Starting /dee2/code/volunteer_pipeline.sh ERR6133394 current disk space = 1547303837696 free memory = 1604387796 ERR6133394 SRAfilesize 00acdc11b38eac77001959f496fa6c6a ERR6133394.sra ERR6133394.sra file validated ERR6133394 is single end ERR6133394 is conventional basespace ERR6133394 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133394_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.85475 33.0 27.0 33.0 15.0 37.0 2 33.444 33.0 33.0 37.0 27.0 37.0 3 33.7305 37.0 33.0 37.0 27.0 37.0 4 34.0695 37.0 33.0 37.0 27.0 37.0 5 34.15775 37.0 33.0 37.0 27.0 37.0 6 34.558 37.0 33.0 37.0 27.0 37.0 7 35.35725 37.0 33.0 40.0 27.0 40.0 8 35.46525 37.0 33.0 40.0 33.0 40.0 9 35.535 37.0 33.0 40.0 33.0 40.0 10-11 35.428375 37.0 33.0 40.0 30.0 40.0 12-13 35.13075 37.0 33.0 38.5 27.0 40.0 14-15 35.144999999999996 37.0 33.0 38.5 27.0 40.0 16-17 34.952625 37.0 33.0 37.0 27.0 40.0 18-19 34.89425 37.0 33.0 37.0 27.0 40.0 20-21 34.248000000000005 37.0 33.0 37.0 27.0 40.0 22-23 34.170500000000004 37.0 33.0 37.0 27.0 40.0 24-25 33.515125 37.0 33.0 37.0 22.0 40.0 26-27 33.26275 37.0 33.0 37.0 22.0 40.0 28-29 32.854625 37.0 33.0 37.0 22.0 40.0 30-31 32.60175 35.0 33.0 37.0 22.0 40.0 32-33 32.309625 35.0 33.0 37.0 22.0 40.0 34-35 31.584 33.0 27.0 37.0 18.5 40.0 36-37 31.2065 33.0 27.0 37.0 15.0 38.5 38-39 31.535 33.0 27.0 37.0 22.0 40.0 40-41 31.818125000000002 33.0 27.0 37.0 22.0 40.0 42-43 31.313625000000002 33.0 27.0 37.0 18.5 40.0 44-45 31.0635 33.0 27.0 37.0 15.0 40.0 46-47 30.365000000000002 33.0 27.0 37.0 15.0 37.0 48-49 30.13875 33.0 27.0 37.0 15.0 37.0 50-51 29.912625 33.0 27.0 37.0 15.0 37.0 52-53 29.55975 33.0 27.0 37.0 15.0 37.0 54-55 29.43425 33.0 27.0 37.0 15.0 37.0 56-57 28.676250000000003 33.0 27.0 37.0 15.0 37.0 58-59 28.598875 33.0 27.0 35.0 15.0 37.0 60-61 28.048125 33.0 22.0 33.0 15.0 37.0 62-63 27.807000000000002 33.0 22.0 33.0 15.0 37.0 64-65 27.24225 33.0 22.0 33.0 10.5 37.0 66-67 26.74975 30.0 22.0 33.0 6.0 37.0 68-69 26.644 27.0 22.0 33.0 10.5 35.0 70-71 28.360233986435567 33.0 27.0 33.0 15.0 37.0 72-73 28.64159919591996 33.0 27.0 33.0 15.0 37.0 74-75 28.579943660495527 33.0 27.0 33.0 15.0 37.0 76-77 28.21392451126563 33.0 27.0 33.0 15.0 37.0 78-79 27.863711228869615 33.0 27.0 33.0 10.5 37.0 80-81 27.030316924595255 33.0 24.5 33.0 6.0 37.0 82-83 26.08320430169907 33.0 22.0 33.0 2.0 37.0 84-85 25.54939267812388 33.0 22.0 33.0 2.0 37.0 86-87 24.61622807017544 33.0 15.0 33.0 2.0 37.0 88-89 23.867461622807017 30.0 15.0 33.0 2.0 37.0 90-91 22.497121710526315 27.0 2.0 33.0 2.0 35.0 92-93 21.300986842105264 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 86.0 21 90.0 22 125.0 23 146.0 24 187.0 25 190.0 26 228.0 27 244.0 28 247.0 29 266.0 30 291.0 31 269.0 32 292.0 33 289.0 34 282.0 35 298.0 36 250.0 37 180.0 38 40.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 74.825 5.25 5.925 14.000000000000002 2 54.525 23.65 14.149999999999999 7.675 3 28.975 39.050000000000004 18.0 13.975000000000001 4 30.25 26.25 22.475 21.025 5 23.674999999999997 26.400000000000002 31.75 18.175 6 19.25 33.650000000000006 27.3 19.8 7 30.725 28.299999999999997 22.625 18.35 8 27.450000000000003 28.849999999999998 28.7 15.0 9 24.125 28.125 29.349999999999998 18.4 10-11 22.85 27.3875 30.275000000000002 19.4875 12-13 22.35 29.2 29.6625 18.787499999999998 14-15 20.95 29.675 30.099999999999998 19.275000000000002 16-17 22.725 30.337500000000002 25.1 21.837500000000002 18-19 21.9625 26.987499999999997 30.7875 20.2625 20-21 24.3 25.1875 29.9875 20.525 22-23 26.8125 23.2875 27.725 22.175 24-25 24.45 27.1625 28.237499999999997 20.150000000000002 26-27 22.55 25.95 31.974999999999998 19.525000000000002 28-29 24.8125 27.925 27.762500000000003 19.5 30-31 24.6625 27.0875 27.474999999999998 20.775 32-33 24.1125 24.7875 30.2875 20.8125 34-35 21.7 30.4625 27.1625 20.674999999999997 36-37 23.325000000000003 28.237499999999997 26.35 22.0875 38-39 26.724999999999998 24.2625 29.7 19.3125 40-41 24.9375 25.224999999999998 28.1875 21.65 42-43 25.474999999999998 28.299999999999997 27.450000000000003 18.775 44-45 21.5375 28.3875 28.825 21.25 46-47 22.900000000000002 28.549999999999997 27.737499999999997 20.8125 48-49 22.375 26.85 29.599999999999998 21.175 50-51 21.3625 28.1375 29.65 20.849999999999998 52-53 22.725 30.4375 26.687499999999996 20.150000000000002 54-55 22.95 29.025000000000002 29.7375 18.2875 56-57 24.8 27.200000000000003 27.700000000000003 20.3 58-59 24.3 27.712500000000002 26.687499999999996 21.3 60-61 24.9375 28.599999999999998 27.800000000000004 18.6625 62-63 21.762500000000003 29.275000000000002 28.875 20.0875 64-65 20.962500000000002 32.3125 28.1875 18.5375 66-67 23.5 27.525 28.3875 20.5875 68-69 20.325 29.0875 27.875 22.7125 70-71 23.718832226538026 28.37990226788623 27.452700162886856 20.448565342688887 72-73 24.189463019250255 26.545086119554206 29.15400202634245 20.11144883485309 74-75 24.77604299974405 28.01382134630151 27.55310980291784 19.6570258510366 76-77 23.428201811125486 26.9987063389392 28.15006468305304 21.423027166882278 78-79 21.747090362233557 27.95867660520466 29.880999084608344 20.413233947953447 80-81 21.192052980132452 31.642384105960264 27.933774834437088 19.2317880794702 82-83 21.233337821462232 27.777029756294603 28.544499798034202 22.445132624208966 84-85 22.272292776184624 25.590604943329236 30.35641130684146 21.78069097364468 86-87 22.25877192982456 29.221491228070175 27.700109649122805 20.819627192982455 88-89 21.080043859649123 29.015899122807014 28.85142543859649 21.052631578947366 90-91 24.451754385964914 28.71436403508772 27.15186403508772 19.682017543859647 92-93 20.545504385964914 33.34703947368421 26.398026315789476 19.709429824561404 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 2.0 18 4.0 19 4.0 20 3.0 21 3.0 22 5.0 23 6.0 24 7.5 25 12.0 26 19.0 27 26.0 28 36.0 29 43.0 30 39.0 31 45.0 32 59.0 33 67.0 34 77.0 35 94.0 36 136.5 37 211.5 38 250.5 39 216.0 40 208.0 41 229.5 42 237.0 43 245.5 44 216.5 45 203.0 46 198.0 47 151.0 48 122.0 49 117.5 50 110.0 51 106.5 52 104.5 53 113.0 54 126.0 55 117.0 56 101.5 57 95.0 58 73.5 59 43.5 60 30.0 61 21.5 62 16.0 63 13.5 64 13.5 65 15.0 66 11.5 67 7.0 68 7.5 69 14.5 70 13.0 71 5.0 72 4.5 73 2.5 74 1.0 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 19.0 71 19.0 72 28.0 73 20.0 74 14.0 75 28.0 76 14.0 77 22.0 78 25.0 79 23.0 80 26.0 81 35.0 82 27.0 83 25.0 84 27.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3648.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.125 #Duplication Level Percentage of deduplicated Percentage of total 1 91.36593591905566 67.72500000000001 2 4.418212478920742 6.550000000000001 3 1.0792580101180438 2.4 4 0.9106239460370995 2.7 5 0.5059021922428331 1.875 6 0.4721753794266442 2.1 7 0.2360876897133221 1.225 8 0.1011804384485666 0.6 9 0.06745362563237774 0.44999999999999996 >10 0.8094435075885328 12.8 >50 0.03372681281618887 1.575 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 63 1.575 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 45 1.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 40 1.0 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 37 0.9249999999999999 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 35 0.8750000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 35 0.8750000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 28 0.7000000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 26 0.65 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 25 0.625 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 23 0.575 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 22 0.5499999999999999 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 20 0.5 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 17 0.42500000000000004 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 17 0.42500000000000004 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 17 0.42500000000000004 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 16 0.4 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 15 0.375 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 14 0.35000000000000003 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 14 0.35000000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 13 0.325 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 12 0.3 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 11 0.27499999999999997 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 10 0.25 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 10 0.25 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 10 0.25 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 9 0.22499999999999998 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 9 0.22499999999999998 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 8 0.2 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 7 0.17500000000000002 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 7 0.17500000000000002 No Hit GTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCA 6 0.15 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 6 0.15 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 6 0.15 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 6 0.15 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 6 0.15 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 5 0.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 5 0.125 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit CACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATA 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit CAAGTCGAACGGGAAGTGGTGTTTCCAGTGGCGAACGGGTGAGTAACGCG 5 0.125 No Hit GGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0125 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAAATA 20 0.002921389 64.14375 7 AAATAAG 20 0.002921389 64.14375 9 AAAATAA 20 0.002921389 64.14375 8 TGAAAAT 25 0.00706927 51.315002 6 TAAAAAA 15 0.009905079 47.513885 86-87 >>END_MODULE Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra Rejected 42428 READS because READLEN < 1 Read 42428 spots for ERR6133394.sra Written 42428 spots for ERR6133394.sra SRR ids: ['ERR6133394.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ultbq_nn ERR6133394.sra spots: 848560 blocks: [[1, 42428], [42429, 84856], [84857, 127284], [127285, 169712], [169713, 212140], [212141, 254568], [254569, 296996], [296997, 339424], [339425, 381852], [381853, 424280], [424281, 466708], [466709, 509136], [509137, 551564], [551565, 593992], [593993, 636420], [636421, 678848], [678849, 721276], [721277, 763704], [763705, 806132], [806133, 848560]] ERR6133394 file size 184803 ERR6133394 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o ERR6133394 ERR6133394_1.fastq Input file: ERR6133394_1.fastq trimmed: ERR6133394-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 02:49:09 2024 >> started Sat Dec 7 02:49:10 2024 >> done (0.681s) 848560 reads processed; of these: 28 ( 0.00%) short reads filtered out after trimming by size control 4 ( 0.00%) empty reads filtered out after trimming by size control 848528 (100.00%) reads available; of these: 214164 (25.24%) trimmed reads available after processing 634364 (74.76%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 3 0.00% 21 0 0.00% 22 2 0.00% 23 1 0.00% 24 0 0.00% 25 1 0.00% 26 0 0.00% 27 0 0.00% 28 0 0.00% 29 10 0.00% 30 0 0.00% 31 4 0.00% 32 13 0.00% 33 3 0.00% 34 4 0.00% 35 2 0.00% 36 2 0.00% 37 1 0.00% 38 8 0.00% 39 17 0.00% 40 30 0.00% 41 11 0.00% 42 4 0.00% 43 8 0.00% 44 19 0.00% 45 18 0.00% 46 33 0.00% 47 37 0.00% 48 76 0.01% 49 86 0.01% 50 117 0.01% 51 161 0.02% 52 212 0.02% 53 268 0.03% 54 342 0.04% 55 497 0.06% 56 608 0.07% 57 938 0.11% 58 640 0.08% 59 868 0.10% 60 930 0.11% 61 1135 0.13% 62 1193 0.14% 63 1291 0.15% 64 1448 0.17% 65 1402 0.17% 66 1509 0.18% 67 1504 0.18% 68 1403 0.17% 69 1600 0.19% 70 5887 0.69% 71 5824 0.69% 72 7203 0.85% 73 7335 0.86% 74 7679 0.90% 75 8060 0.95% 76 8227 0.97% 77 9115 1.07% 78 9735 1.15% 79 10578 1.25% 80 11084 1.31% 81 13507 1.59% 82 14523 1.71% 83 14097 1.66% 84 15947 1.88% 85 10919 1.29% 86 11246 1.33% 87 12458 1.47% 88 14301 1.69% 89 15823 1.86% 90 16779 1.98% 91 17910 2.11% 92 15123 1.78% 93 566702 66.79% 848528 reads passed initial QC criterion=sequence-density sequence-density=4.38 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=22 prefix-density=4.46 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=31.69 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=1.6 sequence=CAAGATAATAATTTTTCGCTATTTACGATTTTATATTCTTGTTACTAGATACTCTATAGGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTTCGAAAGTCTTTTTTTTTAA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 02:49:23 Started mapping on | Dec 07 02:49:23 Finished on | Dec 07 02:49:29 Mapping speed, Million of reads per hour | 509.12 Number of input reads | 848528 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 361954 Uniquely mapped reads % | 42.66% Average mapped length | 88.44 Number of splices: Total | 15916 Number of splices: Annotated (sjdb) | 13202 Number of splices: GT/AG | 15383 Number of splices: GC/AG | 279 Number of splices: AT/AC | 16 Number of splices: Non-canonical | 238 Mismatch rate per base, % | 0.82% Deletion rate per base | 0.04% Deletion average length | 1.73 Insertion rate per base | 0.01% Insertion average length | 1.60 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 398236 % of reads mapped to multiple loci | 46.93% Number of reads mapped to too many loci | 42961 % of reads mapped to too many loci | 5.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.50% % of reads unmapped: other | 0.85% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 88338 88338 88338 N_multimapping 398236 398236 398236 N_noFeature 38192 42091 346498 N_ambiguous 14507 2912 110 UnstrandedReadsAssigned:309255 PositiveStrandReadsAssigned:316951 NegativeStrandReadsAssigned:15346 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=85 echo kmer=81 ERR6133394 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133394-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 848,528 reads, 573,444 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 802 rounds 52973 ERR6133394.ke.tsv 35125 ERR6133394.se.tsv 88098 total ==> ERR6133394.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 3 4.96389 PNS24243 293 194 0 0 KQK14069 1603 1504 6 9.05647 KQK14071 474 375 0 0 ==> ERR6133394.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 3 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 5 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR6133394 completed mapping pipeline successfully