 202642 Apr 11 11:07 20180411_metagenome_filters.jpg\n", "drwxrwxr-x 3 sean sean 0 Apr 11 14:32 20180411_trimgalore_10bp_Cvirginica_MBD\n", "drwxr-xr-x 2 root users 0 Apr 24 10:37 20180419_kmergenie_diploid_geoduck\n", "drwxr-xr-x 2 root users 0 Apr 24 10:37 20180419_kmergenie_diploid_k301_geoduck\n", "drwxr-xr-x 2 root users 0 Apr 19 14:23 20180419_kmergenie_geoduck\n", "drwxrwxr-x 6 sean sean 0 May 3 08:56 20180421_geoduck_hi-c\n", "drwxr-xr-x 2 root users 0 Apr 24 10:48 20180421_kmergenie_k301_geoduck\n", "drwxr-xr-x 2 root users 0 Apr 22 07:36 20180422_sparseassembler_kmer131_geoduck\n", "drwxr-xr-x 2 root users 0 Apr 23 06:58 20180423_sparseassembler_kmer111_geoduck\n", "drwxr-xr-x 2 root users 0 May 10 13:57 20180423_sparseassembler_kmer95_geoduck\n", "drwxrwxr-x 8 sean sean 0 Apr 25 07:29 20180424_yaamini_TA\n", "-rw-rw-r-- 1 sean users 270380 Apr 26 08:52 20180425_metagenome_filters.jpg\n", "-rw-rw-r-- 1 sean users 109676 Apr 30 11:49 20180430_quast_pga_assemblies.png\n", "-rw-rw-r-- 1 sean users 98255 Apr 30 11:59 20180430_quast_sparse_sn_pga_comparison.png\n", "drwxrwxr-x 3 steven steven 0 May 9 13:49 20180503_oly_genome_pbjelly_sjw_01_bismark\n", "drwxrwxr-x 3 steven steven 0 May 9 13:57 20180503_oly_methylseq_trimgalore\n", "drwxrwxr-x 4 steven steven 0 May 7 08:16 20180503_trimgalore\n", "drwxrwxr-x 2 steven steven 0 May 9 14:01 20180507_oly_methylseq_bismark\n", "drwxrwxr-x 2 sam sam 0 May 9 14:10 20180508_geoduck_assemblies_bowtie2_indexes\n", "drwxrwxr-x 2 sam sam 0 May 9 14:14 20180508_geoduck_mapping_nova_to_10x\n", "drwxrwxr-x 2 sam sam 0 May 9 14:15 20180508_geoduck_mapping_nova_to_Hi-C\n", "drwxrwxr-x 2 sam sam 0 May 9 14:16 20180508_geoduck_mapping_nova_to_sparse\n", "drwxr-xr-x 2 root users 0 May 12 15:21 20180512_geoduck_fasta_subsets\n", "drwx------ 2 root users 0 May 16 09:29 20180514_geoduck_trimgalore_rrbs\n", "drwxr-sr-x 2 root users 0 May 15 09:15 20180515_oly_bowtie2_pbjelly_sjw_01_genome_index\n", "-rw-rw-rw- 1 1027 users 711192 Dec 11 14:02 2100 expert_DNA 12000_DE72902486_2017-12-11_13-45-31.xad\n", "drwxrwsrwx 4 1026 users 0 May 25 2016 ftp2.genewiz.com\n", "drwxrwxrwx 10 1026 users 0 Jan 22 2014 GenBankSRA\n", "-rw-rw-rw- 1 1026 users 1429 May 25 2016 oly_gbs.barcodes\n", "drwxr-xr-x 18 root users 0 May 14 06:53 quast_results\n", "-rw-rw-rw- 1 1026 users 16571 Jan 17 2016 readme.md\n", "-rwxrwxrwx 1 1027 users 51712 Feb 1 13:19 Thumbs.db\n" ] } ], "source": [ "%%bash\n", "ls -l /mnt/owl/Athaliana/" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 24\n", "drwxrwxrwx 55 1026 users 0 May 16 09:29 Athaliana\n", "drwxrwsrwx 7 1024 dialout 0 Oct 29 2015 btea\n", "drwxrwsrwx 2 1024 users 0 Dec 9 2015 cicese\n", "drwxrwsrwx 3 1024 users 0 Oct 2 2012 dlf\n", "drwxrwsrwx 6 1050 users 0 Jan 7 2015 eimd\n", "drwxrwxrwx 8 1024 65538 0 Nov 8 2016 fish546\n", "drwxrwsrwx 6 1060 65539 0 Jul 31 2017 generosa\n", "drwxrwxrwx 26 1024 users 0 Mar 3 07:37 halfshell\n", "-rwxrwxrwx 1 1062 users 9195 Dec 31 2013 index.html\n", "-rwxrwxrwx 1 1024 users 15019 Oct 2 2012 index.php\n", "drwxrwsrwx 5 1050 users 0 Aug 20 2014 lilmax\n", "drwxr-xr-x 27 1024 users 0 Jan 17 10:05 nightingales\n", "drwxrwsrwx 6 1026 dialout 0 Dec 6 2016 O_lurida_genome_assemblies_BGI\n", "drwxrwsrwx 6 1026 dialout 0 Dec 6 2016 P_generosa_genome_assemblies_BGI\n", "drwxrwsrwx 6 1024 dialout 0 Sep 7 2017 phainopepla\n", "drwxrwsrwx 3 1026 users 0 Sep 8 2016 porites\n", "drwxrwsrwx 2 1063 65539 0 Jan 17 2017 sam\n", "drwxrwsrwx 8 1052 65539 0 Mar 21 10:06 scaphapoda\n", "drwxrwxrwx 19 1059 65539 0 Jan 18 15:08 spartina\n", "drwxrwxrwx 5 1026 users 0 Jan 4 2017 symbiodinium\n", "drwxr-sr-x 2 1026 dialout 0 May 31 2016 testing\n", "drwxrwsrwx 5 1058 65539 0 Dec 13 2016 trochophora\n", "drwx--s--x 2 1023 1023 0 Aug 29 2016 web_images\n", "drwxrwxrwx 12 1026 users 0 Mar 6 13:31 wetgenes\n", "drwxrwsrwx 15 1024 users 0 Oct 24 2017 whale\n" ] } ], "source": [ "%%bash\n", "ls -l /mnt/owl/" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "sam adm sudo lpadmin sambashare\n" ] } ], "source": [ "%%bash\n", "groups" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Copied to owl/Athaliana outside of notebook for use with ```sudo```." ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "find: paths must precede expression: /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/\n", "Usage: find [-H] [-L] [-P] [-Olevel] [-D help|tree|search|stat|rates|opt|exec|time] [path...] [expression]\n" ] } ], "source": [ "%%bash\n", "find type -d /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Cut cell out due to excessively long output, due to mistyped command. Proper command is below." ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "find: Arguments to -type should contain only one letter\n" ] } ], "source": [ "%%bash\n", "find /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/ \\\n", "-type -d" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/\n", "/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc\n", "/mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/20180514_geoduck_trimmed_fastqc/multiqc_data\n" ] } ], "source": [ "%%bash\n", "find /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/ \\\n", "-type d" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "##### Realized I never verified checksums after transfer to owl" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Wed May 16 10:51:40 PDT 2018\n" ] } ], "source": [ "%%bash\n", "date" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1,104c1,104\n", "< 0137130ff79ba54ebe4de76ddbfbbf98 /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-154_S5_L002_R1_001_val_1.fq.gz\n", "< 015e566c9f429ac1adfdf416da8fb7be /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-42_S39_L005_R1_001_val_1.fq.gz\n", "< 03026cab1cf9a2b03588879f374acab3 /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-208_S28_L004_R1_001_val_1.fq.gz\n", "< 038e33efea49851078b3f1a411566ed6 /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-206_S27_L004_R1_001_val_1.fq.gz\n", "< 0640d03836c69dc738d2bc678353778d /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/EPI-169_S12_L002_R1_001_val_1.fq.gz\n", "< 08df55124a5098b33d01202fa04ffbe6 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7795503d512020745a8875e9b1fcfce8 EPI-135_S35_L005_R2_001_val_2.fq.gz\n", "> 77cb77f28446531fb10573a5b1c891bb EPI-194_S23_L003_R2_001_val_2.fq.gz\n", "> 78bdfe95946e10f3d98c827125cfef7e EPI-170_S13_L002_R1_001_val_1.fq.gz\n", "> 7d40dd664fc0a35194377be415ccec2f EPI-205_S26_L004_R1_001_val_1.fq.gz\n", "> 7ef206ffbffb83a91c17922d311c36d5 EPI-161_S8_L002_R2_001_val_2.fq.gz\n", "> 7fd7eb223a32396672c5a899beefeb1f EPI-41_S38_L005_R2_001_val_2.fq.gz\n", "> 8028ba1e13070f316677969b49c1afa1 EPI-175_S14_L003_R2_001_val_2.fq.gz\n", "> 81631d536f2bca57a005199960b5840b EPI-104_S28_L005_R2_001_val_2.fq.gz\n", "> 83aed870b0c1c0e379da1d43fe0dfc61 EPI-160_S7_L002_R1_001_val_1.fq.gz\n", "> 83d184984902d2abb9ef18bdb476df1f EPI-194_S23_L003_R1_001_val_1.fq.gz\n", "> 84a7f590648447a961cd8f2460b00642 EPI-154_S5_L002_R2_001_val_2.fq.gz\n", "> 8aca334f7b7c90351ccb65807f901586 EPI-226_S34_L004_R1_001_val_1.fq.gz\n", "> 9445ee52b4563228a04b4d7ec718f67b EPI-185_S19_L003_R1_001_val_1.fq.gz\n", "> 95084943e42c97720b204a7b65bd9082 EPI-175_S14_L003_R1_001_val_1.fq.gz\n", "> 978a1c9362478a2484300eae8d3c63cf EPI-160_S7_L002_R2_001_val_2.fq.gz\n", "> 9bb57c07cc49130941ecca1d31b66c04 EPI-145_S38_L005_R2_001_val_2.fq.gz\n", "> 9bcba9ff91a5d93a0917c73c2cf53380 EPI-136_S36_L005_R2_001_val_2.fq.gz\n", "> 9c875dc103b79765489fecfbe13f7608 EPI-170_S13_L002_R2_001_val_2.fq.gz\n", "> a777203f0f3ecc5c6a2f1b2f565b4b83 EPI-167_S10_L002_R2_001_val_2.fq.gz\n", "> a7f5db1fd296c8ecfbf271798810de70 EPI-127_S33_L005_R2_001_val_2.fq.gz\n", "> b0f23ba088e407e395615a40b514ec8b EPI-145_S38_L005_R1_001_val_1.fq.gz\n", "> b1ce73ce1c526b08448b5aaab43f5f72 EPI-181_S16_L003_R2_001_val_2.fq.gz\n", "> b77dfa577ac8c9a43fdde3d0b8d8a49b EPI-162_S9_L002_R1_001_val_1.fq.gz\n", "> b7d751f9e97f2e5972f68bd3343bc6b3 EPI-205_S26_L004_R2_001_val_2.fq.gz\n", "> b876a7e891058c2f6d42e18af9196dbf EPI-226_S34_L004_R2_001_val_2.fq.gz\n", "> bbb15f7aa27376f3b6ab9b06ecc7ac7f EPI-111_S29_L005_R1_001_val_1.fq.gz\n", "> be112018de7d6b9acd2f9d6a6b456db5 EPI-199_S24_L003_R1_001_val_1.fq.gz\n", "> c1e554e4f94f64b7f0faca1e291004c7 EPI-111_S29_L005_R2_001_val_2.fq.gz\n", "> c777c66ae787c516cea6f091439a8ea9 EPI-143_S37_L005_R1_001_val_1.fq.gz\n", "> c8849a046cbeba9414404cf9d77d66c5 EPI-159_S6_L002_R2_001_val_2.fq.gz\n", "> cb4e5b8fc1c3d87adb4f96f7f6050f63 EPI-200_S25_L003_R1_001_val_1.fq.gz\n", "> cef1bdb7d39eb552a80fed0c5e02d701 EPI-193_S22_L003_R1_001_val_1.fq.gz\n", "> d0effb97fa3c9b6e128c06d0a5f94739 EPI-206_S27_L004_R2_001_val_2.fq.gz\n", "> d9c02e95da8e1ed8e2764508ba0ac9b0 EPI-229_S36_L004_R1_001_val_1.fq.gz\n", "> daeb67f7ec0306743775bb50722bb630 EPI-44_S41_L005_R1_001_val_1.fq.gz\n", "> dbe3842870647cf96c9643bffffe828c EPI-136_S36_L005_R1_001_val_1.fq.gz\n", "> dbee52f3a94b6c391109f5d144b454f8 EPI-227_S35_L004_R2_001_val_2.fq.gz\n", "> dcc14a7d1e13179eb0ba10e9fb3cbf38 EPI-119_S31_L005_R2_001_val_2.fq.gz\n", "> e4086ea3cd5b0a0aada67ef64c3aeaa3 EPI-182_S17_L003_R2_001_val_2.fq.gz\n", "> ea2666959910c47db78db94e55a6a72a EPI-181_S16_L003_R1_001_val_1.fq.gz\n", "> ecf8b4c16df4e4dbbe67b40e2d1a409d EPI-229_S36_L004_R2_001_val_2.fq.gz\n", "> edf42d84e4f5e97f52aa2b9748298cff EPI-113_S30_L005_R2_001_val_2.fq.gz\n", "> ef9866b6a612642277311c35f8f02641 EPI-103_S27_L005_R2_001_val_2.fq.gz\n", "> f0fca9b0d0cf78804764c66dc51a3fe3 EPI-159_S6_L002_R1_001_val_1.fq.gz\n", "> f1eb760fd147143d63b54f5c89e1d5af EPI-120_S32_L005_R2_001_val_2.fq.gz\n", "> f2d3b92853a1b9f08686652cde404605 EPI-230_S37_L004_R2_001_val_2.fq.gz\n", "> f47b496bba977efe969ce230152085d0 EPI-215_S31_L004_R2_001_val_2.fq.gz\n", "> f5a6ca5a8a7bc4bb2a5ca3855d013dce EPI-120_S32_L005_R1_001_val_1.fq.gz\n", "> f682c0f4c328c3f3580904d3476fb385 EPI-119_S31_L005_R1_001_val_1.fq.gz\n", "> f6c4b020b630208f12bbe86a740db2a1 EPI-209_S29_L004_R2_001_val_2.fq.gz\n", "> f787b24dbbd69875d91bff5495cca6fa EPI-193_S22_L003_R2_001_val_2.fq.gz\n", "> fcf914bb22022e9ba9345c95135bd21e EPI-187_S20_L003_R1_001_val_1.fq.gz\n", "> ff3715f13717e62aae23b8511aefcc7f EPI-153_S4_L002_R2_001_val_2.fq.gz\n", "> ff6ec2a7f720dddd48a049c1b6bb4382 EPI-221_S33_L004_R1_001_val_1.fq.gz\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t24m31.033s\n", "user\t4m46.304s\n", "sys\t0m32.640s\n" ] } ], "source": [ "%%bash\n", "time \\\n", "for trim_fq in /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/*val*.gz\n", "do md5sum \"$trim_fq\" >> /home/sam/Downloads/20180516_tmp_checksums.md5\n", "done\n", "\n", "diff <(sort /home/sam/Downloads/20180516_tmp_checksums.md5) <(sort /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/checksums.md5)\n", "\n", "sed '/^Subject:/ s/ / checksums JOB COMPLETE/' ~/.default-subject.mail | msmtp \"$EMAIL\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Having dealt with the above issue twice in the same notebook, I decided to look into avoiding this situation.\n", "\n", "It turns out that md5sum has a built in checking option!!!" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "bash: line 2: cd: /mnt/owl/Athaliana//mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/: No such file or directory\n", "md5sum: checksums.md5: No such file or directory\n", "\n", "real\t0m0.002s\n", "user\t0m0.000s\n", "sys\t0m0.000s\n" ] } ], "source": [ "%%bash\n", "\n", "cd /mnt/owl/Athaliana//mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/\n", "\n", "time \\\n", "md5sum -c checksums.md5" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "EPI-103_S27_L005_R1_001_val_1.fq.gz: OK\n", "EPI-103_S27_L005_R2_001_val_2.fq.gz: OK\n", "EPI-104_S28_L005_R1_001_val_1.fq.gz: OK\n", "EPI-104_S28_L005_R2_001_val_2.fq.gz: OK\n", "EPI-111_S29_L005_R1_001_val_1.fq.gz: OK\n", "EPI-111_S29_L005_R2_001_val_2.fq.gz: OK\n", "EPI-113_S30_L005_R1_001_val_1.fq.gz: OK\n", "EPI-113_S30_L005_R2_001_val_2.fq.gz: OK\n", "EPI-119_S31_L005_R1_001_val_1.fq.gz: OK\n", "EPI-119_S31_L005_R2_001_val_2.fq.gz: OK\n", "EPI-120_S32_L005_R1_001_val_1.fq.gz: OK\n", "EPI-120_S32_L005_R2_001_val_2.fq.gz: OK\n", "EPI-127_S33_L005_R1_001_val_1.fq.gz: OK\n", "EPI-127_S33_L005_R2_001_val_2.fq.gz: OK\n", "EPI-128_S34_L005_R1_001_val_1.fq.gz: OK\n", "EPI-128_S34_L005_R2_001_val_2.fq.gz: OK\n", "EPI-135_S35_L005_R1_001_val_1.fq.gz: OK\n", "EPI-135_S35_L005_R2_001_val_2.fq.gz: OK\n", "EPI-136_S36_L005_R1_001_val_1.fq.gz: OK\n", "EPI-136_S36_L005_R2_001_val_2.fq.gz: OK\n", "EPI-143_S37_L005_R1_001_val_1.fq.gz: OK\n", "EPI-143_S37_L005_R2_001_val_2.fq.gz: OK\n", "EPI-145_S38_L005_R1_001_val_1.fq.gz: OK\n", "EPI-145_S38_L005_R2_001_val_2.fq.gz: OK\n", "EPI-151_S2_L002_R1_001_val_1.fq.gz: OK\n", "EPI-151_S2_L002_R2_001_val_2.fq.gz: OK\n", "EPI-152_S3_L002_R1_001_val_1.fq.gz: OK\n", "EPI-152_S3_L002_R2_001_val_2.fq.gz: OK\n", "EPI-153_S4_L002_R1_001_val_1.fq.gz: OK\n", "EPI-153_S4_L002_R2_001_val_2.fq.gz: OK\n", "EPI-154_S5_L002_R1_001_val_1.fq.gz: OK\n", "EPI-154_S5_L002_R2_001_val_2.fq.gz: OK\n", "EPI-159_S6_L002_R1_001_val_1.fq.gz: OK\n", "EPI-159_S6_L002_R2_001_val_2.fq.gz: OK\n", "EPI-160_S7_L002_R1_001_val_1.fq.gz: OK\n", "EPI-160_S7_L002_R2_001_val_2.fq.gz: OK\n", "EPI-161_S8_L002_R1_001_val_1.fq.gz: OK\n", "EPI-161_S8_L002_R2_001_val_2.fq.gz: OK\n", "EPI-162_S9_L002_R1_001_val_1.fq.gz: OK\n", "EPI-162_S9_L002_R2_001_val_2.fq.gz: OK\n", "EPI-167_S10_L002_R1_001_val_1.fq.gz: OK\n", "EPI-167_S10_L002_R2_001_val_2.fq.gz: OK\n", "EPI-168_S11_L002_R1_001_val_1.fq.gz: OK\n", "EPI-168_S11_L002_R2_001_val_2.fq.gz: OK\n", "EPI-169_S12_L002_R1_001_val_1.fq.gz: OK\n", "EPI-169_S12_L002_R2_001_val_2.fq.gz: OK\n", "EPI-170_S13_L002_R1_001_val_1.fq.gz: OK\n", "EPI-170_S13_L002_R2_001_val_2.fq.gz: OK\n", "EPI-175_S14_L003_R1_001_val_1.fq.gz: OK\n", "EPI-175_S14_L003_R2_001_val_2.fq.gz: OK\n", "EPI-176_S15_L003_R1_001_val_1.fq.gz: OK\n", "EPI-176_S15_L003_R2_001_val_2.fq.gz: OK\n", "EPI-181_S16_L003_R1_001_val_1.fq.gz: OK\n", "EPI-181_S16_L003_R2_001_val_2.fq.gz: OK\n", "EPI-182_S17_L003_R1_001_val_1.fq.gz: OK\n", "EPI-182_S17_L003_R2_001_val_2.fq.gz: OK\n", "EPI-184_S18_L003_R1_001_val_1.fq.gz: OK\n", "EPI-184_S18_L003_R2_001_val_2.fq.gz: OK\n", "EPI-185_S19_L003_R1_001_val_1.fq.gz: OK\n", "EPI-185_S19_L003_R2_001_val_2.fq.gz: OK\n", "EPI-187_S20_L003_R1_001_val_1.fq.gz: OK\n", "EPI-187_S20_L003_R2_001_val_2.fq.gz: OK\n", "EPI-188_S21_L003_R1_001_val_1.fq.gz: OK\n", "EPI-188_S21_L003_R2_001_val_2.fq.gz: OK\n", "EPI-193_S22_L003_R1_001_val_1.fq.gz: OK\n", "EPI-193_S22_L003_R2_001_val_2.fq.gz: OK\n", "EPI-194_S23_L003_R1_001_val_1.fq.gz: OK\n", "EPI-194_S23_L003_R2_001_val_2.fq.gz: OK\n", "EPI-199_S24_L003_R1_001_val_1.fq.gz: OK\n", "EPI-199_S24_L003_R2_001_val_2.fq.gz: OK\n", "EPI-200_S25_L003_R1_001_val_1.fq.gz: OK\n", "EPI-200_S25_L003_R2_001_val_2.fq.gz: OK\n", "EPI-205_S26_L004_R1_001_val_1.fq.gz: OK\n", "EPI-205_S26_L004_R2_001_val_2.fq.gz: OK\n", "EPI-206_S27_L004_R1_001_val_1.fq.gz: OK\n", "EPI-206_S27_L004_R2_001_val_2.fq.gz: OK\n", "EPI-208_S28_L004_R1_001_val_1.fq.gz: OK\n", "EPI-208_S28_L004_R2_001_val_2.fq.gz: OK\n", "EPI-209_S29_L004_R1_001_val_1.fq.gz: OK\n", "EPI-209_S29_L004_R2_001_val_2.fq.gz: OK\n", "EPI-214_S30_L004_R1_001_val_1.fq.gz: OK\n", "EPI-214_S30_L004_R2_001_val_2.fq.gz: OK\n", "EPI-215_S31_L004_R1_001_val_1.fq.gz: OK\n", "EPI-215_S31_L004_R2_001_val_2.fq.gz: OK\n", "EPI-220_S32_L004_R1_001_val_1.fq.gz: OK\n", "EPI-220_S32_L004_R2_001_val_2.fq.gz: OK\n", "EPI-221_S33_L004_R1_001_val_1.fq.gz: OK\n", "EPI-221_S33_L004_R2_001_val_2.fq.gz: OK\n", "EPI-226_S34_L004_R1_001_val_1.fq.gz: OK\n", "EPI-226_S34_L004_R2_001_val_2.fq.gz: OK\n", "EPI-227_S35_L004_R1_001_val_1.fq.gz: OK\n", "EPI-227_S35_L004_R2_001_val_2.fq.gz: OK\n", "EPI-229_S36_L004_R1_001_val_1.fq.gz: OK\n", "EPI-229_S36_L004_R2_001_val_2.fq.gz: OK\n", "EPI-230_S37_L004_R1_001_val_1.fq.gz: OK\n", "EPI-230_S37_L004_R2_001_val_2.fq.gz: OK\n", "EPI-41_S38_L005_R1_001_val_1.fq.gz: OK\n", "EPI-41_S38_L005_R2_001_val_2.fq.gz: OK\n", "EPI-42_S39_L005_R1_001_val_1.fq.gz: OK\n", "EPI-42_S39_L005_R2_001_val_2.fq.gz: OK\n", "EPI-43_S40_L005_R1_001_val_1.fq.gz: OK\n", "EPI-43_S40_L005_R2_001_val_2.fq.gz: OK\n", "EPI-44_S41_L005_R1_001_val_1.fq.gz: OK\n", "EPI-44_S41_L005_R2_001_val_2.fq.gz: OK\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n", "real\t23m52.712s\n", "user\t4m47.840s\n", "sys\t0m32.472s\n" ] } ], "source": [ "%%bash\n", "\n", "cd /mnt/owl/Athaliana/20180514_geoduck_trimgalore_rrbs/\n", "\n", "time \\\n", "md5sum -c checksums.md5" ] }, { "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 }