{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Get the data" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/sr320/Documents/GitHub/nb-2021/O_lurida/data\n" ] } ], "source": [ "cd ../data" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [], "source": [ "ls" ] }, { "cell_type": "raw", "metadata": {}, "source": [ "wget -r \\\n", "--no-directories --no-parent \\\n", "--no-check-certificate \\\n", "-P . \\\n", "-A .fastq https://gannet.fish.washington.edu/generosa/O.lurida_QuantSeq2020/Trimmed/\n" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "34.trim.fastq 47.trim.fastq\n", "35.trim.fastq Olurida_v081-bowtie-index.1.bt2\n", "37.trim.fastq Olurida_v081-bowtie-index.2.bt2\n", "39.trim.fastq Olurida_v081-bowtie-index.3.bt2\n", "41.trim.fastq Olurida_v081-bowtie-index.4.bt2\n", "43.trim.fastq Olurida_v081-bowtie-index.rev.1.bt2\n", "44.trim.fastq Olurida_v081-bowtie-index.rev.2.bt2\n", "45.trim.fastq Olurida_v081.fa\n", "46.trim.fastq\n" ] } ], "source": [ "!ls" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Bowtie 2 version 2.3.5 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)\n", "Usage: \n", " bowtie2 [options]* -x {-1 -2 | -U | --interleaved } [-S ]\n", "\n", " Index filename prefix (minus trailing .X.bt2).\n", " NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.\n", " Files with #1 mates, paired with files in .\n", " Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).\n", " Files with #2 mates, paired with files in .\n", " Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).\n", " Files with unpaired reads.\n", " Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).\n", " Files with interleaved paired-end FASTQ/FASTA reads\n", " Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).\n", " File for SAM output (default: stdout)\n", "\n", " , , can be comma-separated lists (no whitespace) and can be\n", " specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.\n", "\n", "Options (defaults in parentheses):\n", "\n", " Input:\n", " -q query input files are FASTQ .fq/.fastq (default)\n", " --tab5 query input files are TAB5 .tab5\n", " --tab6 query input files are TAB6 .tab6\n", " --qseq query input files are in Illumina's qseq format\n", " -f query input files are (multi-)FASTA .fa/.mfa\n", " -r query input files are raw one-sequence-per-line\n", " -F k:,i: query input files are continuous FASTA where reads\n", " are substrings (k-mers) extracted from a FASTA file \n", " and aligned at offsets 1, 1+i, 1+2i ... end of reference\n", " -c , , are sequences themselves, not files\n", " -s/--skip skip the first reads/pairs in the input (none)\n", " -u/--upto stop after first reads/pairs (no limit)\n", " -5/--trim5 trim bases from 5'/left end of reads (0)\n", " -3/--trim3 trim bases from 3'/right end of reads (0)\n", " --trim-to [3:|5:] trim reads exceeding bases from either 3' or 5' end\n", " If the read end is not specified then it defaults to 3 (0)\n", " --phred33 qualities are Phred+33 (default)\n", " --phred64 qualities are Phred+64\n", " --int-quals qualities encoded as space-delimited integers\n", "\n", " Presets: Same as:\n", " For --end-to-end:\n", " --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50\n", " --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50\n", " --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)\n", " --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50\n", "\n", " For --local:\n", " --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00\n", " --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75\n", " --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)\n", " --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50\n", "\n", " Alignment:\n", " -N max # mismatches in seed alignment; can be 0 or 1 (0)\n", " -L length of seed substrings; must be >3, <32 (22)\n", " -i interval between seed substrings w/r/t read len (S,1,1.15)\n", " --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)\n", " --dpad include extra ref chars on sides of DP table (15)\n", " --gbar disallow gaps within nucs of read extremes (4)\n", " --ignore-quals treat all quality values as 30 on Phred scale (off)\n", " --nofw do not align forward (original) version of read (off)\n", " --norc do not align reverse-complement version of read (off)\n", " --no-1mm-upfront do not allow 1 mismatch alignments before attempting to\n", " scan for the optimal seeded alignments\n", " --end-to-end entire read must align; no clipping (on)\n", " OR\n", " --local local alignment; ends might be soft clipped (off)\n", "\n", " Scoring:\n", " --ma match bonus (0 for --end-to-end, 2 for --local) \n", " --mp max penalty for mismatch; lower qual = lower penalty (6)\n", " --np penalty for non-A/C/G/Ts in read/ref (1)\n", " --rdg , read gap open, extend penalties (5,3)\n", " --rfg , reference gap open, extend penalties (5,3)\n", " --score-min min acceptable alignment score w/r/t read length\n", " (G,20,8 for local, L,-0.6,-0.6 for end-to-end)\n", "\n", " Reporting:\n", " (default) look for multiple alignments, report best, with MAPQ\n", " OR\n", " -k report up to alns per read; MAPQ not meaningful\n", " OR\n", " -a/--all report all alignments; very slow, MAPQ not meaningful\n", "\n", " Effort:\n", " -D give up extending after failed extends in a row (15)\n", " -R for reads w/ repetitive seeds, try sets of seeds (2)\n", "\n", " Paired-end:\n", " -I/--minins minimum fragment length (0)\n", " -X/--maxins maximum fragment length (500)\n", " --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)\n", " --no-mixed suppress unpaired alignments for paired reads\n", " --no-discordant suppress discordant alignments for paired reads\n", " --dovetail concordant when mates extend past each other\n", " --no-contain not concordant when one mate alignment contains other\n", " --no-overlap not concordant when mates overlap at all\n", "\n", " Output:\n", " -t/--time print wall-clock time taken by search phases\n", " --un write unpaired reads that didn't align to \n", " --al write unpaired reads that aligned at least once to \n", " --un-conc write pairs that didn't align concordantly to \n", " --al-conc write pairs that aligned concordantly at least once to \n", " (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.\n", " --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.)\n", " --quiet print nothing to stderr except serious errors\n", " --met-file send metrics to file at (off)\n", " --met-stderr send metrics to stderr (off)\n", " --met report internal counters & metrics every secs (1)\n", " --no-unal suppress SAM records for unaligned reads\n", " --no-head suppress header lines, i.e. lines starting with @\n", " --no-sq suppress @SQ header lines\n", " --rg-id set read group id, reflected in @RG line and RG:Z: opt field\n", " --rg add (\"lab:value\") to @RG line of SAM header.\n", " Note: @RG line only printed when --rg-id is set.\n", " --omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.\n", " --sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace \n", " at the expense of generating non-standard SAM.\n", " --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.\n", " --soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN\n", "\n", " Performance:\n", " -p/--threads number of alignment threads to launch (1)\n", " --reorder force SAM output order to match order of input reads\n", " --mm use memory-mapped I/O for index; many 'bowtie's can share\n", "\n", " Other:\n", " --qc-filter filter out reads that are bad according to QSEQ filter\n", " --seed seed for random number generator (0)\n", " --non-deterministic seed rand. gen. arbitrarily instead of using read attributes\n", " --version print version information and quit\n", " -h/--help print this usage message\n" ] } ], "source": [ "!/Applications/bioinfo/bowtie2-235/bowtie2 -h\n", "\n" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "data": { "text/plain": [ "'/Users/sr320/Documents/GitHub/nb-2021/O_lurida/code'" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pwd" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "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 1090M 100 1090M 0 0 2226k 0 0:08:21 0:08:21 --:--:-- 2313k 0 2024k 0 0:09:11 0:00:15 0:08:56 2395k1:29 0:06:47 1934k0:06:43 1513k 0 2156k 0 0:08:37 0:01:58 0:06:39 1730k 0 0:08:38 0:02:02 0:06:36 2114k 0:08:38 0:02:04 0:06:34 2047k0 0:08:40 0:02:09 0:06:31 1989k81k 0 0:08:56 0:03:16 0:05:40 2185kk 0 0:08:32 0:04:13 0:04:19 2765k 2199k 0 0:08:27 0:04:29 0:03:58 2518k 0 0:08:26 0:04:35 0:03:51 2367k 0 2214k 0 0:08:24 0:06:01 0:02:23 2166k 2213k 0 0:08:24 0:06:13 0:02:11 2113k 0 0 2218k 0 0:08:23 0:06:22 0:02:01 2372k 0 0:08:23 0:06:23 0:02:00 2258k 2202k 0 0:08:26 0:07:01 0:01:25 2637kM 90 983M 0 0 2221k 0 0:08:22 0:07:33 0:00:49 2546k\n" ] } ], "source": [ "!curl http://owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081.fa > ../data/Olurida_v081.fa" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "!curl 156.trim.fastq 34.trim.fastq 43.trim.fastq Olurida_v081.fa\n", "137.trim.fastq 159.trim.fastq 35.trim.fastq 44.trim.fastq\n", "139.trim.fastq 161.trim.fastq 37.trim.fastq 45.trim.fastq\n", "140.trim.fastq 162.trim.fastq 39.trim.fastq 46.trim.fastq\n", "141.trim.fastq 168.trim.fastq 41.trim.fastq 47.trim.fastq\n" ] } ], "source": [ "!ls ../data/" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": true, "jupyter": { "outputs_hidden": true } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Settings:\n", " Output files: \"../data/Olurida_v081-bowtie-index.*.bt2\"\n", " Line rate: 6 (line is 64 bytes)\n", " Lines per side: 1 (side is 64 bytes)\n", " Offset rate: 4 (one in 16)\n", " FTable chars: 10\n", " Strings: unpacked\n", " Max bucket size: default\n", " Max bucket size, sqrt multiplier: default\n", " Max bucket size, len divisor: 32\n", " Difference-cover sample period: 1024\n", " Endianness: little\n", " Actual local endianness: little\n", " Sanity checking: disabled\n", " Assertions: disabled\n", " Random seed: 0\n", " Sizeofs: void*:8, int:4, long:8, size_t:8\n", "Input files DNA, FASTA:\n", " ../data/Olurida_v081.fa\n", "Building a SMALL index\n", "Reading reference sizes\n", " Time reading reference sizes: 00:00:09\n", "Calculating joined length\n", "Writing header\n", "Reserving space for joined string\n", "Joining reference sequences\n", " Time to join reference sequences: 00:00:05\n", "bmax according to bmaxDivN setting: 33664221\n", "Using parameters --bmax 25248166 --dcv 1024\n", " Doing ahead-of-time memory usage test\n", " Passed! Constructing with these parameters: --bmax 25248166 --dcv 1024\n", "Constructing suffix-array element generator\n", "Building DifferenceCoverSample\n", " Building sPrime\n", " Building sPrimeOrder\n", " V-Sorting samples\n", " V-Sorting samples time: 00:00:06\n", " Allocating rank array\n", " Ranking v-sort output\n", " Ranking v-sort output time: 00:00:04\n", " Invoking Larsson-Sadakane on ranks\n", " Invoking Larsson-Sadakane on ranks time: 00:00:06\n", " Sanity-checking and returning\n", "Building samples\n", "Reserving space for 86 sample suffixes\n", "Generating random suffixes\n", "QSorting 86 sample offsets, eliminating duplicates\n", "QSorting sample offsets, eliminating duplicates time: 00:00:00\n", "Multikey QSorting 86 samples\n", " (Using difference cover)\n", " Multikey QSorting samples time: 00:00:00\n", "Calculating bucket sizes\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Split 10, merged 41; iterating...\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Split 7, merged 3; iterating...\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Split 1, merged 2; iterating...\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Avg bucket size: 1.82586e+07 (target: 25248165)\n", "Converting suffix-array elements to index image\n", "Allocating ftab, absorbFtab\n", "Entering Ebwt loop\n", "Getting block 1 of 59\n", "Getting block 2 of 59\n", " Reserving size (25248166) for bucket 1\n", " Reserving size (25248166) for bucket 2\n", "Getting block 3 of 59\n", "Getting block 4 of 59\n", "Getting block 5 of 59\n", "Getting block 6 of 59\n", "Getting block 7 of 59\n", " Calculating Z arrays for bucket 1\n", " Calculating Z arrays for bucket 2\n", " Reserving size (25248166) for bucket 3\n", " Reserving size (25248166) for bucket 4\n", " Reserving size (25248166) for bucket 5\n", " Reserving size (25248166) for bucket 6\n", " Reserving size (25248166) for bucket 7\n", " Entering block accumulator loop for bucket 1:\n", " Calculating Z arrays for bucket 3\n", " Entering block accumulator loop for bucket 2:\n", " Calculating Z arrays for bucket 4\n", " Calculating Z arrays for bucket 5\n", " Calculating Z arrays for bucket 6\n", " Calculating Z arrays for bucket 7\n", " Entering block accumulator loop for bucket 3:\n", " Entering block accumulator loop for bucket 4:\n", " Entering block accumulator loop for bucket 5:\n", " Entering block accumulator loop for bucket 6:\n", " Entering block accumulator loop for bucket 7:\n", " bucket 1: 10%\n", " bucket 2: 10%\n", " bucket 3: 10%\n", " bucket 4: 10%\n", " bucket 6: 10%\n", " bucket 5: 10%\n", " bucket 7: 10%\n", " bucket 1: 20%\n", " bucket 2: 20%\n", " bucket 3: 20%\n", " bucket 4: 20%\n", " bucket 6: 20%\n", " bucket 5: 20%\n", " bucket 7: 20%\n", " bucket 1: 30%\n", " bucket 2: 30%\n", " bucket 3: 30%\n", " bucket 4: 30%\n", " bucket 6: 30%\n", " bucket 5: 30%\n", " bucket 7: 30%\n", " bucket 1: 40%\n", " bucket 2: 40%\n", " bucket 3: 40%\n", " bucket 4: 40%\n", " bucket 5: 40%\n", " bucket 6: 40%\n", " bucket 1: 50%\n", " bucket 7: 40%\n", " bucket 2: 50%\n", " bucket 3: 50%\n", " bucket 4: 50%\n", " bucket 5: 50%\n", " bucket 6: 50%\n", " bucket 1: 60%\n", " bucket 7: 50%\n", " bucket 2: 60%\n", " bucket 3: 60%\n", " bucket 4: 60%\n", " bucket 5: 60%\n", " bucket 1: 70%\n", " bucket 6: 60%\n", " bucket 2: 70%\n", " bucket 7: 60%\n", " bucket 3: 70%\n", " bucket 4: 70%\n", " bucket 1: 80%\n", " bucket 5: 70%\n", " bucket 6: 70%\n", " bucket 2: 80%\n", " bucket 3: 80%\n", " bucket 7: 70%\n", " bucket 1: 90%\n", " bucket 4: 80%\n", " bucket 5: 80%\n", " bucket 6: 80%\n", " bucket 2: 90%\n", " bucket 3: 90%\n", " bucket 1: 100%\n", " Sorting block of length 10546021 for bucket 1\n", " (Using difference cover)\n", " bucket 7: 80%\n", " bucket 4: 90%\n", " bucket 2: 100%\n", " Sorting block of length 17069038 for bucket 2\n", " (Using difference cover)\n", " bucket 6: 90%\n", " bucket 5: 90%\n", " bucket 3: 100%\n", " Sorting block of length 23992684 for bucket 3\n", " (Using difference cover)\n", " bucket 7: 90%\n", " bucket 4: 100%\n", " Sorting block of length 10615649 for bucket 4\n", " (Using difference cover)\n", " bucket 5: 100%\n", " Sorting block of length 25141453 for bucket 5\n", " (Using difference cover)\n", " bucket 6: 100%\n", " Sorting block of length 13738781 for bucket 6\n", " (Using difference cover)\n", " Sorting block time: 00:00:03\n", "Returning block of 10546022 for bucket 1\n", " bucket 7: 100%\n", " Sorting block of length 24015573 for bucket 7\n", " (Using difference cover)\n", "Getting block 8 of 59\n", " Reserving size (25248166) for bucket 8\n", " Calculating Z arrays for bucket 8\n", " Entering block accumulator loop for bucket 8:\n", " Sorting block time: 00:00:04\n", "Returning block of 10615650 for bucket 4\n", " bucket 8: 10%\n", "Getting block 9 of 59\n", " Reserving size (25248166) for bucket 9\n", " Calculating Z arrays for bucket 9\n", " Entering block accumulator loop for bucket 9:\n", " Sorting block time: 00:00:06\n", "Returning block of 17069039 for bucket 2\n", " Sorting block time: 00:00:04\n", "Returning block of 13738782 for bucket 6\n", "Getting block 10 of 59\n", " Reserving size (25248166) for bucket 10\n", " Calculating Z arrays for bucket 10\n", " Entering block accumulator loop for bucket 10:\n", "Getting block 11 of 59\n", " Reserving size (25248166) for bucket 11\n", " Calculating Z arrays for bucket 11\n", " Entering block accumulator loop for bucket 11:\n", " bucket 8: 20%\n", " bucket 9: 10%\n", " Sorting block time: 00:00:07\n", "Returning block of 23992685 for bucket 3\n", " bucket 10: 10%\n", " bucket 11: 10%\n", " Sorting block time: 00:00:07\n", "Returning block of 25141454 for bucket 5\n", " bucket 8: 30%\n", " bucket 9: 20%\n", "Getting block 12 of 59\n", " Reserving size (25248166) for bucket 12\n", " Calculating Z arrays for bucket 12\n", " Entering block accumulator loop for bucket 12:\n", " Sorting block time: 00:00:07\n", "Returning block of 24015574 for bucket 7\n", "Getting block 13 of 59\n", " Reserving size (25248166) for bucket 13\n", " Calculating Z arrays for bucket 13\n", " Entering block accumulator loop for bucket 13:\n", " bucket 10: 20%\n", " bucket 11: 20%\n", "Getting block 14 of 59\n", " Reserving size (25248166) for bucket 14\n", " Calculating Z arrays for bucket 14\n", " Entering block accumulator loop for bucket 14:\n", " bucket 8: 40%\n", " bucket 9: 30%\n", " bucket 12: 10%\n", " bucket 13: 10%\n", " bucket 10: 30%\n", " bucket 11: 30%\n", " bucket 8: 50%\n", " bucket 9: 40%\n", " bucket 14: 10%\n", " bucket 12: 20%\n", " bucket 13: 20%\n", " bucket 10: 40%\n", " bucket 11: 40%\n", " bucket 8: 60%\n", " bucket 9: 50%\n", " bucket 14: 20%\n", " bucket 12: 30%\n", " bucket 13: 30%\n", " bucket 11: 50%\n", " bucket 10: 50%\n", " bucket 8: 70%\n", " bucket 9: 60%\n", " bucket 14: 30%\n", " bucket 12: 40%\n", " bucket 13: 40%\n", " bucket 8: 80%\n", " bucket 11: 60%\n", " bucket 10: 60%\n", " bucket 9: 70%\n", " bucket 14: 40%\n", " bucket 12: 50%\n", " bucket 13: 50%\n", " bucket 8: 90%\n", " bucket 11: 70%\n", " bucket 9: 80%\n", " bucket 10: 70%\n", " bucket 14: 50%\n", " bucket 12: 60%\n", " bucket 8: 100%\n", " Sorting block of length 22581806 for bucket 8\n", " (Using difference cover)\n", " bucket 13: 60%\n", " bucket 11: 80%\n", " bucket 9: 90%\n", " bucket 10: 80%\n", " bucket 14: 60%\n", " bucket 12: 70%\n", " bucket 11: 90%\n", " bucket 13: 70%\n", " bucket 9: 100%\n", " Sorting block of length 17277554 for bucket 9\n", " (Using difference cover)\n", " bucket 10: 90%\n", " bucket 14: 70%\n", " bucket 12: 80%\n", " bucket 11: 100%\n", " Sorting block of length 6801184 for bucket 11\n", " (Using difference cover)\n", " bucket 13: 80%\n", " bucket 10: 100%\n", " Sorting block of length 22247097 for bucket 10\n", " (Using difference cover)\n", " bucket 12: 90%\n", " bucket 14: 80%\n", " bucket 13: 90%\n", " Sorting block time: 00:00:02\n", "Returning block of 6801185 for bucket 11\n", "Getting block 15 of 59\n", " Reserving size (25248166) for bucket 15\n", " Calculating Z arrays for bucket 15\n", " Entering block accumulator loop for bucket 15:\n", " Sorting block time: 00:00:05\n", "Returning block of 22581807 for bucket 8\n", " bucket 12: 100%\n", " Sorting block of length 18775712 for bucket 12\n", " (Using difference cover)\n", " bucket 14: 90%\n", "Getting block 16 of 59\n", " Reserving size (25248166) for bucket 16\n", " Calculating Z arrays for bucket 16\n", " Entering block accumulator loop for bucket 16:\n", " Sorting block time: 00:00:04\n", "Returning block of 17277555 for bucket 9\n", " bucket 13: 100%\n", " Sorting block of length 14196298 for bucket 13\n", " (Using difference cover)\n", "Getting block 17 of 59\n", " Reserving size (25248166) for bucket 17\n", " Calculating Z arrays for bucket 17\n", " Entering block accumulator loop for bucket 17:\n", " bucket 15: 10%\n", " bucket 14: 100%\n", " Sorting block of length 21943106 for bucket 14\n", " (Using difference cover)\n", " bucket 16: 10%\n", " Sorting block time: 00:00:07\n", "Returning block of 22247098 for bucket 10\n", " bucket 15: 20%\n", " bucket 17: 10%\n", "Getting block 18 of 59\n", " Reserving size (25248166) for bucket 18\n", " Calculating Z arrays for bucket 18\n", " Entering block accumulator loop for bucket 18:\n", " Sorting block time: 00:00:04\n", "Returning block of 14196299 for bucket 13\n", " Sorting block time: 00:00:05\n", "Returning block of 18775713 for bucket 12\n", " bucket 16: 20%\n", "Getting block 19 of 59\n", " Reserving size (25248166) for bucket 19\n", " Calculating Z arrays for bucket 19\n", " Entering block accumulator loop for bucket 19:\n", "Getting block 20 of 59\n", " Reserving size (25248166) for bucket 20\n", " Calculating Z arrays for bucket 20\n", " Entering block accumulator loop for bucket 20:\n", " bucket 15: 30%\n", " bucket 17: 20%\n", " bucket 18: 10%\n", " bucket 16: 30%\n", " Sorting block time: 00:00:06\n", "Returning block of 21943107 for bucket 14\n", " bucket 19: 10%\n", " bucket 20: 10%\n", " bucket 15: 40%\n", " bucket 17: 30%\n", "Getting block 21 of 59\n", " Reserving size (25248166) for bucket 21\n", " Calculating Z arrays for bucket 21\n", " Entering block accumulator loop for bucket 21:\n", " bucket 18: 20%\n", " bucket 16: 40%\n", " bucket 20: 20%\n", " bucket 19: 20%\n", " bucket 15: 50%\n", " bucket 21: 10%\n", " bucket 17: 40%\n", " bucket 18: 30%\n", " bucket 16: 50%\n", " bucket 20: 30%\n", " bucket 15: 60%\n", " bucket 19: 30%\n", " bucket 17: 50%\n", " bucket 21: 20%\n", " bucket 18: 40%\n", " bucket 16: 60%\n", " bucket 20: 40%\n", " bucket 15: 70%\n", " bucket 21: 30%\n", " bucket 19: 40%\n", " bucket 17: 60%\n", " bucket 16: 70%\n", " bucket 18: 50%\n", " bucket 15: 80%\n", " bucket 20: 50%\n", " bucket 21: 40%\n", " bucket 17: 70%\n", " bucket 19: 50%\n", " bucket 16: 80%\n", " bucket 15: 90%\n", " bucket 20: 60%\n", " bucket 18: 60%\n", " bucket 21: 50%\n", " bucket 17: 80%\n", " bucket 19: 60%\n", " bucket 16: 90%\n", " bucket 20: 70%\n", " bucket 15: 100%\n", " Sorting block of length 19906911 for bucket 15\n", " (Using difference cover)\n", " bucket 18: 70%\n", " bucket 21: 60%\n", " bucket 17: 90%\n", " bucket 19: 70%\n", " bucket 16: 100%\n", " Sorting block of length 22116162 for bucket 16\n", " (Using difference cover)\n", " bucket 20: 80%\n", " bucket 18: 80%\n", " bucket 21: 70%\n", " bucket 17: 100%\n", " Sorting block of length 24966571 for bucket 17\n", " (Using difference cover)\n", " bucket 19: 80%\n", " bucket 20: 90%\n", " bucket 18: 90%\n", " bucket 21: 80%\n", " Sorting block time: 00:00:05\n", "Returning block of 19906912 for bucket 15\n", " bucket 20: 100%\n", " Sorting block of length 11930681 for bucket 20\n", " (Using difference cover)\n", " bucket 19: 90%\n", " bucket 18: 100%\n", " Sorting block of length 24850666 for bucket 18\n", " (Using difference cover)\n", "Getting block 22 of 59\n", " Reserving size (25248166) for bucket 22\n", " Calculating Z arrays for bucket 22\n", " Entering block accumulator loop for bucket 22:\n", " bucket 21: 90%\n", " Sorting block time: 00:00:06\n", "Returning block of 22116163 for bucket 16\n", " bucket 19: 100%\n", " Sorting block of length 21722129 for bucket 19\n", " (Using difference cover)\n", " bucket 22: 10%\n", "Getting block 23 of 59\n", " Reserving size (25248166) for bucket 23\n", " Calculating Z arrays for bucket 23\n", " Entering block accumulator loop for bucket 23:\n", " Sorting block time: 00:00:03\n", "Returning block of 11930682 for bucket 20\n", " bucket 21: 100%\n", " Sorting block of length 20971416 for bucket 21\n", " (Using difference cover)\n", "Getting block 24 of 59\n", " Reserving size (25248166) for bucket 24\n", " Calculating Z arrays for bucket 24\n", " Entering block accumulator loop for bucket 24:\n", " Sorting block time: 00:00:07\n", "Returning block of 24966572 for bucket 17\n", "Getting block 25 of 59\n", " Reserving size (25248166) for bucket 25\n", " Calculating Z arrays for bucket 25\n", " Entering block accumulator loop for bucket 25:\n", " bucket 22: 20%\n", " bucket 23: 10%\n", " bucket 24: 10%\n", " Sorting block time: 00:00:07\n", "Returning block of 24850667 for bucket 18\n", " bucket 23: 20%\n", " bucket 22: 30%\n", " bucket 25: 10%\n", "Getting block 26 of 59\n", " Reserving size (25248166) for bucket 26\n", " Calculating Z arrays for bucket 26\n", " Entering block accumulator loop for bucket 26:\n", " Sorting block time: 00:00:06\n", "Returning block of 21722130 for bucket 19\n", " bucket 24: 20%\n", " Sorting block time: 00:00:06\n", "Returning block of 20971417 for bucket 21\n", "Getting block 27 of 59\n", " Reserving size (25248166) for bucket 27\n", " Calculating Z arrays for bucket 27\n", " Entering block accumulator loop for bucket 27:\n", "Getting block 28 of 59\n", " Reserving size (25248166) for bucket 28\n", " Calculating Z arrays for bucket 28\n", " Entering block accumulator loop for bucket 28:\n", " bucket 25: 20%\n", " bucket 22: 40%\n", " bucket 23: 30%\n", " bucket 26: 10%\n", " bucket 24: 30%\n", " bucket 27: 10%\n", " bucket 28: 10%\n", " bucket 25: 30%\n", " bucket 23: 40%\n", " bucket 22: 50%\n", " bucket 26: 20%\n", " bucket 24: 40%\n", " bucket 27: 20%\n", " bucket 28: 20%\n", " bucket 23: 50%\n", " bucket 25: 40%\n", " bucket 22: 60%\n", " bucket 26: 30%\n", " bucket 24: 50%\n", " bucket 27: 30%\n", " bucket 28: 30%\n", " bucket 23: 60%\n", " bucket 25: 50%\n", " bucket 22: 70%\n", " bucket 24: 60%\n", " bucket 26: 40%\n", " bucket 27: 40%\n", " bucket 23: 70%\n", " bucket 28: 40%\n", " bucket 25: 60%\n", " bucket 24: 70%\n", " bucket 22: 80%\n", " bucket 26: 50%\n", " bucket 27: 50%\n", " bucket 23: 80%\n", " bucket 25: 70%\n", " bucket 28: 50%\n", " bucket 24: 80%\n", " bucket 22: 90%\n", " bucket 26: 60%\n", " bucket 27: 60%\n", " bucket 23: 90%\n", " bucket 25: 80%\n", " bucket 28: 60%\n", " bucket 22: 100%\n", " Sorting block of length 17486475 for bucket 22\n", " (Using difference cover)\n", " bucket 24: 90%\n", " bucket 26: 70%\n", " bucket 23: 100%\n", " Sorting block of length 24394510 for bucket 23\n", " (Using difference cover)\n", " bucket 27: 70%\n", " bucket 25: 90%\n", " bucket 28: 70%\n", " bucket 24: 100%\n", " Sorting block of length 22064542 for bucket 24\n", " (Using difference cover)\n", " bucket 26: 80%\n", " bucket 27: 80%\n", " bucket 25: 100%\n", " Sorting block of length 23791711 for bucket 25\n", " (Using difference cover)\n", " bucket 28: 80%\n", " bucket 26: 90%\n", " Sorting block time: 00:00:04\n", "Returning block of 17486476 for bucket 22\n", "Getting block 29 of 59\n", " Reserving size (25248166) for bucket 29\n", " Calculating Z arrays for bucket 29\n", " Entering block accumulator loop for bucket 29:\n", " bucket 27: 90%\n", " bucket 26: 100%\n", " Sorting block of length 21414401 for bucket 26\n", " (Using difference cover)\n", " bucket 28: 90%\n", " bucket 27: 100%\n", " Sorting block of length 15146305 for bucket 27\n", " (Using difference cover)\n", " bucket 29: 10%\n", " Sorting block time: 00:00:07\n", "Returning block of 24394511 for bucket 23\n", " Sorting block time: 00:00:06\n", "Returning block of 22064543 for bucket 24\n", " bucket 28: 100%\n", " Sorting block of length 11081348 for bucket 28\n", " (Using difference cover)\n", "Getting block 30 of 59\n", " Reserving size (25248166) for bucket 30\n", " Calculating Z arrays for bucket 30\n", " Entering block accumulator loop for bucket 30:\n", "Getting block 31 of 59\n", " Reserving size (25248166) for bucket 31\n", " Calculating Z arrays for bucket 31\n", " Entering block accumulator loop for bucket 31:\n", " bucket 29: 20%\n", " Sorting block time: 00:00:07\n", "Returning block of 23791712 for bucket 25\n", " bucket 31: 10%\n", " bucket 30: 10%\n", "Getting block 32 of 59\n", " Reserving size (25248166) for bucket 32\n", " Calculating Z arrays for bucket 32\n", " Entering block accumulator loop for bucket 32:\n", " Sorting block time: 00:00:04\n", "Returning block of 15146306 for bucket 27\n", " Sorting block time: 00:00:03\n", "Returning block of 11081349 for bucket 28\n", " Sorting block time: 00:00:06\n", "Returning block of 21414402 for bucket 26\n", "Getting block 33 of 59\n", " Reserving size (25248166) for bucket 33\n", " Calculating Z arrays for bucket 33\n", " Entering block accumulator loop for bucket 33:\n", "Getting block 34 of 59\n", " Reserving size (25248166) for bucket 34\n", " Calculating Z arrays for bucket 34\n", " Entering block accumulator loop for bucket 34:\n", "Getting block 35 of 59\n", " Reserving size (25248166) for bucket 35\n", " Calculating Z arrays for bucket 35\n", " Entering block accumulator loop for bucket 35:\n", " bucket 29: 30%\n", " bucket 30: 20%\n", " bucket 31: 20%\n", " bucket 32: 10%\n", " bucket 33: 10%\n", " bucket 34: 10%\n", " bucket 35: 10%\n", " bucket 29: 40%\n", " bucket 30: 30%\n", " bucket 31: 30%\n", " bucket 32: 20%\n", " bucket 33: 20%\n", " bucket 34: 20%\n", " bucket 35: 20%\n", " bucket 30: 40%\n", " bucket 29: 50%\n", " bucket 31: 40%\n", " bucket 32: 30%\n", " bucket 33: 30%\n", " bucket 34: 30%\n", " bucket 35: 30%\n", " bucket 30: 50%\n", " bucket 29: 60%\n", " bucket 31: 50%\n", " bucket 33: 40%\n", " bucket 32: 40%\n", " bucket 35: 40%\n", " bucket 34: 40%\n", " bucket 30: 60%\n", " bucket 31: 60%\n", " bucket 33: 50%\n", " bucket 29: 70%\n", " bucket 32: 50%\n", " bucket 35: 50%\n", " bucket 34: 50%\n", " bucket 30: 70%\n", " bucket 31: 70%\n", " bucket 33: 60%\n", " bucket 32: 60%\n", " bucket 35: 60%\n", " bucket 29: 80%\n", " bucket 34: 60%\n", " bucket 30: 80%\n", " bucket 31: 80%\n", " bucket 33: 70%\n", " bucket 32: 70%\n", " bucket 35: 70%\n", " bucket 29: 90%\n", " bucket 34: 70%\n", " bucket 30: 90%\n", " bucket 31: 90%\n", " bucket 33: 80%\n", " bucket 32: 80%\n", " bucket 35: 80%\n", " bucket 34: 80%\n", " bucket 29: 100%\n", " Sorting block of length 21516020 for bucket 29\n", " (Using difference cover)\n", " bucket 30: 100%\n", " Sorting block of length 9933788 for bucket 30\n", " (Using difference cover)\n", " bucket 31: 100%\n", " Sorting block of length 24998546 for bucket 31\n", " (Using difference cover)\n", " bucket 33: 90%\n", " bucket 35: 90%\n", " bucket 32: 90%\n", " bucket 34: 90%\n", " Sorting block time: 00:00:02\n", "Returning block of 9933789 for bucket 30\n", " bucket 33: 100%\n", " Sorting block of length 8343621 for bucket 33\n", " (Using difference cover)\n", "Getting block 36 of 59\n", " Reserving size (25248166) for bucket 36\n", " Calculating Z arrays for bucket 36\n", " Entering block accumulator loop for bucket 36:\n", " bucket 35: 100%\n", " Sorting block of length 11260437 for bucket 35\n", " (Using difference cover)\n", " bucket 32: 100%\n", " Sorting block of length 22409734 for bucket 32\n", " (Using difference cover)\n", " bucket 34: 100%\n", " Sorting block of length 19972565 for bucket 34\n", " (Using difference cover)\n", " bucket 36: 10%\n", " Sorting block time: 00:00:03\n", "Returning block of 8343622 for bucket 33\n", "Getting block 37 of 59\n", " Reserving size (25248166) for bucket 37\n", " Calculating Z arrays for bucket 37\n", " Entering block accumulator loop for bucket 37:\n", " Sorting block time: 00:00:06\n", "Returning block of 21516021 for bucket 29\n", " Sorting block time: 00:00:03\n", "Returning block of 11260438 for bucket 35\n", "Getting block 38 of 59\n", " Reserving size (25248166) for bucket 38\n", " Calculating Z arrays for bucket 38\n", " Entering block accumulator loop for bucket 38:\n", " bucket 36: 20%\n", "Getting block 39 of 59\n", " Reserving size (25248166) for bucket 39\n", " Calculating Z arrays for bucket 39\n", " Entering block accumulator loop for bucket 39:\n", " Sorting block time: 00:00:07\n", "Returning block of 24998547 for bucket 31\n", " bucket 37: 10%\n", "Getting block 40 of 59\n", " Reserving size (25248166) for bucket 40\n", " Calculating Z arrays for bucket 40\n", " Entering block accumulator loop for bucket 40:\n", " Sorting block time: 00:00:06\n", "Returning block of 19972566 for bucket 34\n", " bucket 38: 10%\n", " bucket 36: 30%\n", " Sorting block time: 00:00:06\n", "Returning block of 22409735 for bucket 32\n", "Getting block 41 of 59\n", " Reserving size (25248166) for bucket 41\n", " Calculating Z arrays for bucket 41\n", " Entering block accumulator loop for bucket 41:\n", " bucket 39: 10%\n", "Getting block 42 of 59\n", " Reserving size (25248166) for bucket 42\n", " Calculating Z arrays for bucket 42\n", " Entering block accumulator loop for bucket 42:\n", " bucket 37: 20%\n", " bucket 40: 10%\n", " bucket 38: 20%\n", " bucket 36: 40%\n", " bucket 41: 10%\n", " bucket 39: 20%\n", " bucket 42: 10%\n", " bucket 37: 30%\n", " bucket 36: 50%\n", " bucket 38: 30%\n", " bucket 40: 20%\n", " bucket 39: 30%\n", " bucket 41: 20%\n", " bucket 37: 40%\n", " bucket 42: 20%\n", " bucket 36: 60%\n", " bucket 38: 40%\n", " bucket 40: 30%\n", " bucket 39: 40%\n", " bucket 41: 30%\n", " bucket 37: 50%\n", " bucket 42: 30%\n", " bucket 36: 70%\n", " bucket 38: 50%\n", " bucket 39: 50%\n", " bucket 41: 40%\n", " bucket 40: 40%\n", " bucket 37: 60%\n", " bucket 42: 40%\n", " bucket 36: 80%\n", " bucket 38: 60%\n", " bucket 39: 60%\n", " bucket 37: 70%\n", " bucket 41: 50%\n", " bucket 42: 50%\n", " bucket 40: 50%\n", " bucket 36: 90%\n", " bucket 38: 70%\n", " bucket 39: 70%\n", " bucket 37: 80%\n", " bucket 41: 60%\n", " bucket 42: 60%\n", " bucket 40: 60%\n", " bucket 36: 100%\n", " Sorting block of length 21333788 for bucket 36\n", " (Using difference cover)\n", " bucket 38: 80%\n", " bucket 39: 80%\n", " bucket 37: 90%\n", " bucket 42: 70%\n", " bucket 41: 70%\n", " bucket 40: 70%\n", " bucket 38: 90%\n", " bucket 39: 90%\n", " bucket 37: 100%\n", " Sorting block of length 15645687 for bucket 37\n", " (Using difference cover)\n", " bucket 42: 80%\n", " bucket 41: 80%\n", " bucket 38: 100%\n", " Sorting block of length 10973099 for bucket 38\n", " (Using difference cover)\n", " bucket 40: 80%\n", " Sorting block time: 00:00:05\n", "Returning block of 21333789 for bucket 36\n", " bucket 39: 100%\n", " Sorting block of length 23397444 for bucket 39\n", " (Using difference cover)\n", " bucket 41: 90%\n", " bucket 42: 90%\n", "Getting block 43 of 59\n", " Reserving size (25248166) for bucket 43\n", " Calculating Z arrays for bucket 43\n", " Entering block accumulator loop for bucket 43:\n", " bucket 40: 90%\n", " Sorting block time: 00:00:03\n", "Returning block of 10973100 for bucket 38\n", " Sorting block time: 00:00:04\n", "Returning block of 15645688 for bucket 37\n", "Getting block 44 of 59\n", " Reserving size (25248166) for bucket 44\n", " Calculating Z arrays for bucket 44\n", " Entering block accumulator loop for bucket 44:\n", "Getting block 45 of 59\n", " Reserving size (25248166) for bucket 45\n", " Calculating Z arrays for bucket 45\n", " Entering block accumulator loop for bucket 45:\n", " bucket 42: 100%\n", " Sorting block of length 17693709 for bucket 42\n", " (Using difference cover)\n", " bucket 43: 10%\n", " bucket 41: 100%\n", " Sorting block of length 18460410 for bucket 41\n", " (Using difference cover)\n", " bucket 40: 100%\n", " Sorting block of length 15383856 for bucket 40\n", " (Using difference cover)\n", " bucket 44: 10%\n", " bucket 43: 20%\n", " bucket 45: 10%\n", " Sorting block time: 00:00:06\n", "Returning block of 23397445 for bucket 39\n", "Getting block 46 of 59\n", " Reserving size (25248166) for bucket 46\n", " Calculating Z arrays for bucket 46\n", " Entering block accumulator loop for bucket 46:\n", " bucket 44: 20%\n", " Sorting block time: 00:00:05\n", "Returning block of 17693710 for bucket 42\n", " Sorting block time: 00:00:05\n", "Returning block of 18460411 for bucket 41\n", " bucket 43: 30%\n", " bucket 45: 20%\n", " Sorting block time: 00:00:05\n", "Returning block of 15383857 for bucket 40\n", "Getting block 47 of 59\n", " Reserving size (25248166) for bucket 47\n", " Calculating Z arrays for bucket 47\n", " Entering block accumulator loop for bucket 47:\n", "Getting block 48 of 59\n", " Reserving size (25248166) for bucket 48\n", " Calculating Z arrays for bucket 48\n", " Entering block accumulator loop for bucket 48:\n", "Getting block 49 of 59\n", " Reserving size (25248166) for bucket 49\n", " Calculating Z arrays for bucket 49\n", " Entering block accumulator loop for bucket 49:\n", " bucket 46: 10%\n", " bucket 44: 30%\n", " bucket 43: 40%\n", " bucket 45: 30%\n", " bucket 48: 10%\n", " bucket 47: 10%\n", " bucket 49: 10%\n", " bucket 44: 40%\n", " bucket 46: 20%\n", " bucket 43: 50%\n", " bucket 45: 40%\n", " bucket 47: 20%\n", " bucket 48: 20%\n", " bucket 49: 20%\n", " bucket 44: 50%\n", " bucket 46: 30%\n", " bucket 43: 60%\n", " bucket 45: 50%\n", " bucket 47: 30%\n", " bucket 48: 30%\n", " bucket 49: 30%\n", " bucket 44: 60%\n", " bucket 46: 40%\n", " bucket 43: 70%\n", " bucket 45: 60%\n", " bucket 47: 40%\n", " bucket 48: 40%\n", " bucket 49: 40%\n", " bucket 44: 70%\n", " bucket 46: 50%\n", " bucket 43: 80%\n", " bucket 45: 70%\n", " bucket 47: 50%\n", " bucket 48: 50%\n", " bucket 44: 80%\n", " bucket 49: 50%\n", " bucket 46: 60%\n", " bucket 43: 90%\n", " bucket 45: 80%\n", " bucket 47: 60%\n", " bucket 44: 90%\n", " bucket 48: 60%\n", " bucket 49: 60%\n", " bucket 46: 70%\n", " bucket 43: 100%\n", " Sorting block of length 23716207 for bucket 43\n", " (Using difference cover)\n", " bucket 45: 90%\n", " bucket 44: 100%\n", " Sorting block of length 10821533 for bucket 44\n", " (Using difference cover)\n", " bucket 47: 70%\n", " bucket 48: 70%\n", " bucket 49: 70%\n", " bucket 46: 80%\n", " bucket 45: 100%\n", " Sorting block of length 20554306 for bucket 45\n", " (Using difference cover)\n", " bucket 47: 80%\n", " bucket 49: 80%\n", " bucket 48: 80%\n", " Sorting block time: 00:00:03\n", "Returning block of 10821534 for bucket 44\n", " bucket 46: 90%\n", "Getting block 50 of 59\n", " Reserving size (25248166) for bucket 50\n", " Calculating Z arrays for bucket 50\n", " Entering block accumulator loop for bucket 50:\n", " bucket 47: 90%\n", " bucket 49: 90%\n", " bucket 48: 90%\n", " bucket 46: 100%\n", " Sorting block of length 7815363 for bucket 46\n", " (Using difference cover)\n", " Sorting block time: 00:00:06\n", "Returning block of 23716208 for bucket 43\n", " bucket 50: 10%\n", "Getting block 51 of 59\n", " Reserving size (25248166) for bucket 51\n", " Calculating Z arrays for bucket 51\n", " Entering block accumulator loop for bucket 51:\n", " bucket 47: 100%\n", " Sorting block of length 21977571 for bucket 47\n", " (Using difference cover)\n", " Sorting block time: 00:00:02\n", "Returning block of 7815364 for bucket 46\n", " bucket 49: 100%\n", " Sorting block of length 21076245 for bucket 49\n", " (Using difference cover)\n", " bucket 48: 100%\n", " Sorting block of length 24859881 for bucket 48\n", " (Using difference cover)\n", " Sorting block time: 00:00:05\n", "Returning block of 20554307 for bucket 45\n", "Getting block 52 of 59\n", " Reserving size (25248166) for bucket 52\n", " Calculating Z arrays for bucket 52\n", " Entering block accumulator loop for bucket 52:\n", " bucket 50: 20%\n", "Getting block 53 of 59\n", " Reserving size (25248166) for bucket 53\n", " Calculating Z arrays for bucket 53\n", " Entering block accumulator loop for bucket 53:\n", " bucket 51: 10%\n", " bucket 52: 10%\n", " bucket 50: 30%\n", " bucket 53: 10%\n", " bucket 51: 20%\n", " Sorting block time: 00:00:07\n", "Returning block of 21977572 for bucket 47\n", " Sorting block time: 00:00:07\n", "Returning block of 21076246 for bucket 49\n", " bucket 52: 20%\n", " bucket 50: 40%\n", " bucket 53: 20%\n", "Getting block 54 of 59\n", " Reserving size (25248166) for bucket 54\n", " Calculating Z arrays for bucket 54\n", " Entering block accumulator loop for bucket 54:\n", "Getting block 55 of 59\n", " Reserving size (25248166) for bucket 55\n", " Calculating Z arrays for bucket 55\n", " Entering block accumulator loop for bucket 55:\n", " Sorting block time: 00:00:08\n", "Returning block of 24859882 for bucket 48\n", " bucket 51: 30%\n", "Getting block 56 of 59\n", " Reserving size (25248166) for bucket 56\n", " Calculating Z arrays for bucket 56\n", " Entering block accumulator loop for bucket 56:\n", " bucket 52: 30%\n", " bucket 50: 50%\n", " bucket 53: 30%\n", " bucket 54: 10%\n", " bucket 55: 10%\n", " bucket 51: 40%\n", " bucket 56: 10%\n", " bucket 52: 40%\n", " bucket 50: 60%\n", " bucket 53: 40%\n", " bucket 54: 20%\n", " bucket 55: 20%\n", " bucket 51: 50%\n", " bucket 56: 20%\n", " bucket 52: 50%\n", " bucket 50: 70%\n", " bucket 54: 30%\n", " bucket 53: 50%\n", " bucket 55: 30%\n", " bucket 51: 60%\n", " bucket 56: 30%\n", " bucket 52: 60%\n", " bucket 50: 80%\n", " bucket 54: 40%\n", " bucket 53: 60%\n", " bucket 55: 40%\n", " bucket 51: 70%\n", " bucket 56: 40%\n", " bucket 52: 70%\n", " bucket 50: 90%\n", " bucket 54: 50%\n", " bucket 53: 70%\n", " bucket 55: 50%\n", " bucket 56: 50%\n", " bucket 51: 80%\n", " bucket 52: 80%\n", " bucket 50: 100%\n", " Sorting block of length 12117388 for bucket 50\n", " (Using difference cover)\n", " bucket 54: 60%\n", " bucket 53: 80%\n", " bucket 55: 60%\n", " bucket 56: 60%\n", " bucket 51: 90%\n", " bucket 52: 90%\n", " bucket 54: 70%\n", " bucket 53: 90%\n", " bucket 55: 70%\n", " Sorting block time: 00:00:03\n", "Returning block of 12117389 for bucket 50\n", " bucket 56: 70%\n", " bucket 51: 100%\n", " Sorting block of length 20042929 for bucket 51\n", " (Using difference cover)\n", "Getting block 57 of 59\n", " Reserving size (25248166) for bucket 57\n", " Calculating Z arrays for bucket 57\n", " Entering block accumulator loop for bucket 57:\n", " bucket 52: 100%\n", " Sorting block of length 12185793 for bucket 52\n", " (Using difference cover)\n", " bucket 54: 80%\n", " bucket 53: 100%\n", " Sorting block of length 25037652 for bucket 53\n", " (Using difference cover)\n", " bucket 55: 80%\n", " bucket 56: 80%\n", " bucket 57: 10%\n", " Sorting block time: 00:00:03\n", "Returning block of 12185794 for bucket 52\n", " bucket 54: 90%\n", "Getting block 58 of 59\n", " Reserving size (25248166) for bucket 58\n", " Calculating Z arrays for bucket 58\n", " Entering block accumulator loop for bucket 58:\n", " bucket 55: 90%\n", " bucket 56: 90%\n", " bucket 57: 20%\n", " Sorting block time: 00:00:05\n", "Returning block of 20042930 for bucket 51\n", " bucket 54: 100%\n", " Sorting block of length 13367001 for bucket 54\n", " (Using difference cover)\n", " bucket 58: 10%\n", " bucket 55: 100%\n", " Sorting block of length 20956898 for bucket 55\n", " (Using difference cover)\n", "Getting block 59 of 59\n", " Reserving size (25248166) for bucket 59\n", " Calculating Z arrays for bucket 59\n", " Entering block accumulator loop for bucket 59:\n", " bucket 56: 100%\n", " Sorting block of length 7524981 for bucket 56\n", " (Using difference cover)\n", " bucket 57: 30%\n", " bucket 59: 10%\n", " Sorting block time: 00:00:07\n", "Returning block of 25037653 for bucket 53\n", " bucket 58: 20%\n", " Sorting block time: 00:00:02\n", "Returning block of 7524982 for bucket 56\n", " Sorting block time: 00:00:04\n", "Returning block of 13367002 for bucket 54\n", " bucket 59: 20%\n", " bucket 57: 40%\n", " bucket 59: 30%\n", " bucket 58: 30%\n", " Sorting block time: 00:00:06\n", "Returning block of 20956899 for bucket 55\n", " bucket 57: 50%\n", " bucket 59: 40%\n", " bucket 58: 40%\n", " bucket 59: 50%\n", " bucket 57: 60%\n", " bucket 59: 60%\n", " bucket 58: 50%\n", " bucket 57: 70%\n", " bucket 59: 70%\n", " bucket 58: 60%\n", " bucket 59: 80%\n", " bucket 57: 80%\n", " bucket 58: 70%\n", " bucket 59: 90%\n", " bucket 57: 90%\n", " bucket 59: 100%\n", " Sorting block of length 24028122 for bucket 59\n", " (Using difference cover)\n", " bucket 58: 80%\n", " bucket 57: 100%\n", " Sorting block of length 23089971 for bucket 57\n", " (Using difference cover)\n", " bucket 58: 90%\n", " bucket 58: 100%\n", " Sorting block of length 15974712 for bucket 58\n", " (Using difference cover)\n", " Sorting block time: 00:00:04\n", "Returning block of 24028123 for bucket 59\n", " Sorting block time: 00:00:04\n", "Returning block of 23089972 for bucket 57\n", " Sorting block time: 00:00:03\n", "Returning block of 15974713 for bucket 58\n", "Exited Ebwt loop\n", "fchr[A]: 0\n", "fchr[C]: 341519526\n", "fchr[G]: 538577822\n", "fchr[T]: 735626959\n", "fchr[$]: 1077255099\n", "Exiting Ebwt::buildToDisk()\n", "Returning from initFromVector\n", "Wrote 371984998 bytes to primary EBWT file: ../data/Olurida_v081-bowtie-index.1.bt2\n", "Wrote 269313780 bytes to secondary EBWT file: ../data/Olurida_v081-bowtie-index.2.bt2\n", "Re-opening _in1 and _in2 as input streams\n", "Returning from Ebwt constructor\n", "Headers:\n", " len: 1077255099\n", " bwtLen: 1077255100\n", " sz: 269313775\n", " bwtSz: 269313775\n", " lineRate: 6\n", " offRate: 4\n", " offMask: 0xfffffff0\n", " ftabChars: 10\n", " eftabLen: 20\n", " eftabSz: 80\n", " ftabLen: 1048577\n", " ftabSz: 4194308\n", " offsLen: 67328444\n", " offsSz: 269313776\n", " lineSz: 64\n", " sideSz: 64\n", " sideBwtSz: 48\n", " sideBwtLen: 192\n", " numSides: 5610704\n", " numLines: 5610704\n", " ebwtTotLen: 359085056\n", " ebwtTotSz: 359085056\n", " color: 0\n", " reverse: 0\n", "Total time for call to driver() for forward index: 00:05:17\n", "Reading reference sizes\n", " Time reading reference sizes: 00:00:05\n", "Calculating joined length\n", "Writing header\n", "Reserving space for joined string\n", "Joining reference sequences\n", " Time to join reference sequences: 00:00:05\n", " Time to reverse reference sequence: 00:00:00\n", "bmax according to bmaxDivN setting: 33664221\n", "Using parameters --bmax 25248166 --dcv 1024\n", " Doing ahead-of-time memory usage test\n", " Passed! Constructing with these parameters: --bmax 25248166 --dcv 1024\n", "Constructing suffix-array element generator\n", "Building DifferenceCoverSample\n", " Building sPrime\n", " Building sPrimeOrder\n", " V-Sorting samples\n", " V-Sorting samples time: 00:00:07\n", " Allocating rank array\n", " Ranking v-sort output\n", " Ranking v-sort output time: 00:00:05\n", " Invoking Larsson-Sadakane on ranks\n", " Invoking Larsson-Sadakane on ranks time: 00:00:06\n", " Sanity-checking and returning\n", "Building samples\n", "Reserving space for 86 sample suffixes\n", "Generating random suffixes\n", "QSorting 86 sample offsets, eliminating duplicates\n", "QSorting sample offsets, eliminating duplicates time: 00:00:00\n", "Multikey QSorting 86 samples\n", " (Using difference cover)\n", " Multikey QSorting samples time: 00:00:00\n", "Calculating bucket sizes\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Split 10, merged 40; iterating...\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Split 7, merged 4; iterating...\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Split 3, merged 4; iterating...\n", "Splitting and merging\n", " Splitting and merging time: 00:00:00\n", "Avg bucket size: 1.88992e+07 (target: 25248165)\n", "Converting suffix-array elements to index image\n", "Allocating ftab, absorbFtab\n", "Entering Ebwt loop\n", "Getting block 1 of 57\n", " Reserving size (25248166) for bucket 1\n", "Getting block 2 of 57\n", "Getting block 3 of 57\n", " Calculating Z arrays for bucket 1\n", "Getting block 4 of 57\n", "Getting block 5 of 57\n", "Getting block 6 of 57\n", "Getting block 7 of 57\n", " Reserving size (25248166) for bucket 2\n", " Reserving size (25248166) for bucket 3\n", " Entering block accumulator loop for bucket 1:\n", " Reserving size (25248166) for bucket 4\n", " Reserving size (25248166) for bucket 5\n", " Reserving size (25248166) for bucket 6\n", " Reserving size (25248166) for bucket 7\n", " Calculating Z arrays for bucket 2\n", " Calculating Z arrays for bucket 3\n", " Calculating Z arrays for bucket 4\n", " Calculating Z arrays for bucket 5\n", " Calculating Z arrays for bucket 6\n", " Calculating Z arrays for bucket 7\n", " Entering block accumulator loop for bucket 2:\n", " Entering block accumulator loop for bucket 3:\n", " Entering block accumulator loop for bucket 4:\n", " Entering block accumulator loop for bucket 6:\n", " Entering block accumulator loop for bucket 5:\n", " Entering block accumulator loop for bucket 7:\n", " bucket 1: 10%\n", " bucket 2: 10%\n", " bucket 4: 10%\n", " bucket 3: 10%\n", " bucket 7: 10%\n", " bucket 5: 10%\n", " bucket 6: 10%\n", " bucket 1: 20%\n", " bucket 2: 20%\n", " bucket 4: 20%\n", " bucket 7: 20%\n", " bucket 3: 20%\n", " bucket 5: 20%\n", " bucket 6: 20%\n", " bucket 1: 30%\n", " bucket 2: 30%\n", " bucket 4: 30%\n", " bucket 7: 30%\n", " bucket 3: 30%\n", " bucket 5: 30%\n", " bucket 6: 30%\n", " bucket 1: 40%\n", " bucket 2: 40%\n", " bucket 4: 40%\n", " bucket 7: 40%\n", " bucket 3: 40%\n", " bucket 5: 40%\n", " bucket 6: 40%\n", " bucket 1: 50%\n", " bucket 2: 50%\n", " bucket 4: 50%\n", " bucket 7: 50%\n", " bucket 3: 50%\n", " bucket 5: 50%\n", " bucket 1: 60%\n", " bucket 6: 50%\n", " bucket 2: 60%\n", " bucket 4: 60%\n", " bucket 3: 60%\n", " bucket 1: 70%\n", " bucket 5: 60%\n", " bucket 7: 60%\n", " bucket 6: 60%\n", " bucket 2: 70%\n", " bucket 4: 70%\n", " bucket 1: 80%\n", " bucket 3: 70%\n", " bucket 5: 70%\n", " bucket 7: 70%\n", " bucket 6: 70%\n", " bucket 2: 80%\n", " bucket 1: 90%\n", " bucket 4: 80%\n", " bucket 3: 80%\n", " bucket 7: 80%\n", " bucket 5: 80%\n", " bucket 6: 80%\n", " bucket 2: 90%\n", " bucket 1: 100%\n", " Sorting block of length 10559074 for bucket 1\n", " (Using difference cover)\n", " bucket 4: 90%\n", " bucket 3: 90%\n", " bucket 7: 90%\n", " bucket 5: 90%\n", " bucket 2: 100%\n", " Sorting block of length 21152320 for bucket 2\n", " (Using difference cover)\n", " bucket 6: 90%\n", " bucket 4: 100%\n", " Sorting block of length 13446392 for bucket 4\n", " (Using difference cover)\n", " bucket 3: 100%\n", " Sorting block of length 21250998 for bucket 3\n", " (Using difference cover)\n", " bucket 7: 100%\n", " Sorting block of length 6172379 for bucket 7\n", " (Using difference cover)\n", " bucket 5: 100%\n", " Sorting block of length 16676481 for bucket 5\n", " (Using difference cover)\n", " bucket 6: 100%\n", " Sorting block of length 25021024 for bucket 6\n", " (Using difference cover)\n", " Sorting block time: 00:00:03\n", "Returning block of 10559075 for bucket 1\n", "Getting block 8 of 57\n", " Reserving size (25248166) for bucket 8\n", " Calculating Z arrays for bucket 8\n", " Entering block accumulator loop for bucket 8:\n", " Sorting block time: 00:00:02\n", "Returning block of 6172380 for bucket 7\n", "Getting block 9 of 57\n", " Reserving size (25248166) for bucket 9\n", " Calculating Z arrays for bucket 9\n", " Entering block accumulator loop for bucket 9:\n", " bucket 8: 10%\n", " Sorting block time: 00:00:04\n", "Returning block of 13446393 for bucket 4\n", " bucket 9: 10%\n", "Getting block 10 of 57\n", " Reserving size (25248166) for bucket 10\n", " Calculating Z arrays for bucket 10\n", " Entering block accumulator loop for bucket 10:\n", " Sorting block time: 00:00:06\n", "Returning block of 21152321 for bucket 2\n", " bucket 8: 20%\n", " Sorting block time: 00:00:05\n", "Returning block of 16676482 for bucket 5\n", "Getting block 11 of 57\n", " Reserving size (25248166) for bucket 11\n", " Calculating Z arrays for bucket 11\n", " Entering block accumulator loop for bucket 11:\n", " bucket 9: 20%\n", "Getting block 12 of 57\n", " Reserving size (25248166) for bucket 12\n", " Calculating Z arrays for bucket 12\n", " Entering block accumulator loop for bucket 12:\n", " Sorting block time: 00:00:06\n", "Returning block of 21250999 for bucket 3\n", " bucket 10: 10%\n", " bucket 8: 30%\n", "Getting block 13 of 57\n", " Reserving size (25248166) for bucket 13\n", " Calculating Z arrays for bucket 13\n", " Entering block accumulator loop for bucket 13:\n", " Sorting block time: 00:00:07\n", "Returning block of 25021025 for bucket 6\n", " bucket 11: 10%\n", " bucket 9: 30%\n", " bucket 12: 10%\n", "Getting block 14 of 57\n", " Reserving size (25248166) for bucket 14\n", " Calculating Z arrays for bucket 14\n", " Entering block accumulator loop for bucket 14:\n", " bucket 10: 20%\n", " bucket 8: 40%\n", " bucket 13: 10%\n", " bucket 11: 20%\n", " bucket 9: 40%\n", " bucket 12: 20%\n", " bucket 8: 50%\n", " bucket 10: 30%\n", " bucket 14: 10%\n", " bucket 13: 20%\n", " bucket 11: 30%\n", " bucket 9: 50%\n", " bucket 12: 30%\n", " bucket 8: 60%\n", " bucket 10: 40%\n", " bucket 14: 20%\n", " bucket 13: 30%\n", " bucket 9: 60%\n", " bucket 11: 40%\n", " bucket 12: 40%\n", " bucket 8: 70%\n", " bucket 10: 50%\n", " bucket 14: 30%\n", " bucket 13: 40%\n", " bucket 9: 70%\n", " bucket 11: 50%\n", " bucket 12: 50%\n", " bucket 8: 80%\n", " bucket 10: 60%\n", " bucket 14: 40%\n", " bucket 9: 80%\n", " bucket 13: 50%\n", " bucket 11: 60%\n", " bucket 8: 90%\n", " bucket 12: 60%\n", " bucket 10: 70%\n", " bucket 14: 50%\n", " bucket 9: 90%\n", " bucket 13: 60%\n", " bucket 11: 70%\n", " bucket 8: 100%\n", " Sorting block of length 23388029 for bucket 8\n", " (Using difference cover)\n", " bucket 12: 70%\n", " bucket 10: 80%\n", " bucket 14: 60%\n", " bucket 9: 100%\n", " Sorting block of length 18376933 for bucket 9\n", " (Using difference cover)\n", " bucket 13: 70%\n", " bucket 11: 80%\n", " bucket 12: 80%\n", " bucket 10: 90%\n", " bucket 14: 70%\n", " bucket 13: 80%\n", " bucket 11: 90%\n", " bucket 12: 90%\n", " bucket 10: 100%\n", " Sorting block of length 22920864 for bucket 10\n", " (Using difference cover)\n", " bucket 14: 80%\n", " bucket 13: 90%\n", " bucket 11: 100%\n", " Sorting block of length 19988871 for bucket 11\n", " (Using difference cover)\n", " bucket 12: 100%\n", " Sorting block of length 19363583 for bucket 12\n", " (Using difference cover)\n", " Sorting block time: 00:00:05\n", "Returning block of 18376934 for bucket 9\n", " bucket 14: 90%\n", " Sorting block time: 00:00:06\n", "Returning block of 23388030 for bucket 8\n", "Getting block 15 of 57\n", " Reserving size (25248166) for bucket 15\n", " Calculating Z arrays for bucket 15\n", " Entering block accumulator loop for bucket 15:\n", " bucket 13: 100%\n", " Sorting block of length 24366422 for bucket 13\n", " (Using difference cover)\n", "Getting block 16 of 57\n", " Reserving size (25248166) for bucket 16\n", " Calculating Z arrays for bucket 16\n", " Entering block accumulator loop for bucket 16:\n", " bucket 14: 100%\n", " Sorting block of length 17168338 for bucket 14\n", " (Using difference cover)\n", " bucket 15: 10%\n", " bucket 16: 10%\n", " Sorting block time: 00:00:07\n", "Returning block of 22920865 for bucket 10\n", " bucket 15: 20%\n", " Sorting block time: 00:00:06\n", "Returning block of 19363584 for bucket 12\n", " Sorting block time: 00:00:06\n", "Returning block of 19988872 for bucket 11\n", "Getting block 17 of 57\n", " Reserving size (25248166) for bucket 17\n", " Calculating Z arrays for bucket 17\n", " Entering block accumulator loop for bucket 17:\n", "Getting block 18 of 57\n", " Reserving size (25248166) for bucket 18\n", " Calculating Z arrays for bucket 18\n", " Entering block accumulator loop for bucket 18:\n", "Getting block 19 of 57\n", " Reserving size (25248166) for bucket 19\n", " Calculating Z arrays for bucket 19\n", " Entering block accumulator loop for bucket 19:\n", " bucket 16: 20%\n", " Sorting block time: 00:00:06\n", "Returning block of 17168339 for bucket 14\n", " bucket 15: 30%\n", "Getting block 20 of 57\n", " Reserving size (25248166) for bucket 20\n", " Calculating Z arrays for bucket 20\n", " Entering block accumulator loop for bucket 20:\n", " Sorting block time: 00:00:07\n", "Returning block of 24366423 for bucket 13\n", " bucket 17: 10%\n", " bucket 18: 10%\n", " bucket 16: 30%\n", " bucket 19: 10%\n", "Getting block 21 of 57\n", " Reserving size (25248166) for bucket 21\n", " Calculating Z arrays for bucket 21\n", " Entering block accumulator loop for bucket 21:\n", " bucket 15: 40%\n", " bucket 20: 10%\n", " bucket 16: 40%\n", " bucket 17: 20%\n", " bucket 18: 20%\n", " bucket 19: 20%\n", " bucket 21: 10%\n", " bucket 15: 50%\n", " bucket 16: 50%\n", " bucket 20: 20%\n", " bucket 18: 30%\n", " bucket 17: 30%\n", " bucket 19: 30%\n", " bucket 21: 20%\n", " bucket 15: 60%\n", " bucket 16: 60%\n", " bucket 20: 30%\n", " bucket 18: 40%\n", " bucket 17: 40%\n", " bucket 19: 40%\n", " bucket 21: 30%\n", " bucket 15: 70%\n", " bucket 16: 70%\n", " bucket 20: 40%\n", " bucket 17: 50%\n", " bucket 18: 50%\n", " bucket 21: 40%\n", " bucket 19: 50%\n", " bucket 15: 80%\n", " bucket 16: 80%\n", " bucket 17: 60%\n", " bucket 20: 50%\n", " bucket 18: 60%\n", " bucket 21: 50%\n", " bucket 15: 90%\n", " bucket 16: 90%\n", " bucket 19: 60%\n", " bucket 17: 70%\n", " bucket 20: 60%\n", " bucket 18: 70%\n", " bucket 21: 60%\n", " bucket 15: 100%\n", " Sorting block of length 24352796 for bucket 15\n", " (Using difference cover)\n", " bucket 16: 100%\n", " Sorting block of length 8837753 for bucket 16\n", " (Using difference cover)\n", " bucket 19: 70%\n", " bucket 17: 80%\n", " bucket 20: 70%\n", " bucket 18: 80%\n", " bucket 21: 70%\n", " Sorting block time: 00:00:02\n", "Returning block of 8837754 for bucket 16\n", " bucket 19: 80%\n", "Getting block 22 of 57\n", " Reserving size (25248166) for bucket 22\n", " Calculating Z arrays for bucket 22\n", " Entering block accumulator loop for bucket 22:\n", " bucket 20: 80%\n", " bucket 17: 90%\n", " bucket 18: 90%\n", " bucket 21: 80%\n", " bucket 19: 90%\n", " bucket 22: 10%\n", " bucket 20: 90%\n", " bucket 17: 100%\n", " Sorting block of length 17135649 for bucket 17\n", " (Using difference cover)\n", " bucket 18: 100%\n", " Sorting block of length 18530279 for bucket 18\n", " (Using difference cover)\n", " bucket 21: 90%\n", " Sorting block time: 00:00:06\n", "Returning block of 24352797 for bucket 15\n", " bucket 20: 100%\n", " Sorting block of length 24240163 for bucket 20\n", " (Using difference cover)\n", " bucket 19: 100%\n", " Sorting block of length 17866069 for bucket 19\n", " (Using difference cover)\n", " bucket 22: 20%\n", "Getting block 23 of 57\n", " Reserving size (25248166) for bucket 23\n", " Calculating Z arrays for bucket 23\n", " Entering block accumulator loop for bucket 23:\n", " bucket 21: 100%\n", " Sorting block of length 17572140 for bucket 21\n", " (Using difference cover)\n", " bucket 22: 30%\n", " bucket 23: 10%\n", " Sorting block time: 00:00:05\n", "Returning block of 17135650 for bucket 17\n", "Getting block 24 of 57\n", " Reserving size (25248166) for bucket 24\n", " Calculating Z arrays for bucket 24\n", " Entering block accumulator loop for bucket 24:\n", " Sorting block time: 00:00:06\n", "Returning block of 18530280 for bucket 18\n", " bucket 22: 40%\n", "Getting block 25 of 57\n", " Reserving size (25248166) for bucket 25\n", " Calculating Z arrays for bucket 25\n", " Entering block accumulator loop for bucket 25:\n", " bucket 23: 20%\n", " Sorting block time: 00:00:05\n", "Returning block of 17866070 for bucket 19\n", " Sorting block time: 00:00:05\n", "Returning block of 17572141 for bucket 21\n", "Getting block 26 of 57\n", " Reserving size (25248166) for bucket 26\n", " Calculating Z arrays for bucket 26\n", " Entering block accumulator loop for bucket 26:\n", " bucket 24: 10%\n", " bucket 22: 50%\n", "Getting block 27 of 57\n", " Reserving size (25248166) for bucket 27\n", " Calculating Z arrays for bucket 27\n", " Entering block accumulator loop for bucket 27:\n", " Sorting block time: 00:00:07\n", "Returning block of 24240164 for bucket 20\n", " bucket 25: 10%\n", " bucket 23: 30%\n", "Getting block 28 of 57\n", " Reserving size (25248166) for bucket 28\n", " Calculating Z arrays for bucket 28\n", " Entering block accumulator loop for bucket 28:\n", " bucket 26: 10%\n", " bucket 24: 20%\n", " bucket 22: 60%\n", " bucket 27: 10%\n", " bucket 25: 20%\n", " bucket 23: 40%\n", " bucket 28: 10%\n", " bucket 26: 20%\n", " bucket 24: 30%\n", " bucket 22: 70%\n", " bucket 25: 30%\n", " bucket 23: 50%\n", " bucket 27: 20%\n", " bucket 28: 20%\n", " bucket 26: 30%\n", " bucket 24: 40%\n", " bucket 22: 80%\n", " bucket 23: 60%\n", " bucket 25: 40%\n", " bucket 27: 30%\n", " bucket 28: 30%\n", " bucket 24: 50%\n", " bucket 26: 40%\n", " bucket 22: 90%\n", " bucket 23: 70%\n", " bucket 25: 50%\n", " bucket 27: 40%\n", " bucket 28: 40%\n", " bucket 26: 50%\n", " bucket 24: 60%\n", " bucket 23: 80%\n", " bucket 22: 100%\n", " Sorting block of length 19018601 for bucket 22\n", " (Using difference cover)\n", " bucket 25: 60%\n", " bucket 27: 50%\n", " bucket 28: 50%\n", " bucket 26: 60%\n", " bucket 24: 70%\n", " bucket 23: 90%\n", " bucket 25: 70%\n", " bucket 27: 60%\n", " bucket 28: 60%\n", " bucket 23: 100%\n", " Sorting block of length 17085345 for bucket 23\n", " (Using difference cover)\n", " bucket 24: 80%\n", " bucket 26: 70%\n", " Sorting block time: 00:00:04\n", "Returning block of 19018602 for bucket 22\n", " bucket 25: 80%\n", " bucket 27: 70%\n", "Getting block 29 of 57\n", " Reserving size (25248166) for bucket 29\n", " Calculating Z arrays for bucket 29\n", " Entering block accumulator loop for bucket 29:\n", " bucket 24: 90%\n", " bucket 28: 70%\n", " bucket 26: 80%\n", " bucket 25: 90%\n", " Sorting block time: 00:00:04\n", "Returning block of 17085346 for bucket 23\n", " bucket 27: 80%\n", " bucket 24: 100%\n", " Sorting block of length 25037061 for bucket 24\n", " (Using difference cover)\n", " bucket 29: 10%\n", " bucket 28: 80%\n", "Getting block 30 of 57\n", " Reserving size (25248166) for bucket 30\n", " Calculating Z arrays for bucket 30\n", " Entering block accumulator loop for bucket 30:\n", " bucket 26: 90%\n", " bucket 25: 100%\n", " Sorting block of length 18146354 for bucket 25\n", " (Using difference cover)\n", " bucket 27: 90%\n", " bucket 29: 20%\n", " bucket 28: 90%\n", " bucket 30: 10%\n", " bucket 26: 100%\n", " Sorting block of length 22667786 for bucket 26\n", " (Using difference cover)\n", " bucket 27: 100%\n", " Sorting block of length 24491772 for bucket 27\n", " (Using difference cover)\n", " bucket 28: 100%\n", " Sorting block of length 16022438 for bucket 28\n", " (Using difference cover)\n", " bucket 30: 20%\n", " bucket 29: 30%\n", " Sorting block time: 00:00:05\n", "Returning block of 18146355 for bucket 25\n", "Getting block 31 of 57\n", " Reserving size (25248166) for bucket 31\n", " Calculating Z arrays for bucket 31\n", " Entering block accumulator loop for bucket 31:\n", " Sorting block time: 00:00:07\n", "Returning block of 25037062 for bucket 24\n", " bucket 30: 30%\n", " bucket 29: 40%\n", "Getting block 32 of 57\n", " Reserving size (25248166) for bucket 32\n", " Calculating Z arrays for bucket 32\n", " Entering block accumulator loop for bucket 32:\n", " bucket 31: 10%\n", " bucket 30: 40%\n", " Sorting block time: 00:00:06\n", "Returning block of 22667787 for bucket 26\n", " Sorting block time: 00:00:05\n", "Returning block of 16022439 for bucket 28\n", "Getting block 33 of 57\n", " Reserving size (25248166) for bucket 33\n", " Calculating Z arrays for bucket 33\n", " Entering block accumulator loop for bucket 33:\n", " bucket 29: 50%\n", "Getting block 34 of 57\n", " Reserving size (25248166) for bucket 34\n", " Calculating Z arrays for bucket 34\n", " Entering block accumulator loop for bucket 34:\n", " bucket 32: 10%\n", " Sorting block time: 00:00:06\n", "Returning block of 24491773 for bucket 27\n", " bucket 31: 20%\n", " bucket 30: 50%\n", "Getting block 35 of 57\n", " Reserving size (25248166) for bucket 35\n", " Calculating Z arrays for bucket 35\n", " Entering block accumulator loop for bucket 35:\n", " bucket 34: 10%\n", " bucket 33: 10%\n", " bucket 32: 20%\n", " bucket 29: 60%\n", " bucket 31: 30%\n", " bucket 30: 60%\n", " bucket 35: 10%\n", " bucket 34: 20%\n", " bucket 33: 20%\n", " bucket 32: 30%\n", " bucket 29: 70%\n", " bucket 31: 40%\n", " bucket 30: 70%\n", " bucket 35: 20%\n", " bucket 34: 30%\n", " bucket 33: 30%\n", " bucket 32: 40%\n", " bucket 29: 80%\n", " bucket 31: 50%\n", " bucket 30: 80%\n", " bucket 35: 30%\n", " bucket 34: 40%\n", " bucket 33: 40%\n", " bucket 32: 50%\n", " bucket 31: 60%\n", " bucket 30: 90%\n", " bucket 29: 90%\n", " bucket 34: 50%\n", " bucket 35: 40%\n", " bucket 33: 50%\n", " bucket 32: 60%\n", " bucket 31: 70%\n", " bucket 30: 100%\n", " Sorting block of length 25015539 for bucket 30\n", " (Using difference cover)\n", " bucket 29: 100%\n", " Sorting block of length 21825456 for bucket 29\n", " (Using difference cover)\n", " bucket 34: 60%\n", " bucket 35: 50%\n", " bucket 33: 60%\n", " bucket 32: 70%\n", " bucket 31: 80%\n", " bucket 34: 70%\n", " bucket 35: 60%\n", " bucket 33: 70%\n", " bucket 32: 80%\n", " bucket 31: 90%\n", " bucket 34: 80%\n", " bucket 35: 70%\n", " bucket 33: 80%\n", " bucket 32: 90%\n", " Sorting block time: 00:00:05\n", "Returning block of 21825457 for bucket 29\n", " bucket 31: 100%\n", " Sorting block of length 19376440 for bucket 31\n", " (Using difference cover)\n", " bucket 34: 90%\n", " Sorting block time: 00:00:06\n", "Returning block of 25015540 for bucket 30\n", " bucket 35: 80%\n", "Getting block 36 of 57\n", " Reserving size (25248166) for bucket 36\n", " Calculating Z arrays for bucket 36\n", " Entering block accumulator loop for bucket 36:\n", " bucket 33: 90%\n", "Getting block 37 of 57\n", " Reserving size (25248166) for bucket 37\n", " Calculating Z arrays for bucket 37\n", " Entering block accumulator loop for bucket 37:\n", " bucket 32: 100%\n", " Sorting block of length 19587746 for bucket 32\n", " (Using difference cover)\n", " bucket 34: 100%\n", " Sorting block of length 2395294 for bucket 34\n", " (Using difference cover)\n", " Sorting block time: 00:00:01\n", "Returning block of 2395295 for bucket 34\n", "Getting block 38 of 57\n", " Reserving size (25248166) for bucket 38\n", " Calculating Z arrays for bucket 38\n", " Entering block accumulator loop for bucket 38:\n", " bucket 35: 90%\n", " bucket 36: 10%\n", " bucket 33: 100%\n", " Sorting block of length 23509819 for bucket 33\n", " (Using difference cover)\n", " bucket 37: 10%\n", " Sorting block time: 00:00:05\n", "Returning block of 19376441 for bucket 31\n", " bucket 38: 10%\n", "Getting block 39 of 57\n", " Reserving size (25248166) for bucket 39\n", " Calculating Z arrays for bucket 39\n", " Entering block accumulator loop for bucket 39:\n", " bucket 35: 100%\n", " Sorting block of length 24977146 for bucket 35\n", " (Using difference cover)\n", " bucket 36: 20%\n", " bucket 37: 20%\n", " Sorting block time: 00:00:05\n", "Returning block of 19587747 for bucket 32\n", "Getting block 40 of 57\n", " Reserving size (25248166) for bucket 40\n", " Calculating Z arrays for bucket 40\n", " Entering block accumulator loop for bucket 40:\n", " bucket 38: 20%\n", " bucket 36: 30%\n", " bucket 39: 10%\n", " bucket 37: 30%\n", " Sorting block time: 00:00:06\n", "Returning block of 23509820 for bucket 33\n", " bucket 40: 10%\n", "Getting block 41 of 57\n", " Reserving size (25248166) for bucket 41\n", " Calculating Z arrays for bucket 41\n", " Entering block accumulator loop for bucket 41:\n", " bucket 38: 30%\n", " bucket 36: 40%\n", " bucket 39: 20%\n", " Sorting block time: 00:00:07\n", "Returning block of 24977147 for bucket 35\n", " bucket 37: 40%\n", " bucket 40: 20%\n", "Getting block 42 of 57\n", " Reserving size (25248166) for bucket 42\n", " Calculating Z arrays for bucket 42\n", " Entering block accumulator loop for bucket 42:\n", " bucket 41: 10%\n", " bucket 38: 40%\n", " bucket 36: 50%\n", " bucket 39: 30%\n", " bucket 37: 50%\n", " bucket 40: 30%\n", " bucket 42: 10%\n", " bucket 41: 20%\n", " bucket 38: 50%\n", " bucket 36: 60%\n", " bucket 39: 40%\n", " bucket 37: 60%\n", " bucket 40: 40%\n", " bucket 42: 20%\n", " bucket 41: 30%\n", " bucket 38: 60%\n", " bucket 36: 70%\n", " bucket 37: 70%\n", " bucket 40: 50%\n", " bucket 39: 50%\n", " bucket 42: 30%\n", " bucket 41: 40%\n", " bucket 38: 70%\n", " bucket 36: 80%\n", " bucket 37: 80%\n", " bucket 40: 60%\n", " bucket 42: 40%\n", " bucket 39: 60%\n", " bucket 41: 50%\n", " bucket 38: 80%\n", " bucket 36: 90%\n", " bucket 37: 90%\n", " bucket 40: 70%\n", " bucket 42: 50%\n", " bucket 41: 60%\n", " bucket 39: 70%\n", " bucket 38: 90%\n", " bucket 36: 100%\n", " Sorting block of length 18554232 for bucket 36\n", " (Using difference cover)\n", " bucket 37: 100%\n", " Sorting block of length 24797373 for bucket 37\n", " (Using difference cover)\n", " bucket 40: 80%\n", " bucket 42: 60%\n", " bucket 41: 70%\n", " bucket 38: 100%\n", " Sorting block of length 24474201 for bucket 38\n", " (Using difference cover)\n", " bucket 39: 80%\n", " bucket 40: 90%\n", " bucket 42: 70%\n", " bucket 41: 80%\n", " bucket 39: 90%\n", " bucket 40: 100%\n", " Sorting block of length 3140042 for bucket 40\n", " (Using difference cover)\n", " Sorting block time: 00:00:04\n", "Returning block of 18554233 for bucket 36\n", " bucket 42: 80%\n", " Sorting block time: 00:00:01\n", "Returning block of 3140043 for bucket 40\n", "Getting block 43 of 57\n", " Reserving size (25248166) for bucket 43\n", " Calculating Z arrays for bucket 43\n", " Entering block accumulator loop for bucket 43:\n", "Getting block 44 of 57\n", " Reserving size (25248166) for bucket 44\n", " Calculating Z arrays for bucket 44\n", " Entering block accumulator loop for bucket 44:\n", " bucket 41: 90%\n", " bucket 39: 100%\n", " Sorting block of length 23643670 for bucket 39\n", " (Using difference cover)\n", " Sorting block time: 00:00:06\n", "Returning block of 24797374 for bucket 37\n", "Getting block 45 of 57\n", " Reserving size (25248166) for bucket 45\n", " Calculating Z arrays for bucket 45\n", " Entering block accumulator loop for bucket 45:\n", " bucket 42: 90%\n", " Sorting block time: 00:00:07\n", "Returning block of 24474202 for bucket 38\n", " bucket 44: 10%\n", " bucket 43: 10%\n", " bucket 41: 100%\n", " Sorting block of length 22243200 for bucket 41\n", " (Using difference cover)\n", "Getting block 46 of 57\n", " Reserving size (25248166) for bucket 46\n", " Calculating Z arrays for bucket 46\n", " Entering block accumulator loop for bucket 46:\n", " bucket 45: 10%\n", " bucket 42: 100%\n", " Sorting block of length 21125246 for bucket 42\n", " (Using difference cover)\n", " bucket 44: 20%\n", " bucket 43: 20%\n", " bucket 46: 10%\n", " Sorting block time: 00:00:06\n", "Returning block of 23643671 for bucket 39\n", " bucket 45: 20%\n", " bucket 44: 30%\n", " bucket 43: 30%\n", "Getting block 47 of 57\n", " Reserving size (25248166) for bucket 47\n", " Calculating Z arrays for bucket 47\n", " Entering block accumulator loop for bucket 47:\n", " Sorting block time: 00:00:06\n", "Returning block of 22243201 for bucket 41\n", "Getting block 48 of 57\n", " Reserving size (25248166) for bucket 48\n", " Calculating Z arrays for bucket 48\n", " Entering block accumulator loop for bucket 48:\n", " bucket 46: 20%\n", " Sorting block time: 00:00:05\n", "Returning block of 21125247 for bucket 42\n", " bucket 43: 40%\n", " bucket 45: 30%\n", " bucket 44: 40%\n", "Getting block 49 of 57\n", " Reserving size (25248166) for bucket 49\n", " Calculating Z arrays for bucket 49\n", " Entering block accumulator loop for bucket 49:\n", " bucket 47: 10%\n", " bucket 48: 10%\n", " bucket 46: 30%\n", " bucket 43: 50%\n", " bucket 44: 50%\n", " bucket 45: 40%\n", " bucket 49: 10%\n", " bucket 47: 20%\n", " bucket 48: 20%\n", " bucket 46: 40%\n", " bucket 43: 60%\n", " bucket 44: 60%\n", " bucket 49: 20%\n", " bucket 45: 50%\n", " bucket 47: 30%\n", " bucket 48: 30%\n", " bucket 46: 50%\n", " bucket 44: 70%\n", " bucket 43: 70%\n", " bucket 49: 30%\n", " bucket 45: 60%\n", " bucket 47: 40%\n", " bucket 48: 40%\n", " bucket 43: 80%\n", " bucket 46: 60%\n", " bucket 44: 80%\n", " bucket 49: 40%\n", " bucket 45: 70%\n", " bucket 47: 50%\n", " bucket 48: 50%\n", " bucket 43: 90%\n", " bucket 44: 90%\n", " bucket 46: 70%\n", " bucket 49: 50%\n", " bucket 45: 80%\n", " bucket 47: 60%\n", " bucket 48: 60%\n", " bucket 43: 100%\n", " Sorting block of length 20977586 for bucket 43\n", " (Using difference cover)\n", " bucket 44: 100%\n", " Sorting block of length 8662558 for bucket 44\n", " (Using difference cover)\n", " bucket 46: 80%\n", " bucket 49: 60%\n", " bucket 45: 90%\n", " bucket 47: 70%\n", " bucket 48: 70%\n", " Sorting block time: 00:00:02\n", "Returning block of 8662559 for bucket 44\n", " bucket 49: 70%\n", " bucket 46: 90%\n", "Getting block 50 of 57\n", " Reserving size (25248166) for bucket 50\n", " Calculating Z arrays for bucket 50\n", " Entering block accumulator loop for bucket 50:\n", " bucket 45: 100%\n", " Sorting block of length 19791304 for bucket 45\n", " (Using difference cover)\n", " bucket 47: 80%\n", " bucket 48: 80%\n", " bucket 49: 80%\n", " bucket 46: 100%\n", " Sorting block of length 20443289 for bucket 46\n", " (Using difference cover)\n", " bucket 50: 10%\n", " Sorting block time: 00:00:05\n", "Returning block of 20977587 for bucket 43\n", " bucket 47: 90%\n", " bucket 48: 90%\n", "Getting block 51 of 57\n", " Reserving size (25248166) for bucket 51\n", " Calculating Z arrays for bucket 51\n", " Entering block accumulator loop for bucket 51:\n", " bucket 49: 90%\n", " bucket 50: 20%\n", " bucket 47: 100%\n", " Sorting block of length 23214824 for bucket 47\n", " (Using difference cover)\n", " Sorting block time: 00:00:05\n", "Returning block of 19791305 for bucket 45\n", " bucket 48: 100%\n", " Sorting block of length 17230678 for bucket 48\n", " (Using difference cover)\n", " bucket 51: 10%\n", "Getting block 52 of 57\n", " Reserving size (25248166) for bucket 52\n", " Calculating Z arrays for bucket 52\n", " Entering block accumulator loop for bucket 52:\n", " bucket 49: 100%\n", " Sorting block of length 13670010 for bucket 49\n", " (Using difference cover)\n", " bucket 50: 30%\n", " Sorting block time: 00:00:05\n", "Returning block of 20443290 for bucket 46\n", "Getting block 53 of 57\n", " Reserving size (25248166) for bucket 53\n", " Calculating Z arrays for bucket 53\n", " Entering block accumulator loop for bucket 53:\n", " bucket 51: 20%\n", " bucket 52: 10%\n", " bucket 50: 40%\n", " Sorting block time: 00:00:05\n", "Returning block of 17230679 for bucket 48\n", " Sorting block time: 00:00:04\n", "Returning block of 13670011 for bucket 49\n", "Getting block 54 of 57\n", " Reserving size (25248166) for bucket 54\n", " Calculating Z arrays for bucket 54\n", " Entering block accumulator loop for bucket 54:\n", "Getting block 55 of 57\n", " Reserving size (25248166) for bucket 55\n", " Calculating Z arrays for bucket 55\n", " Entering block accumulator loop for bucket 55:\n", " bucket 53: 10%\n", " Sorting block time: 00:00:06\n", "Returning block of 23214825 for bucket 47\n", " bucket 51: 30%\n", " bucket 52: 20%\n", " bucket 50: 50%\n", "Getting block 56 of 57\n", " Reserving size (25248166) for bucket 56\n", " Calculating Z arrays for bucket 56\n", " Entering block accumulator loop for bucket 56:\n", " bucket 55: 10%\n", " bucket 54: 10%\n", " bucket 53: 20%\n", " bucket 51: 40%\n", " bucket 52: 30%\n", " bucket 56: 10%\n", " bucket 50: 60%\n", " bucket 55: 20%\n", " bucket 54: 20%\n", " bucket 53: 30%\n", " bucket 51: 50%\n", " bucket 52: 40%\n", " bucket 56: 20%\n", " bucket 50: 70%\n", " bucket 55: 30%\n", " bucket 54: 30%\n", " bucket 53: 40%\n", " bucket 52: 50%\n", " bucket 51: 60%\n", " bucket 56: 30%\n", " bucket 50: 80%\n", " bucket 55: 40%\n", " bucket 54: 40%\n", " bucket 53: 50%\n", " bucket 56: 40%\n", " bucket 52: 60%\n", " bucket 51: 70%\n", " bucket 50: 90%\n", " bucket 55: 50%\n", " bucket 54: 50%\n", " bucket 53: 60%\n", " bucket 56: 50%\n", " bucket 52: 70%\n", " bucket 51: 80%\n", " bucket 50: 100%\n", " Sorting block of length 16274666 for bucket 50\n", " (Using difference cover)\n", " bucket 55: 60%\n", " bucket 54: 60%\n", " bucket 53: 70%\n", " bucket 56: 60%\n", " bucket 52: 80%\n", " bucket 51: 90%\n", " bucket 55: 70%\n", " bucket 54: 70%\n", " bucket 53: 80%\n", " bucket 56: 70%\n", " bucket 52: 90%\n", " Sorting block time: 00:00:04\n", "Returning block of 16274667 for bucket 50\n", " bucket 51: 100%\n", " Sorting block of length 17578616 for bucket 51\n", " (Using difference cover)\n", "Getting block 57 of 57\n", " Reserving size (25248166) for bucket 57\n", " Calculating Z arrays for bucket 57\n", " Entering block accumulator loop for bucket 57:\n", " bucket 55: 80%\n", " bucket 54: 80%\n", " bucket 56: 80%\n", " bucket 53: 90%\n", " bucket 52: 100%\n", " Sorting block of length 11195422 for bucket 52\n", " (Using difference cover)\n", " bucket 57: 10%\n", " bucket 55: 90%\n", " bucket 57: 20%\n", " bucket 54: 90%\n", " bucket 56: 90%\n", " bucket 53: 100%\n", " Sorting block of length 24732783 for bucket 53\n", " (Using difference cover)\n", " Sorting block time: 00:00:04\n", "Returning block of 17578617 for bucket 51\n", " Sorting block time: 00:00:03\n", "Returning block of 11195423 for bucket 52\n", " bucket 57: 30%\n", " bucket 55: 100%\n", " Sorting block of length 24975973 for bucket 55\n", " (Using difference cover)\n", " bucket 54: 100%\n", " Sorting block of length 20586938 for bucket 54\n", " (Using difference cover)\n", " bucket 56: 100%\n", " Sorting block of length 12698050 for bucket 56\n", " (Using difference cover)\n", " bucket 57: 40%\n", " bucket 57: 50%\n", " bucket 57: 60%\n", " Sorting block time: 00:00:03\n", "Returning block of 12698051 for bucket 56\n", " bucket 57: 70%\n", " Sorting block time: 00:00:06\n", "Returning block of 24732784 for bucket 53\n", " Sorting block time: 00:00:05\n", "Returning block of 20586939 for bucket 54\n", " bucket 57: 80%\n", " Sorting block time: 00:00:05\n", "Returning block of 24975974 for bucket 55\n", " bucket 57: 90%\n", " bucket 57: 100%\n", " Sorting block of length 19701028 for bucket 57\n", " (Using difference cover)\n", " Sorting block time: 00:00:03\n", "Returning block of 19701029 for bucket 57\n", "Exited Ebwt loop\n", "fchr[A]: 0\n", "fchr[C]: 341519526\n", "fchr[G]: 538577822\n", "fchr[T]: 735626959\n", "fchr[$]: 1077255099\n", "Exiting Ebwt::buildToDisk()\n", "Returning from initFromVector\n", "Wrote 371984998 bytes to primary EBWT file: ../data/Olurida_v081-bowtie-index.rev.1.bt2\n", "Wrote 269313780 bytes to secondary EBWT file: ../data/Olurida_v081-bowtie-index.rev.2.bt2\n", "Re-opening _in1 and _in2 as input streams\n", "Returning from Ebwt constructor\n", "Headers:\n", " len: 1077255099\n", " bwtLen: 1077255100\n", " sz: 269313775\n", " bwtSz: 269313775\n", " lineRate: 6\n", " offRate: 4\n", " offMask: 0xfffffff0\n", " ftabChars: 10\n", " eftabLen: 20\n", " eftabSz: 80\n", " ftabLen: 1048577\n", " ftabSz: 4194308\n", " offsLen: 67328444\n", " offsSz: 269313776\n", " lineSz: 64\n", " sideSz: 64\n", " sideBwtSz: 48\n", " sideBwtLen: 192\n", " numSides: 5610704\n", " numLines: 5610704\n", " ebwtTotLen: 359085056\n", " ebwtTotSz: 359085056\n", " color: 0\n", " reverse: 1\n", "Total time for backward call to driver() for mirror index: 00:05:03\n" ] } ], "source": [ "!/Applications/bioinfo/bowtie2-2.4.2-macos-x86_64/bowtie2-build \\\n", "--threads 8 \\\n", "../data/Olurida_v081.fa \\\n", "../data/Olurida_v081-bowtie-index" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "https://nbviewer.jupyter.org/github/sr320/student-fish546-2016/blob/1cfbc742fe2811f0b1ac8558a4579fb788f0a0b0/jupyter/02.6-Oly-Bowtie.ipynb" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [], "source": [ "!mkdir ../analyses" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "2162122 reads; of these:\n", " 2162122 (100.00%) were unpaired; of these:\n", " 1448808 (67.01%) aligned 0 times\n", " 471780 (21.82%) aligned exactly 1 time\n", " 241534 (11.17%) aligned >1 times\n", "32.99% overall alignment rate\n" ] } ], "source": [ "!/Applications/bioinfo/bowtie2-2.4.2-macos-x86_64/bowtie2 \\\n", "-x ../data/Olurida_v081-bowtie-index \\\n", "../data/35.trim.fastq \\\n", "-p 8 \\\n", "--very-sensitive \\\n", "-S ../analyses/35.trim.sam" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "2162122 reads; of these:\n", " 2162122 (100.00%) were unpaired; of these:\n", " 1574651 (72.83%) aligned 0 times\n", " 440284 (20.36%) aligned exactly 1 time\n", " 147187 (6.81%) aligned >1 times\n", "27.17% overall alignment rate\n" ] } ], "source": [ "!/Applications/bioinfo/bowtie2-2.4.2-macos-x86_64/bowtie2 \\\n", "-x ../data/Olurida_v081-bowtie-index \\\n", "../data/35.trim.fastq \\\n", "-p 8 \\\n", "--very-fast \\\n", "-S ../analyses/35.trim-fast.sam" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "6737872 reads; of these:\n", " 6737872 (100.00%) were unpaired; of these:\n", " 2704482 (40.14%) aligned 0 times\n", " 2939124 (43.62%) aligned exactly 1 time\n", " 1094266 (16.24%) aligned >1 times\n", "59.86% overall alignment rate\n" ] } ], "source": [ "!/Applications/bioinfo/bowtie2-2.4.2-macos-x86_64/bowtie2 \\\n", "-x ../data/Olurida_v081-bowtie-index \\\n", "../data/34.trim.fastq \\\n", "-p 8 \\\n", "--very-sensitive \\\n", "-S ../analyses/34.trim.sam" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "7420499 reads; of these:\n", " 7420499 (100.00%) were unpaired; of these:\n", " 4486297 (60.46%) aligned 0 times\n", " 2176262 (29.33%) aligned exactly 1 time\n", " 757940 (10.21%) aligned >1 times\n", "39.54% overall alignment rate\n" ] } ], "source": [ "!/Applications/bioinfo/bowtie2-2.4.2-macos-x86_64/bowtie2 \\\n", "-x ../data/Olurida_v081-bowtie-index \\\n", "../data/37.trim.fastq \\\n", "-p 8 \\\n", "--very-sensitive \\\n", "-S ../analyses/37.trim.sam" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "5800354 reads; of these:\n", " 5800354 (100.00%) were unpaired; of these:\n", " 2488107 (42.90%) aligned 0 times\n", " 2527877 (43.58%) aligned exactly 1 time\n", " 784370 (13.52%) aligned >1 times\n", "57.10% overall alignment rate\n" ] } ], "source": [ "!/Applications/bioinfo/bowtie2-2.4.2-macos-x86_64/bowtie2 \\\n", "-x ../data/Olurida_v081-bowtie-index \\\n", "../data/39.trim.fastq \\\n", "-p 8 \\\n", "--very-sensitive \\\n", "-S ../analyses/39.trim.sam" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "samtools view: invalid option -- 'e'\n", "\n", "Usage: samtools view [options] || [region ...]\n", "\n", "Options:\n", " -b output BAM\n", " -C output CRAM (requires -T)\n", " -1 use fast BAM compression (implies -b)\n", " -u uncompressed BAM output (implies -b)\n", " -h include header in SAM output\n", " -H print SAM header only (no alignments)\n", " -c print only the count of matching records\n", " -o FILE output file name [stdout]\n", " -U FILE output reads not selected by filters to FILE [null]\n", " -t FILE FILE listing reference names and lengths (see long help) [null]\n", " -X include customized index file\n", " -L FILE only include reads overlapping this BED FILE [null]\n", " -r STR only include reads in read group STR [null]\n", " -R FILE only include reads with read group listed in FILE [null]\n", " -d STR:STR\n", " only include reads with tag STR and associated value STR [null]\n", " -D STR:FILE\n", " only include reads with tag STR and associated values listed in\n", " FILE [null]\n", " -q INT only include reads with mapping quality >= INT [0]\n", " -l STR only include reads in library STR [null]\n", " -m INT only include reads with number of CIGAR operations consuming\n", " query sequence >= INT [0]\n", " -f INT only include reads with all of the FLAGs in INT present [0]\n", " -F INT only include reads with none of the FLAGS in INT present [0]\n", " -G INT only EXCLUDE reads with all of the FLAGs in INT present [0]\n", " -s FLOAT subsample reads (given INT.FRAC option value, 0.FRAC is the\n", " fraction of templates/read pairs to keep; INT part sets seed)\n", " -M use the multi-region iterator (increases the speed, removes\n", " duplicates and outputs the reads as they are ordered in the file)\n", " -x STR read tag to strip (repeatable) [null]\n", " -B collapse the backward CIGAR operation\n", " -? print long help, including note about region specification\n", " -S ignored (input format is auto-detected)\n", " --no-PG do not add a PG line\n", " --input-fmt-option OPT[=VAL]\n", " Specify a single input file format option in the form\n", " of OPTION or OPTION=VALUE\n", " -O, --output-fmt FORMAT[,OPT[=VAL]]...\n", " Specify output format (SAM, BAM, CRAM)\n", " --output-fmt-option OPT[=VAL]\n", " Specify a single output file format option in the form\n", " of OPTION or OPTION=VALUE\n", " -T, --reference FILE\n", " Reference sequence FASTA FILE [null]\n", " -@, --threads INT\n", " Number of additional threads to use [0]\n", " --write-index\n", " Automatically index the output files [off]\n", " --verbosity INT\n", " Set level of verbosity\n", "\n" ] } ], "source": [ "!/Applications/bioinfo/samtools-1.11/samtools view -help" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[bam_sort_core] merging from 1 files and 1 in-memory blocks...\n" ] } ], "source": [ "!/Applications/bioinfo/samtools-1.11/samtools view -b ../analyses/39.trim.sam \\\n", "| /Applications/bioinfo/samtools-1.11/samtools sort -o ../analyses/39.trim.bam\n", "\n", "!/Applications/bioinfo/samtools-1.11/samtools index ../analyses/39.trim.bam" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "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": "3.8.5" } }, "nbformat": 4, "nbformat_minor": 4 }