{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\r\n", "BSMAP v2.74\r\n", "Usage:\tbsmap [options]\r\n", " -a query a file, FASTA/FASTQ/BAM format\r\n", " -d reference sequences file, FASTA format\r\n", " -o output alignment file, BSP/SAM/BAM format, if omitted, the output will be written to STDOUT in SAM format.\r\n", "\r\n", " Options for alignment:\r\n", " -s seed size, default=16(WGBS mode), 12(RRBS mode). min=8, max=16.\r\n", " -v if this value is between 0 and 1, it's interpreted as the mismatch rate w.r.t to the read length.\r\n", " otherwise it's interpreted as the maximum number of mismatches allowed on a read, <=15.\r\n", " example: -v 5 (max #mismatches = 5), -v 0.1 (max #mismatches = read_length * 10%)\r\n", " default=0.08.\r\n", " -g gap size, BSMAP only allow 1 continuous gap (insert or deletion) with up to 3 nucleotides\r\n", " default=0\r\n", " -w maximum number of equal best hits to count, <=1000\r\n", " -3 using 3-nucleotide mapping approach\r\n", " -B start from the Nth read or read pair, default: 1\r\n", " -E end at the Nth read or read pair, default: 4,294,967,295\r\n", " -I index interval, default=4\r\n", " -k set the cut-off ratio for over-represented kmers, default=5e-07\r\n", " example: -k 1e-6 means the top 0.0001% over-represented kmer will be skipped in alignment\r\n", " -p number of processors to use, default=8\r\n", " -D activating RRBS mapping mode and set restriction enzyme digestion sites. \r\n", " digestion position marked by '-', example: -D C-CGG for MspI digestion.\r\n", " default: none (whole genome shotgun bisulfite mapping mode)\r\n", " -S seed for random number generation used in selecting multiple hits\r\n", " other seed values generate pseudo random number based on read index number, to allow reproducible mapping results. \r\n", " default=0. (get seed from system clock, mapping results not resproducible.)\r\n", " -n [0,1] set mapping strand information. default: 0\r\n", " -n 0: only map to 2 forward strands, i.e. BSW(++) and BSC(-+), \r\n", " for PE sequencing, map read#1 to ++ and -+, read#2 to +- and --.\r\n", " -n 1: map SE or PE reads to all 4 strands, i.e. ++, +-, -+, -- \r\n", " -M set alignment information for the additional nucleotide transition. \r\n", " is in the form of two different nucleotides N1N2, \r\n", " indicating N1 in the reads could be mapped to N2 in the reference sequences.\r\n", " default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. \r\n", " example: -M GA could be used to detect A=>I(G) transition in RNA editing. \r\n", "\r\n", " Options for trimming:\r\n", " -q quality threshold in trimming, 0-40, default=0 (no trim)\r\n", " -z base quality, default=33 [Illumina is using 64, Sanger Institute is using 33]\r\n", " -f filter low-quality reads containing >n Ns, default=5\r\n", " -A 3-end adapter sequence, default: none (no trim)\r\n", " -L map the first N nucleotides of the read, default:144 (map the whole read).\r\n", "\r\n", " Options for reporting:\r\n", " -r [0,1] how to report repeat hits, 0=none(unique hit/pair only); 1=random one, default:1.\r\n", " -R print corresponding reference sequences in SAM output, default=off\r\n", " -u report unmapped reads, default=off\r\n", " -H do not print header information in SAM format output\r\n", "\r\n", " Options for pair-end alignment:\r\n", " -b query b file\r\n", " -m minimal insert size allowed, default=28\r\n", " -x maximal insert size allowed, default=500\r\n", "\r\n", " -h help\r\n", "\r\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " % Total % Received % Xferd Average Speed Time Time Time Current\n", " Dload Upload Total Spent Left Speed\n", "100 541M 100 541M 0 0 94.5M 0 0:00:05 0:00:05 --:--:-- 99.0M\n" ] } ], "source": [ "!curl http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_ensembl_tracks/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n", "> /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa " ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "^C\r\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Users/sr320/data-genomic/tentacle/2112_Cv_LSU.fastq \\\n", "-d /Users/sr320/git-repos/nb-2015/Cv/data/cvir.v1.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapoutcvir.v1.sam \\\n", "-p 8 \\\n", "2> /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapoutcvir.v1-error" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "BSMAP v2.74\n", "Start at: Wed Feb 11 15:14:42 2015\n", "\n", "Input reference file: /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \t(format: FASTA)\n", "Load in 7658 db seqs, total size 557717710 bp. 6 secs passed\n", "total_kmers: 43046721\n", "Create seed table. 22 secs passed\n", "max number of mismatches: read_length * 8% \tmax gap size: 0\n", "kmer cut-off ratio: 5e-07\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\n", "quality cutoff: 0\tbase quality char: '!'\n", "min fragment size:28\tmax fragemt size:500\n", "start from read #1\tend at read #4294967295\n", "additional alignment: T in reads => C in reference\n", "mapping strand: ++,-+\n", "Single-end alignment(8 threads)\n", "Input read file: /Users/sr320/data-genomic/tentacle/2112_Cv_LSU.fastq \t(format: FASTQ)\n", "Output file: /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapout.sam\t (format: SAM)\n", "Thread #4: \t300000 reads finished. 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\t18850000 reads finished. 801 secs passed\n", "Thread #6: \t18900000 reads finished. 801 secs passed\n", "Thread #4: \t18950000 reads finished. 803 secs passed\n", "Thread #3: \t19000000 reads finished. 803 secs passed\n", "Thread #7: \t19050000 reads finished. 804 secs passed\n", "Thread #0: \t19100000 reads finished. 804 secs passed\n", "Thread #5: \t19150000 reads finished. 805 secs passed\n", "Thread #2: \t19200000 reads finished. 810 secs passed\n", "Thread #1: \t19250000 reads finished. 816 secs passed\n", "Thread #6: \t19300000 reads finished. 816 secs passed\n", "Thread #4: \t19350000 reads finished. 818 secs passed\n", "Thread #3: \t19400000 reads finished. 819 secs passed\n", "Thread #0: \t19500000 reads finished. 819 secs passed\n", "Thread #7: \t19450000 reads finished. 819 secs passed\n", "Thread #5: \t19550000 reads finished. 820 secs passed\n", "Thread #2: \t19600000 reads finished. 825 secs passed\n", "Thread #1: \t19650000 reads finished. 831 secs passed\n", "Thread 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"Thread #3: \t20550000 reads finished. 866 secs passed\n", "Thread #4: \t20600000 reads finished. 867 secs passed\n", "Thread #7: \t20650000 reads finished. 869 secs passed\n", "Thread #0: \t20700000 reads finished. 869 secs passed\n", "Thread #5: \t20750000 reads finished. 869 secs passed\n", "Thread #2: \t20800000 reads finished. 875 secs passed\n", "Thread #1: \t20850000 reads finished. 880 secs passed\n", "Thread #6: \t20900000 reads finished. 880 secs passed\n", "Thread #3: \t20950000 reads finished. 883 secs passed\n", "Thread #4: \t21000000 reads finished. 884 secs passed\n", "Thread #7: \t21050000 reads finished. 885 secs passed\n", "Thread #0: \t21100000 reads finished. 886 secs passed\n", "Thread #5: \t21150000 reads finished. 886 secs passed\n", "Thread #2: \t21200000 reads finished. 892 secs passed\n", "Thread #1: \t21250000 reads finished. 897 secs passed\n", "Thread #6: \t21300000 reads finished. 897 secs passed\n", "Thread #3: \t21350000 reads finished. 899 secs 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finished. 1567 secs passed\n", "Thread #3: \t38950000 reads finished. 1569 secs passed\n", "Thread #7: \t39000000 reads finished. 1570 secs passed\n", "Thread #4: \t39050000 reads finished. 1572 secs passed\n", "Thread #5: \t39100000 reads finished. 1572 secs passed\n", "Thread #0: \t39150000 reads finished. 1573 secs passed\n", "Thread #2: \t39200000 reads finished. 1579 secs passed\n", "Thread #1: \t39250000 reads finished. 1580 secs passed\n", "Thread #6: \t39300000 reads finished. 1583 secs passed\n", "Thread #3: \t39350000 reads finished. 1585 secs passed\n", "Thread #7: \t39400000 reads finished. 1586 secs passed\n", "Thread #4: \t39450000 reads finished. 1587 secs passed\n", "Thread #5: \t39500000 reads finished. 1588 secs passed\n", "Thread #0: \t39550000 reads finished. 1589 secs passed\n", "Thread #2: \t39600000 reads finished. 1595 secs passed\n", "Thread #1: \t39650000 reads finished. 1596 secs passed\n", "Thread #6: \t39700000 reads finished. 1599 secs passed\n", "Thread 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finished. 132409 secs passed\n", "Thread #7: \t222450000 reads finished. 132874 secs passed\n", "Thread #5: \t222500000 reads finished. 132874 secs passed\n", "Thread #0: \t222600000 reads finished. 132874 secs passed\n", "Thread #2: \t222550000 reads finished. 132878 secs passed\n", "Thread #4: \t222650000 reads finished. 132878 secs passed\n", "Thread #3: \t222750000 reads finished. 132878 secs passed\n", "Thread #6: \t222700000 reads finished. 132878 secs passed\n", "Thread #1: \t222800000 reads finished. 132878 secs passed\n", "Thread #7: \t222850000 reads finished. 132905 secs passed\n", "Thread #5: \t222900000 reads finished. 132906 secs passed\n", "Thread #0: \t222950000 reads finished. 132907 secs passed\n", "Thread #2: \t223000000 reads finished. 132907 secs passed\n", "Thread #4: \t223050000 reads finished. 132907 secs passed\n", "Thread #3: \t223100000 reads finished. 132908 secs passed\n", "Thread #6: \t223150000 reads finished. 132908 secs passed\n", "Thread #1: \t223200000 reads finished. 132908 secs passed\n", "Thread #7: \t223250000 reads finished. 132929 secs passed\n", "Thread #5: \t223300000 reads finished. 133540 secs passed\n", "Thread #0: \t223350000 reads finished. 133540 secs passed\n", "Thread #4: \t223450000 reads finished. 133541 secs passed\n", "Thread #3: \t223500000 reads finished. 133541 secs passed\n", "Thread #2: \t223400000 reads finished. 133541 secs passed\n", "Thread #6: \t223550000 reads finished. 133541 secs passed\n", "Thread #1: \t223600000 reads finished. 133541 secs passed\n", "Thread #7: \t223650000 reads finished. 133569 secs passed\n", "Thread #5: \t223700000 reads finished. 133570 secs passed\n", "Thread #0: \t223750000 reads finished. 133570 secs passed\n", "Thread #4: \t223800000 reads finished. 133571 secs passed\n", "Thread #3: \t223850000 reads finished. 133571 secs passed\n", "Thread #2: \t223900000 reads finished. 133572 secs passed\n", "Thread #6: \t223950000 reads finished. 133572 secs passed\n", "Thread #1: \t224000000 reads finished. 133572 secs passed\n", "Thread #7: \t224050000 reads finished. 133594 secs passed\n", "Thread #5: \t224100000 reads finished. 133594 secs passed\n", "Thread #0: \t224150000 reads finished. 133595 secs passed\n", "Thread #4: \t224200000 reads finished. 133595 secs passed\n", "Thread #3: \t224250000 reads finished. 133596 secs passed\n", "Thread #2: \t224300000 reads finished. 133596 secs passed\n", "Thread #6: \t224350000 reads finished. 133597 secs passed\n", "Thread #1: \t224400000 reads finished. 133597 secs passed\n", "Thread #0: \t224550000 reads finished. 134118 secs passed\n", "Thread #5: \t224500000 reads finished. 134118 secs passed\n", "Thread #7: \t224450000 reads finished. 134118 secs passed\n", "Thread #4: \t224600000 reads finished. 134119 secs passed\n", "Thread #3: \t224650000 reads finished. 134119 secs passed\n", "Thread #2: \t224700000 reads finished. 134120 secs passed\n", "Thread #6: \t224750000 reads finished. 134121 secs passed\n", "Thread #1: \t224800000 reads finished. 134125 secs passed\n", "Thread #5: \t224881920 reads finished. 134126 secs passed\n", "Thread #0: \t224850000 reads finished. 134129 secs passed\n", "Total number of aligned reads: 805388 (0.36%)\n", "Done.\n", "Finished at Fri Feb 13 04:30:11 2015\n", "Total time consumed: 134129 secs\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Users/sr320/data-genomic/tentacle/2112_Cv_LSU.fastq \\\n", "-d /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapout.sam \\\n", "-p 8" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "BSMAP v2.74\n", "Start at: Wed Mar 4 14:12:29 2015\n", "\n", "Input reference file: /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \t(format: FASTA)\n", "Load in 7658 db seqs, total size 557717710 bp. 7 secs passed\n", "total_kmers: 43046721\n", "Create seed table. 20 secs passed\n", "max number of mismatches: read_length * 20% \tmax gap size: 1\n", "kmer cut-off ratio: 5e-07\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\n", "quality cutoff: 0\tbase quality char: '!'\n", "min fragment size:28\tmax fragemt size:500\n", "start from read #1\tend at read #4294967295\n", "additional alignment: T in reads => C in reference\n", "mapping strand: ++,-+\n", "Single-end alignment(8 threads)\n", "Input read file: /Volumes/web/nightingales/C_virginica/2112_lane1_NoIndex_L001_R1_002.fastq.gz \t(format: gzipped FASTQ)\n", "Output file: /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapout_030415.sam\t (format: SAM)\n", "Thread #0: \t50000 reads finished. 73 secs passed\n", "Thread #3: \t100000 reads finished. 73 secs passed\n", "Thread #4: \t200000 reads finished. 74 secs passed\n", "Thread #1: \t150000 reads finished. 74 secs passed\n", "Thread #5: \t250000 reads finished. 74 secs passed\n", "Thread #6: \t300000 reads finished. 75 secs passed\n", "Thread #7: \t400000 reads finished. 76 secs passed\n", "Thread #2: \t350000 reads finished. 76 secs passed\n", "Thread #0: \t450000 reads finished. 127 secs passed\n", "Thread #1: \t600000 reads finished. 128 secs passed\n", "Thread #3: \t500000 reads finished. 129 secs passed\n", "Thread #4: \t550000 reads finished. 129 secs passed\n", "Thread #6: \t700000 reads finished. 130 secs passed\n", "Thread #2: \t800000 reads finished. 130 secs passed\n", "Thread #5: \t650000 reads finished. 131 secs passed\n", "Thread #7: \t750000 reads finished. 131 secs passed\n", "Thread #3: \t950000 reads finished. 185 secs passed\n", "Thread #0: \t850000 reads finished. 185 secs passed\n", "Thread #6: \t1050000 reads finished. 186 secs passed\n", "Thread #1: \t900000 reads finished. 186 secs passed\n", "Thread #4: \t1000000 reads finished. 186 secs passed\n", "Thread #2: \t1100000 reads finished. 186 secs passed\n", "Thread #5: \t1150000 reads finished. 187 secs passed\n", "Thread #7: \t1200000 reads finished. 187 secs passed\n", "Thread #1: \t1400000 reads finished. 246 secs passed\n", "Thread #3: \t1250000 reads finished. 246 secs passed\n", "Thread #0: \t1300000 reads finished. 247 secs passed\n", "Thread #6: \t1350000 reads finished. 247 secs passed\n", "Thread #4: \t1450000 reads finished. 247 secs passed\n", "Thread #7: \t1600000 reads finished. 247 secs passed\n", "Thread #5: \t1550000 reads finished. 247 secs passed\n", "Thread #2: \t1500000 reads finished. 247 secs passed\n", "Thread #1: \t1650000 reads finished. 304 secs passed\n", "Thread #3: \t1700000 reads finished. 305 secs passed\n", "Thread #0: \t1750000 reads finished. 305 secs passed\n", "Thread #7: \t1900000 reads finished. 305 secs passed\n", "Thread #6: \t1800000 reads finished. 306 secs passed\n", "Thread #4: \t1850000 reads finished. 306 secs passed\n", "Thread #5: \t1950000 reads finished. 307 secs passed\n", "Thread #2: \t2000000 reads finished. 307 secs passed\n", "Thread #1: \t2050000 reads finished. 364 secs passed\n", "Thread #0: \t2150000 reads finished. 364 secs passed\n", "Thread #6: \t2250000 reads finished. 364 secs passed\n", "Thread #7: \t2200000 reads finished. 364 secs passed\n", "Thread #3: \t2100000 reads finished. 364 secs passed\n", "Thread #4: \t2300000 reads finished. 365 secs passed\n", "Thread #2: \t2400000 reads finished. 365 secs passed\n", "Thread #5: \t2350000 reads finished. 365 secs passed\n", "Thread #6: \t2550000 reads finished. 423 secs passed\n", "Thread #1: \t2450000 reads finished. 423 secs passed\n", "Thread #0: \t2500000 reads finished. 423 secs passed\n", "Thread #7: \t2600000 reads finished. 423 secs passed\n", "Thread #3: \t2650000 reads finished. 423 secs passed\n", "Thread #4: \t2700000 reads finished. 424 secs passed\n", "Thread #5: \t2800000 reads finished. 424 secs passed\n", "Thread #2: \t2750000 reads finished. 424 secs passed\n", "Thread #6: \t2850000 reads finished. 481 secs passed\n", "Thread #1: \t2900000 reads finished. 481 secs passed\n", "Thread #0: \t2950000 reads finished. 482 secs passed\n", "Thread #7: \t3000000 reads finished. 482 secs passed\n", "Thread #3: \t3050000 reads finished. 482 secs passed\n", "Thread #4: \t3100000 reads finished. 482 secs passed\n", "Thread #5: \t3150000 reads finished. 483 secs passed\n", "Thread #2: \t3200000 reads finished. 483 secs passed\n", "Thread #6: \t3250000 reads finished. 540 secs passed\n", "Thread #1: \t3300000 reads finished. 541 secs passed\n", "Thread #4: \t3500000 reads finished. 541 secs passed\n", "Thread #0: \t3350000 reads finished. 541 secs passed\n", "Thread #7: \t3400000 reads finished. 541 secs passed\n", "Thread #5: \t3550000 reads finished. 541 secs passed\n", "Thread #2: \t3600000 reads finished. 542 secs passed\n", "Thread #3: \t3450000 reads finished. 542 secs passed\n", "Thread #1: \t3700000 reads finished. 597 secs passed\n", "Thread #6: \t3650000 reads finished. 598 secs passed\n", "Thread #0: \t3800000 reads finished. 598 secs passed\n", "Thread #7: \t3850000 reads finished. 598 secs passed\n", "Thread #4: \t3750000 reads finished. 598 secs passed\n", "Thread #5: \t3900000 reads finished. 598 secs passed\n", "Thread #2: \t3950000 reads finished. 599 secs passed\n", "Thread #3: \t4000000 reads finished. 599 secs passed\n", "Thread #6: \t4100000 reads finished. 656 secs passed\n", "Thread #7: \t4200000 reads finished. 657 secs passed\n", "Thread #0: \t4150000 reads finished. 657 secs passed\n", "Thread #1: \t4050000 reads finished. 657 secs passed\n", "Thread #5: \t4300000 reads finished. 657 secs passed\n", "Thread #3: \t4400000 reads finished. 657 secs passed\n", "Thread #2: \t4350000 reads finished. 658 secs passed\n", "Thread #4: \t4250000 reads finished. 658 secs passed\n", "Thread #7: \t4500000 reads finished. 714 secs passed\n", "Thread #6: \t4450000 reads finished. 715 secs passed\n", "Thread #0: \t4550000 reads finished. 715 secs passed\n", "Thread #1: \t4600000 reads finished. 718 secs passed\n", "Thread #4: \t4800000 reads finished. 722 secs passed\n", "Thread #2: \t4750000 reads finished. 722 secs passed\n", "Thread #5: \t4650000 reads finished. 722 secs passed\n", "Thread #3: \t4700000 reads finished. 724 secs passed\n", "Thread #6: \t4900000 reads finished. 772 secs passed\n", "Thread #0: \t4950000 reads finished. 773 secs passed\n", "Thread #7: \t4850000 reads finished. 773 secs passed\n", "Thread #1: \t5000000 reads finished. 773 secs passed\n", "Thread #2: \t5100000 reads finished. 777 secs passed\n", "Thread #4: \t5050000 reads finished. 777 secs passed\n", "Thread #5: \t5150000 reads finished. 778 secs passed\n", "Thread #3: \t5200000 reads finished. 779 secs passed\n", "Thread #6: \t5250000 reads finished. 844 secs passed\n", "Thread #7: \t5350000 reads finished. 844 secs passed\n", "Thread #1: \t5400000 reads finished. 844 secs passed\n", "Thread #0: \t5300000 reads finished. 844 secs passed\n", "Thread #4: \t5500000 reads finished. 845 secs passed\n", "Thread #2: \t5450000 reads finished. 846 secs passed\n", "Thread #5: \t5550000 reads finished. 846 secs passed\n", "Thread #3: \t5600000 reads finished. 851 secs passed\n", "Thread #7: \t5700000 reads finished. 917 secs passed\n", "Thread #4: \t5850000 reads finished. 917 secs passed\n", "Thread #2: \t5900000 reads finished. 917 secs passed\n", "Thread #1: \t5750000 reads finished. 918 secs passed\n", "Thread #6: \t5650000 reads finished. 918 secs passed\n", "Thread #0: \t5800000 reads finished. 918 secs passed\n", "Thread #5: \t5950000 reads finished. 918 secs passed\n", "Thread #3: \t6000000 reads finished. 919 secs passed\n", "Thread #4: \t6100000 reads finished. 989 secs passed\n", "Thread #1: \t6200000 reads finished. 989 secs passed\n", "Thread #6: \t6250000 reads finished. 990 secs passed\n", "Thread #5: \t6350000 reads finished. 990 secs passed\n", "Thread #7: \t6050000 reads finished. 990 secs passed\n", "Thread #0: \t6300000 reads finished. 990 secs passed\n", "Thread #2: \t6150000 reads finished. 990 secs passed\n", "Thread #3: \t6400000 reads finished. 990 secs passed\n", "Thread #4: \t6450000 reads finished. 1059 secs passed\n", "Thread #1: \t6500000 reads finished. 1061 secs passed\n", "Thread #0: \t6700000 reads finished. 1061 secs passed\n", "Thread #6: \t6550000 reads finished. 1061 secs passed\n", "Thread #5: \t6600000 reads finished. 1061 secs passed\n", "Thread #2: \t6750000 reads finished. 1062 secs passed\n", "Thread #7: \t6650000 reads finished. 1062 secs passed\n", "Thread #3: \t6800000 reads finished. 1062 secs passed\n", "Thread #4: \t6850000 reads finished. 1129 secs passed\n", "Thread #0: \t6950000 reads finished. 1129 secs passed\n", "Thread #1: \t6900000 reads finished. 1129 secs passed\n", "Thread #2: \t7100000 reads finished. 1129 secs passed\n", "Thread #5: \t7050000 reads finished. 1130 secs passed\n", "Thread #6: \t7000000 reads finished. 1130 secs passed\n", "Thread #7: \t7150000 reads finished. 1130 secs passed\n", "Thread #3: \t7200000 reads finished. 1130 secs passed\n", "Thread #0: \t7300000 reads finished. 1200 secs passed\n", "Thread #4: \t7250000 reads finished. 1200 secs passed\n", "Thread #2: \t7400000 reads finished. 1201 secs passed\n", "Thread #5: \t7450000 reads finished. 1201 secs passed\n", "Thread #1: \t7350000 reads finished. 1201 secs passed\n", "Thread #6: \t7500000 reads finished. 1201 secs passed\n", "Thread #3: \t7600000 reads finished. 1202 secs passed\n", "Thread #7: \t7550000 reads finished. 1202 secs passed\n", "Thread #0: \t7650000 reads finished. 1271 secs passed\n", "Thread #2: \t7750000 reads finished. 1271 secs passed\n", "Thread #4: \t7700000 reads finished. 1271 secs passed\n", "Thread #1: \t7850000 reads finished. 1271 secs passed\n", "Thread #5: \t7800000 reads finished. 1271 secs passed\n", "Thread #6: \t7900000 reads finished. 1271 secs passed\n", "Thread #3: \t7950000 reads finished. 1272 secs passed\n", "Thread #7: \t8000000 reads finished. 1272 secs passed\n", "Thread #2: \t8100000 reads finished. 1339 secs passed\n", "Thread #0: \t8050000 reads finished. 1339 secs passed\n", "Thread #4: \t8150000 reads finished. 1340 secs passed\n", "Thread #5: \t8250000 reads finished. 1340 secs passed\n", "Thread #1: \t8200000 reads finished. 1340 secs passed\n", "Thread #3: \t8350000 reads finished. 1341 secs passed\n", "Thread #7: \t8400000 reads finished. 1341 secs passed\n", "Thread #6: \t8300000 reads finished. 1341 secs passed\n", "Thread #2: \t8450000 reads finished. 1408 secs passed\n", "Thread #5: \t8600000 reads finished. 1411 secs passed\n", "Thread #0: \t8500000 reads finished. 1411 secs passed\n", "Thread #1: \t8650000 reads finished. 1411 secs passed\n", "Thread #3: \t8700000 reads finished. 1411 secs passed\n", "Thread #4: \t8550000 reads finished. 1411 secs passed\n", "Thread #7: \t8750000 reads finished. 1412 secs passed\n", "Thread #6: \t8800000 reads finished. 1412 secs passed\n", "Thread #0: \t8950000 reads finished. 1481 secs passed\n", "Thread #1: \t9000000 reads finished. 1481 secs passed\n", "Thread #2: \t8850000 reads finished. 1481 secs passed\n", "Thread #5: \t8900000 reads finished. 1482 secs passed\n", "Thread #3: \t9050000 reads finished. 1482 secs passed\n", "Thread #4: \t9100000 reads finished. 1482 secs passed\n", "Thread #7: \t9150000 reads finished. 1483 secs passed\n", "Thread #6: \t9200000 reads finished. 1483 secs passed\n", "Thread #2: \t9350000 reads finished. 1556 secs passed\n", "Thread #0: \t9250000 reads finished. 1556 secs passed\n", "Thread #5: \t9400000 reads finished. 1557 secs passed\n", "Thread #7: \t9550000 reads finished. 1557 secs passed\n", "Thread #3: \t9450000 reads finished. 1557 secs passed\n", "Thread #4: \t9500000 reads finished. 1557 secs passed\n", "Thread #1: \t9300000 reads finished. 1557 secs passed\n", "Thread #6: \t9600000 reads finished. 1558 secs passed\n", "Thread #2: \t9650000 reads finished. 1630 secs passed\n", "Thread #0: \t9700000 reads finished. 1630 secs passed\n", "Thread #7: \t9800000 reads finished. 1631 secs passed\n", "Thread #5: \t9750000 reads finished. 1631 secs passed\n", "Thread #1: \t9950000 reads finished. 1631 secs passed\n", "Thread #3: \t9850000 reads finished. 1631 secs passed\n", "Thread #4: \t9900000 reads finished. 1631 secs passed\n", "Thread #6: \t10000000 reads finished. 1632 secs passed\n", "Thread #0: \t10100000 reads finished. 1701 secs passed\n", "Thread #2: \t10050000 reads finished. 1701 secs passed\n", "Thread #7: \t10150000 reads finished. 1702 secs passed\n", "Thread #5: \t10200000 reads finished. 1702 secs passed\n", "Thread #3: \t10300000 reads finished. 1702 secs passed\n", "Thread #1: \t10250000 reads finished. 1703 secs passed\n", "Thread #6: \t10400000 reads finished. 1703 secs passed\n", "Thread #4: \t10350000 reads finished. 1703 secs passed\n", "Thread #0: \t10450000 reads finished. 1773 secs passed\n", "Thread #7: \t10550000 reads finished. 1773 secs passed\n", "Thread #2: \t10500000 reads finished. 1773 secs passed\n", "Thread #5: \t10600000 reads finished. 1773 secs passed\n", "Thread #3: \t10650000 reads finished. 1773 secs passed\n", "Thread #4: \t10800000 reads finished. 1773 secs passed\n", "Thread #6: \t10750000 reads finished. 1773 secs passed\n", "Thread #1: \t10700000 reads finished. 1774 secs passed\n", "Thread #0: \t10850000 reads finished. 1842 secs passed\n", "Thread #7: \t10900000 reads finished. 1843 secs passed\n", "Thread #2: \t10950000 reads finished. 1843 secs passed\n", "Thread #5: \t11000000 reads finished. 1843 secs passed\n", "Thread #4: \t11100000 reads finished. 1844 secs passed\n", "Thread #3: \t11050000 reads finished. 1844 secs passed\n", "Thread #1: \t11200000 reads finished. 1844 secs passed\n", "Thread #6: \t11150000 reads finished. 1844 secs passed\n", "Thread #0: \t11250000 reads finished. 1912 secs passed\n", "Thread #2: \t11350000 reads finished. 1913 secs passed\n", "Thread #7: \t11300000 reads finished. 1913 secs passed\n", "Thread #4: \t11450000 reads finished. 1914 secs passed\n", "Thread #5: \t11400000 reads finished. 1914 secs passed\n", "Thread #6: \t11600000 reads finished. 1914 secs passed\n", "Thread #3: \t11500000 reads finished. 1914 secs passed\n", "Thread #1: \t11550000 reads finished. 1915 secs passed\n", "Thread #2: \t11700000 reads finished. 1982 secs passed\n", "Thread #0: \t11650000 reads finished. 1983 secs passed\n", "Thread #5: \t11850000 reads finished. 1983 secs passed\n", "Thread #4: \t11800000 reads finished. 1984 secs passed\n", "Thread #7: \t11750000 reads finished. 1984 secs passed\n", "Thread #6: \t11900000 reads finished. 1984 secs passed\n", "Thread #1: \t12000000 reads finished. 1984 secs passed\n", "Thread #3: \t11950000 reads finished. 1984 secs passed\n", "Thread #7: \t12250000 reads finished. 2052 secs passed\n", "Thread #4: \t12200000 reads finished. 2052 secs passed\n", "Thread #0: \t12100000 reads finished. 2052 secs passed\n", "Thread #2: \t12050000 reads finished. 2052 secs passed\n", "Thread #5: \t12150000 reads finished. 2053 secs passed\n", "Thread #6: \t12300000 reads finished. 2053 secs passed\n", "Thread #1: \t12350000 reads finished. 2053 secs passed\n", "Thread #3: \t12400000 reads finished. 2054 secs passed\n", "Thread #7: \t12450000 reads finished. 2115 secs passed\n", "Thread #2: \t12600000 reads finished. 2116 secs passed\n", "Thread #0: \t12550000 reads finished. 2117 secs passed\n", "Thread #4: \t12500000 reads finished. 2117 secs passed\n", "Thread #1: \t12750000 reads finished. 2117 secs passed\n", "Thread #5: \t12650000 reads finished. 2117 secs passed\n", "Thread #3: \t12800000 reads finished. 2117 secs passed\n", "Thread #6: \t12700000 reads finished. 2118 secs passed\n", "Thread #7: \t12850000 reads finished. 2175 secs passed\n", "Thread #2: \t12900000 reads finished. 2176 secs passed\n", "Thread #0: \t12950000 reads finished. 2177 secs passed\n", "Thread #5: \t13100000 reads finished. 2177 secs passed\n", "Thread #4: \t13000000 reads finished. 2177 secs passed\n", "Thread #1: \t13050000 reads finished. 2177 secs passed\n", "Thread #3: \t13150000 reads finished. 2178 secs passed\n", "Thread #6: \t13200000 reads finished. 2178 secs passed\n", "Thread #2: \t13300000 reads finished. 2236 secs passed\n", "Thread #7: \t13250000 reads finished. 2236 secs passed\n", "Thread #5: \t13400000 reads finished. 2236 secs passed\n", "Thread #0: \t13350000 reads finished. 2236 secs passed\n", "Thread #4: \t13450000 reads finished. 2241 secs passed\n", "Thread #3: \t13550000 reads finished. 2241 secs passed\n", "Thread #1: \t13500000 reads finished. 2241 secs passed\n", "Thread #6: \t13600000 reads finished. 2243 secs passed\n", "Thread #2: \t13650000 reads finished. 3026 secs passed\n", "Thread #5: \t13750000 reads finished. 3026 secs passed\n", "Thread #7: \t13700000 reads finished. 3026 secs passed\n", "Thread #0: \t13800000 reads finished. 3026 secs passed\n", "Thread #1: \t13950000 reads finished. 3026 secs passed\n", "Thread #3: \t13900000 reads finished. 3027 secs passed\n", "Thread #4: \t13850000 reads finished. 3027 secs passed\n", "Thread #6: \t14000000 reads finished. 3028 secs passed\n", "Thread #7: \t14150000 reads finished. 3376 secs passed\n", "Thread #3: \t14300000 reads finished. 3376 secs passed\n", "Thread #4: \t14350000 reads finished. 3376 secs passed\n", "Thread #0: \t14200000 reads finished. 3376 secs passed\n", "Thread #1: \t14250000 reads finished. 3376 secs passed\n", "Thread #2: \t14050000 reads finished. 3377 secs passed\n", "Thread #5: \t14100000 reads finished. 3377 secs passed\n", "Thread #6: \t14400000 reads finished. 3377 secs passed\n", "Thread #3: \t14500000 reads finished. 4843 secs passed\n", "Thread #7: \t14450000 reads finished. 4843 secs passed\n", "Thread #4: \t14550000 reads finished. 4844 secs passed\n", "Thread #0: \t14600000 reads finished. 4844 secs passed\n", "Thread #1: \t14650000 reads finished. 4844 secs passed\n", "Thread #5: \t14750000 reads finished. 4844 secs passed\n", "Thread #2: \t14700000 reads finished. 4844 secs passed\n", "Thread #6: \t14800000 reads finished. 4844 secs passed\n", "Thread #3: \t14800123 reads finished. 4859 secs passed\n", "Total number of aligned reads: 200983 (1.4%)\n", "Done.\n", "Finished at Wed Mar 4 15:33:28 2015\n", "Total time consumed: 4859 secs\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Volumes/web/nightingales/C_virginica/2112_lane1_NoIndex_L001_R1_002.fastq.gz \\\n", "-d /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapout_030415.sam \\\n", "-v 0.2 \\\n", "-g 1 \\\n", "-p 8" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Volumes/web/nightingales/C_virginica/2112_lane1_NoIndex_L001_R1_002.fastq.gz \\\n", "-d /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapout_030515.sam \\\n", "-v 20 \\\n", "-s 8 \\\n", "-g 3 \\\n", "-q 20 \\\n", "-p 8 \\\n", "2> /Users/sr320/data-genomic/tentacle/std-err-2112_Cv_LSU_bsmapout_030515" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [], "source": [ "!cp /Volumes/web-1/nightingales/C_virginica/2112_lane1_NoIndex_L001_R1_002.fastq.gz \\\n", "/Users/sr320/data-genomic/tentacle/2112_lane1_NoIndex_L001_R1_002.fastq.gz\n", "\n" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "BSMAP v2.74\n", "Start at: Sun Mar 8 08:10:40 2015\n", "\n", "Input reference file: /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \t(format: FASTA)\n", "Load in 7658 db seqs, total size 557717710 bp. 6 secs passed\n", "total_kmers: 43046721\n", "Create seed table. 18 secs passed\n", "max number of mismatches: read_length * 8% \tmax gap size: 3\n", "kmer cut-off ratio: 5e-07\n", "max multi-hits: 100\tmax Ns: 5\tseed size: 16\tindex interval: 4\n", "quality cutoff: 20\tbase quality char: '!'\n", "min fragment size:28\tmax fragemt size:500\n", "start from read #1\tend at read #4294967295\n", "additional alignment: T in reads => C in reference\n", "mapping strand: ++,-+\n", "Single-end alignment(8 threads)\n", "Input read file: /Users/sr320/data-genomic/tentacle/2112_lane1_NoIndex_L001_R1_002.fastq.gz \t(format: gzipped FASTQ)\n", "Output file: /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapout_030815.sam\t (format: SAM)\n", "Thread #4: \t100000 reads finished. 45 secs passed\n", "Thread #0: \t50000 reads finished. 45 secs passed\n", "Thread #1: \t200000 reads finished. 45 secs passed\n", "Thread #3: \t150000 reads finished. 45 secs passed\n", "Thread #2: \t300000 reads finished. 45 secs passed\n", "Thread #5: \t350000 reads finished. 45 secs passed\n", "Thread #6: \t250000 reads finished. 45 secs passed\n", "Thread #7: \t400000 reads finished. 46 secs passed\n", "Thread #6: \t750000 reads finished. 70 secs passed\n", "Thread #7: \t800000 reads finished. 71 secs passed\n", "Thread #4: \t450000 reads finished. 71 secs passed\n", "Thread #1: \t550000 reads finished. 71 secs passed\n", "Thread #5: \t700000 reads finished. 71 secs passed\n", "Thread #0: \t500000 reads finished. 71 secs passed\n", "Thread #3: \t600000 reads finished. 71 secs passed\n", "Thread #2: \t650000 reads finished. 72 secs passed\n", "Thread #6: \t850000 reads finished. 94 secs passed\n", "Thread #4: \t950000 reads finished. 95 secs passed\n", 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\t14650000 reads finished. 916 secs passed\n", "Thread #2: \t14600000 reads finished. 916 secs passed\n", "Thread #4: \t14750000 reads finished. 917 secs passed\n", "Thread #1: \t14800000 reads finished. 917 secs passed\n", "Thread #3: \t14700000 reads finished. 917 secs passed\n", "Thread #6: \t14850000 reads finished. 933 secs passed\n", "Thread #7: \t14900000 reads finished. 937 secs passed\n", "Thread #0: \t14950000 reads finished. 938 secs passed\n", "Thread #5: \t15000000 reads finished. 938 secs passed\n", "Thread #2: \t15050000 reads finished. 938 secs passed\n", "Thread #4: \t15100000 reads finished. 939 secs passed\n", "Thread #3: \t15200000 reads finished. 939 secs passed\n", "Thread #1: \t15150000 reads finished. 939 secs passed\n", "Thread #6: \t15250000 reads finished. 954 secs passed\n", "Thread #7: \t15300000 reads finished. 959 secs passed\n", "Thread #5: \t15400000 reads finished. 960 secs passed\n", "Thread #2: \t15450000 reads finished. 960 secs passed\n", "Thread #0: \t15350000 reads finished. 960 secs passed\n", "Thread #4: \t15500000 reads finished. 960 secs passed\n", "Thread #3: \t15550000 reads finished. 961 secs passed\n", "Thread #1: \t15600000 reads finished. 961 secs passed\n", "Thread #6: \t15650000 reads finished. 976 secs passed\n", "Thread #7: \t15700000 reads finished. 980 secs passed\n", "Thread #5: \t15750000 reads finished. 981 secs passed\n", "Thread #0: \t15850000 reads finished. 981 secs passed\n", "Thread #2: \t15800000 reads finished. 981 secs passed\n", "Thread #4: \t15900000 reads finished. 981 secs passed\n", "Thread #3: \t15950000 reads finished. 982 secs passed\n", "Thread #1: \t16000000 reads finished. 982 secs passed\n", "Total number of aligned reads: 79006 (0.49%)\n", "Done.\n", "Finished at Sun Mar 8 08:27:02 2015\n", "Total time consumed: 982 secs\n" ] } ], "source": [ "!/Applications/bioinfo/BSMAP/bsmap-2.74/bsmap \\\n", "-a /Users/sr320/data-genomic/tentacle/2112_lane1_NoIndex_L001_R1_002.fastq.gz \\\n", "-d /Users/sr320/data-genomic/tentacle/Crassostrea_gigas.GCA_000297895.1.22.dna_sm.genome.fa \\\n", "-o /Users/sr320/data-genomic/tentacle/2112_Cv_LSU_bsmapout_030815.sam \\\n", "-g 3 \\\n", "-q 20 \\\n", "-p 8 \n" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# convert fastq to fasta and chop up?" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }