{ "metadata": { "name": "", "signature": "sha256:4b703f8d62db8c6406ec3317683e8511207e987cdfff3b185545dda807d011ac" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Trying to fix tab issue" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!process_radtags" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "You must specify an input file of a directory path to a set of input files.\r\n", "process_radtags 1.24\r\n", "process_radtags [-f in_file | -p in_dir [-P] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir -e enz [-c] [-q] [-r] [-t len] [-D] [-w size] [-s lim] [-h]\r\n", " f: path to the input file if processing single-end sequences.\r\n", " i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fastq', or 'gzfastq' for gzipped Fastq (default 'fastq').\r\n", " y: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default is to match the input file type).\r\n", " p: path to a directory of files.\r\n", " P: files contained within directory specified by '-p' are paired.\r\n", " 1: first input file in a set of paired-end sequences.\r\n", " 2: second input file in a set of paired-end sequences.\r\n", " o: path to output the processed files.\r\n", " b: path to a file containing barcodes for this run.\r\n", " c: clean data, remove any read with an uncalled base.\r\n", " q: discard reads with low quality scores.\r\n", " r: rescue barcodes and RAD-Tags.\r\n", " t: truncate final read length to this value.\r\n", " E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger, default) or 'phred64' (Illumina 1.3 - 1.5).\r\n", " D: capture discarded reads to a file.\r\n", " w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).\r\n", " s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).\r\n", " h: display this help messsage.\r\n", "\r\n", " Barcode options:\r\n", " --inline_null: barcode is inline with sequence, occurs only on single-end read (default).\r\n", " --index_null: barcode is provded in FASTQ header, occurs only on single-end read.\r\n", " --inline_inline: barcode is inline with sequence, occurs on single and paired-end read.\r\n", " --index_index: barcode is provded in FASTQ header, occurs on single and paired-end read.\r\n", " --inline_index: barcode is inline with sequence on single-end read, occurs in FASTQ header for paired-end read.\r\n", " --index_inline: barcode occurs in FASTQ header for single-end read, is inline with sequence on paired-end read.\r\n", "\r\n", " Restriction enzyme options:\r\n", " -e , --renz_1 : provide the restriction enzyme used (cut site occurs on single-end read)\r\n", " --renz_2 : if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read).\r\n", " Currently supported enzymes include:\r\n", " 'apeKI', 'apoI', 'bamHI', 'bgIII', 'bstYI', 'claI', 'dpnII', 'eaeI', \r\n", " 'ecoRI', 'ecoRV', 'ecoT22I', 'hindIII', 'mluCI', 'mseI', 'mspI', 'ndeI', \r\n", " 'nheI', 'nlaIII', 'notI', 'nsiI', 'pstI', 'sacI', 'sau3AI', 'sbfI', \r\n", " 'sexAI', 'sgrAI', 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI'\r\n", " Adapter options:\r\n", " --adapter_1 : provide adaptor sequence that may occur on the single-end read for filtering.\r\n", " --adapter_2 : provide adaptor sequence that may occur on the paired-read for filtering.\r\n", " --adapter_mm : number of mismatches allowed in the adapter sequence.\r\n", "\r\n", " Output options:\r\n", " --merge: if no barcodes are specified, merge all input files into a single output file.\r\n", "\r\n", " Advanced options:\r\n", " --filter_illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing.\r\n", " --disable_rad_check: disable checking if the RAD site is intact.\r\n", " --len_limit : specify a minimum sequence length (useful if your data has already been trimmed).\r\n", " --barcode_dist: provide the nucleotide distance between barcodes. This allows for barcode rescue if \r\n", " there are less than distance-1 sequencing errors in the barcode (default 2).\r\n" ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "!head ./data/barcodes.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "AAACGG\r\n", "AACGTT\r\n", "AACTGA\r\n", "AAGACG\r\n", "AAGCTA\r\n", "AATATC\r\n", "AATGAG\r\n", "ACAAGA\r\n", "ACAGCG\r\n", "ACATAC\r\n" ] } ], "prompt_number": 37 }, { "cell_type": "code", "collapsed": false, "input": [ "!process_radtags \\\n", "-p /Users/sr320/data-genomic/OlyO-rad01/lane1_2 \\\n", "-o /Users/sr320/data-genomic/OlyO-rad01/out_01/ \\\n", "-b ./data/barcodes.txt \\\n", "-e sbfI \\\n", "-r -c -q -D \\\n", "-i gzfastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Using Phred+33 encoding for quality scores.\r\n", "Found 2 input file(s).\r\n", "Searching for single-end, inlined barcodes.\r\n", "Loaded 96 barcodes (6bp).\r\n", "Processing file 1 of 2 [lane1_NoIndex_L001_R1_001.fastq.gz]\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 10000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 20000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 30000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 40000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 50000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 60000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 70000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 80000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 90000 \r" ] }, { "output_type": 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200000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 210000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 220000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 230000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 240000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 250000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 260000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 270000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 280000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 290000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 300000 \r" ] }, { "output_type": "stream", "stream": 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15900000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15910000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15920000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15930000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15940000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15950000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15960000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15970000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15980000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15990000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 16000000 \r", " 16000000 total reads; -7909635 ambiguous barcodes; -6738305 ambiguous RAD-Tags; +6217627 recovered; -293307 low quality reads; 1058753 retained reads.\r\n", "Processing file 2 of 2 [lane1_NoIndex_L001_R1_002.fastq.gz]\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 10000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 20000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 30000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 40000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 50000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 60000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 70000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 80000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 90000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 100000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 110000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 120000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 130000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 140000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 150000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 160000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 170000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 180000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 190000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 200000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 210000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 220000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 230000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 240000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 250000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 260000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 270000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 280000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 290000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 300000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 310000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 320000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 330000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 340000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 350000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 360000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 370000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 380000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 390000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 400000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 410000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 420000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 430000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 440000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 450000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 460000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 470000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 480000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 490000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 500000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 510000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 520000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 530000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 540000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 550000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 560000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 570000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 580000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 590000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 600000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 610000 \r" ] }, { "output_type": "stream", "stream": 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"output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15690000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15700000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15710000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15720000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15730000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15740000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15750000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15760000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15770000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15780000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15790000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15800000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15810000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15820000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15830000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15840000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15850000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15860000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15870000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15880000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15890000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15900000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15910000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15920000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15930000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15940000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15950000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15960000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15970000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15980000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15990000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 16000000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " 16000000 total reads; -7891081 ambiguous barcodes; -6751949 ambiguous RAD-Tags; +6230063 recovered; -269179 low quality reads; 1087791 retained reads.\r\n", "Closing files, flushing buffers...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Outputing details to log: '/Users/sr320/data-genomic/OlyO-rad01/out_01/process_radtags.log'\r\n", "\r\n", "32000000 total sequences;\r\n", " 15800716 ambiguous barcode drops;\r\n", " 562486 low quality read drops;\r\n", " 13490254 ambiguous RAD-Tag drops;\r\n", "2146544 retained reads.\r\n" ] } ], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "!curl https://raw.githubusercontent.com/jheare/Fish546-Jake/master/data/decradbarcodes3.txt > ./data/codewid" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " % Total % Received % Xferd Average Speed Time Time Time Current\r\n", " Dload Upload Total Spent Left Speed\r\n", "\r", " 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "100 1536 100 1536 0 0 6475 0 --:--:-- --:--:-- --:--:-- 6481\r\n" ] } ], "prompt_number": 10 }, { "cell_type": "code", "collapsed": false, "input": [ "!head ./data/codewid" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "AAACGG \t \t HL01\r\n", "AACGTT \t \t HL09\r\n", "AACTGA \t \t HL17\r\n", "AAGACG \t \t HL25\r\n", "AAGCTA \t \t NF01\r\n", "AATATC \t \t NF09\r\n", "AATGAG \t \t NF17\r\n", "ACAAGA \t \t NF25\r\n", "ACAGCG \t \t SN01\r\n", "ACATAC \t \t SN09\r\n" ] } ], "prompt_number": 38 }, { "cell_type": "code", "collapsed": false, "input": [ "!cut -f3 ./data/codewid > ./data/id\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 39 }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Problem - ID column had a space prefix" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head ./data/id" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " HL01\r\n", " HL09\r\n", " HL17\r\n", " HL25\r\n", " NF01\r\n", " NF09\r\n", " NF17\r\n", " NF25\r\n", " SN01\r\n", " SN09\r\n" ] } ], "prompt_number": 67 }, { "cell_type": "code", "collapsed": false, "input": [ "!head ./data/id | cut -c 2-" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "HL01\r\n", "HL09\r\n", "HL17\r\n", "HL25\r\n", "NF01\r\n", "NF09\r\n", "NF17\r\n", "NF25\r\n", "SN01\r\n", "SN09\r\n" ] } ], "prompt_number": 70 }, { "cell_type": "code", "collapsed": false, "input": [ "!cat ./data/id | cut -c 2- > ./data/id_nospace\n", "\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 71 }, { "cell_type": "code", "collapsed": false, "input": [ "!paste ./data/barcodes.txt ./data/id_nospace > ./data/codes_id.txt" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 72 }, { "cell_type": "code", "collapsed": false, "input": [ "!head ./data/codes_id.txt" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "AAACGG\tHL01\r\n", "AACGTT\tHL09\r\n", "AACTGA\tHL17\r\n", "AAGACG\tHL25\r\n", "AAGCTA\tNF01\r\n", "AATATC\tNF09\r\n", "AATGAG\tNF17\r\n", "ACAAGA\tNF25\r\n", "ACAGCG\tSN01\r\n", "ACATAC\tSN09\r\n" ] } ], "prompt_number": 73 }, { "cell_type": "code", "collapsed": false, "input": [ "#mkdir /Users/sr320/data-genomic/OlyO-rad01/out_02" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 25 }, { "cell_type": "code", "collapsed": false, "input": [ "!process_radtags \\\n", "-p /Users/sr320/data-genomic/OlyO-rad01/lane1_2 \\\n", "-o /Users/sr320/data-genomic/OlyO-rad01/out_02/ \\\n", "-b ./data/codes_id.txt \\\n", "-e sbfI \\\n", "-r -c -q -D \\\n", "-i gzfastq" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Using Phred+33 encoding for quality scores.\r\n", "Found 2 input file(s).\r\n", "Searching for single-end, inlined barcodes.\r\n", "Loaded 96 barcodes (6bp).\r\n", "Processing file 1 of 2 [lane1_NoIndex_L001_R1_001.fastq.gz]\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 10000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 20000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 30000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 40000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 50000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 60000 \r" ] }, { "output_type": "stream", "stream": "stdout", 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"output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15780000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15790000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15800000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15810000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15820000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15830000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15840000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15850000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15860000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15870000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15880000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15890000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15900000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15910000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15920000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15930000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15940000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15950000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15960000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15970000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15980000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15990000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 16000000 \r", " 16000000 total reads; -7909635 ambiguous barcodes; -6738305 ambiguous RAD-Tags; +6217627 recovered; -293307 low quality reads; 1058753 retained reads.\r\n", "Processing file 2 of 2 [lane1_NoIndex_L001_R1_002.fastq.gz]\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 10000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 20000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 30000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 40000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 50000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 60000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 70000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 80000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 90000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 100000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 110000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 120000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 130000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 140000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 150000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 160000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " 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380000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 390000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 400000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 410000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 420000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 430000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 440000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 450000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 460000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 470000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 480000 \r" ] }, { "output_type": "stream", "stream": 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910000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 920000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 930000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 940000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 950000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 960000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 970000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 980000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 990000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 1000000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 1010000 \r" ] }, { "output_type": "stream", "stream": 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"stdout", "text": [ " Processing RAD-Tag 15770000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15780000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15790000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15800000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15810000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15820000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15830000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15840000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15850000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15860000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15870000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15880000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15890000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15900000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15910000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15920000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15930000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15940000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15950000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15960000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15970000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15980000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 15990000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " Processing RAD-Tag 16000000 \r" ] }, { "output_type": "stream", "stream": "stdout", "text": [ " 16000000 total reads; -7891081 ambiguous barcodes; -6751949 ambiguous RAD-Tags; +6230063 recovered; -269179 low quality reads; 1087791 retained reads.\r\n", "Closing files, flushing buffers...\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Outputing details to log: '/Users/sr320/data-genomic/OlyO-rad01/out_02/process_radtags.log'\r\n", "\r\n", "32000000 total sequences;\r\n", " 15800716 ambiguous barcode drops;\r\n", " 562486 low quality read drops;\r\n", " 13490254 ambiguous RAD-Tag drops;\r\n", "2146544 retained reads.\r\n" ] } ], "prompt_number": 74 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }