Starting /dee2/code/volunteer_pipeline.sh ERR9452011 current disk space = 1548612304896 free memory = 1601581408 ERR9452011 SRAfilesize 306d290b9d222223ddaaeff569b80798 ERR9452011.sra ERR9452011.sra file validated ERR9452011 is single end ERR9452011 is conventional basespace ERR9452011 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452011_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.14425 37.0 37.0 37.0 37.0 37.0 2 36.5535 37.0 37.0 37.0 37.0 37.0 3 36.60025 37.0 37.0 37.0 37.0 37.0 4 36.625 37.0 37.0 37.0 37.0 37.0 5 36.615 37.0 37.0 37.0 37.0 37.0 6 36.5975 37.0 37.0 37.0 37.0 37.0 7 36.653 37.0 37.0 37.0 37.0 37.0 8 36.613 37.0 37.0 37.0 37.0 37.0 9 36.642 37.0 37.0 37.0 37.0 37.0 10 36.614 37.0 37.0 37.0 37.0 37.0 11 36.62 37.0 37.0 37.0 37.0 37.0 12 36.685 37.0 37.0 37.0 37.0 37.0 13 36.67 37.0 37.0 37.0 37.0 37.0 14 36.671 37.0 37.0 37.0 37.0 37.0 15 36.5905 37.0 37.0 37.0 37.0 37.0 16 36.64 37.0 37.0 37.0 37.0 37.0 17 36.594 37.0 37.0 37.0 37.0 37.0 18 36.6315 37.0 37.0 37.0 37.0 37.0 19 36.6905 37.0 37.0 37.0 37.0 37.0 20 36.585 37.0 37.0 37.0 37.0 37.0 21 36.6035 37.0 37.0 37.0 37.0 37.0 22 36.6105 37.0 37.0 37.0 37.0 37.0 23 36.6665 37.0 37.0 37.0 37.0 37.0 24 36.7205 37.0 37.0 37.0 37.0 37.0 25 36.6805 37.0 37.0 37.0 37.0 37.0 26 36.649 37.0 37.0 37.0 37.0 37.0 27 36.6825 37.0 37.0 37.0 37.0 37.0 28 36.721 37.0 37.0 37.0 37.0 37.0 29 36.7295 37.0 37.0 37.0 37.0 37.0 30 36.714 37.0 37.0 37.0 37.0 37.0 31 36.6845 37.0 37.0 37.0 37.0 37.0 32 36.6645 37.0 37.0 37.0 37.0 37.0 33 36.675 37.0 37.0 37.0 37.0 37.0 34 36.6955 37.0 37.0 37.0 37.0 37.0 35 36.699 37.0 37.0 37.0 37.0 37.0 36 36.723 37.0 37.0 37.0 37.0 37.0 37 36.6775 37.0 37.0 37.0 37.0 37.0 38 36.6185 37.0 37.0 37.0 37.0 37.0 39 36.662 37.0 37.0 37.0 37.0 37.0 40 36.7295 37.0 37.0 37.0 37.0 37.0 41 36.638 37.0 37.0 37.0 37.0 37.0 42 36.677 37.0 37.0 37.0 37.0 37.0 43 36.612 37.0 37.0 37.0 37.0 37.0 44 36.605 37.0 37.0 37.0 37.0 37.0 45 36.614 37.0 37.0 37.0 37.0 37.0 46 36.58 37.0 37.0 37.0 37.0 37.0 47 36.549 37.0 37.0 37.0 37.0 37.0 48 36.6285 37.0 37.0 37.0 37.0 37.0 49 36.6835 37.0 37.0 37.0 37.0 37.0 50 36.611 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 3.0 24 2.0 25 1.0 26 3.0 27 8.0 28 8.0 29 13.0 30 16.0 31 19.0 32 21.0 33 38.0 34 63.0 35 108.0 36 941.0 37 2756.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 17.191039516737984 31.83991945633023 21.973319909388373 28.995721117543415 2 29.725 27.725 21.375 21.175 3 34.858714678669664 26.981745436359088 15.503875968992247 22.655663915978995 4 36.25 31.55 15.675 16.525000000000002 5 21.375 29.65 17.875 31.1 6 25.775 22.675 31.05 20.5 7 27.375 34.55 19.275000000000002 18.8 8 23.1 24.6 32.2 20.1 9 23.825 32.75 22.225 21.2 10 38.45 22.025 19.5 20.025000000000002 11 23.35 24.725 25.374999999999996 26.55 12 22.75 24.474999999999998 31.324999999999996 21.45 13 23.775 22.55 19.775000000000002 33.900000000000006 14 26.625 37.55 19.5 16.325 15 30.4 31.225 20.775 17.599999999999998 16 21.3 35.025 25.7 17.974999999999998 17 23.95 29.425 32.45 14.174999999999999 18 27.150000000000002 26.55 22.525000000000002 23.775 19 38.625 29.775000000000002 17.4 14.2 20 34.975 30.375000000000004 20.424999999999997 14.224999999999998 21 25.874999999999996 44.75 14.099999999999998 15.275 22 28.975 40.300000000000004 14.825 15.9 23 38.375 34.55 14.124999999999998 12.950000000000001 24 32.05 41.05 13.05 13.850000000000001 25 40.225 35.525 10.45 13.8 26 35.825 29.725 12.1 22.35 27 30.55 45.925 6.775 16.75 28 35.85 33.6 7.7 22.85 29 32.25 42.75 4.45 20.549999999999997 30 30.925000000000004 39.85 3.975 25.25 31 38.7 34.825 4.5249999999999995 21.95 32 28.325 36.075 13.325000000000001 22.275 33 23.375 35.125 6.325 35.175 34 28.999999999999996 28.549999999999997 16.125 26.325 35 28.375 30.5 11.525 29.599999999999998 36 21.875 37.525 10.424999999999999 30.175 37 19.400000000000002 33.6 15.299999999999999 31.7 38 20.549999999999997 27.825 15.75 35.875 39 17.125 23.775 25.95 33.15 40 19.400000000000002 24.9 19.825 35.875 41 16.25 21.275 21.75 40.725 42 17.549999999999997 31.825 21.125 29.5 43 22.925 24.099999999999998 22.975 30.0 44 16.25 23.075000000000003 27.1 33.575 45 12.325 28.025 21.224999999999998 38.425 46 15.625 32.975 17.625 33.775 47 10.125 24.224999999999998 19.35 46.300000000000004 48 10.674999999999999 25.15 18.15 46.025 49 10.975 32.925 15.25 40.849999999999994 50 9.725 22.125 17.474999999999998 50.675000000000004 >>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 1.0 16 2.0 17 1.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 1.0 27 0.5 28 0.0 29 0.5 30 1.0 31 1.0 32 1.0 33 1.0 34 1.0 35 3.0 36 5.0 37 10.5 38 16.0 39 35.0 40 54.0 41 72.5 42 91.0 43 112.0 44 133.0 45 237.0 46 341.0 47 561.0 48 781.0 49 629.0 50 477.0 51 473.5 52 470.0 53 641.5 54 813.0 55 632.5 56 452.0 57 319.5 58 187.0 59 147.0 60 107.0 61 69.0 62 31.0 63 23.5 64 16.0 65 12.0 66 8.0 67 9.0 68 10.0 69 6.0 70 2.0 71 1.0 72 0.0 73 0.0 74 0.0 75 0.0 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 0.675 2 0.0 3 0.025 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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 55.15 #Duplication Level Percentage of deduplicated Percentage of total 1 82.7289211242067 45.625 2 10.018132366273798 11.05 3 3.218495013599275 5.325 4 1.087941976427924 2.4 5 0.5893019038984587 1.625 6 0.40797824116047143 1.35 7 0.22665457842248413 0.8750000000000001 8 0.1359927470534905 0.6 9 0.04533091568449683 0.22499999999999998 >10 1.2692656391659112 13.275 >50 0.1813236627379873 6.45 >100 0.09066183136899365 11.200000000000001 >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 AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAC 276 6.9 TruSeq Adapter, Index 7 (97% over 35bp) CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 172 4.3 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAC 73 1.825 TruSeq Adapter, Index 7 (97% over 35bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 72 1.7999999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 60 1.5 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 53 1.325 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 41 1.0250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 36 0.8999999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA 35 0.8750000000000001 TruSeq Adapter, Index 7 (100% over 35bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 31 0.775 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC 27 0.675 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 22 0.5499999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 22 0.5499999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACC 17 0.42500000000000004 TruSeq Adapter, Index 7 (97% over 35bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA 10 0.25 TruSeq Adapter, Index 7 (100% over 35bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CTCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA 7 0.17500000000000002 TruSeq Adapter, Index 7 (100% over 35bp) TGCGGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CGGGGCGTGGACTGTTGTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TTGAGTGCAGCGTTGATGAACAGATCGGAAGAGCACACGTCTGAACTCCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GGGGATGTAGCTCAGATGGTAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGGGTGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 5 0.125 No Hit CGACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCT 5 0.125 TruSeq Adapter, Index 7 (97% over 35bp) TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTT 5 0.125 TruSeq Adapter, Index 7 (97% over 35bp) TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) >>END_MODULE >>Adapter Content fail #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 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10 0.225 0.0 0.0 0.0 0.0 11 0.55 0.0 0.0 0.0 0.0 12 1.1 0.0 0.0 0.0 0.0 13 2.825 0.0 0.0 0.0 0.0 14 13.775 0.0 0.0 0.0 0.0 15 17.275 0.0 0.0 0.0 0.0 16 21.45 0.0 0.0 0.0 0.0 17 28.8 0.0 0.0 0.0 0.0 18 34.1 0.0 0.0 0.0 0.0 19 41.05 0.0 0.0 0.0 0.0 20 49.425 0.0 0.0 0.0 0.0 21 57.15 0.0 0.0 0.0 0.0 22 64.675 0.0 0.0 0.0 0.0 23 73.95 0.0 0.0 0.0 0.0 24 79.425 0.0 0.0 0.0 0.0 25 85.925 0.0 0.0 0.0 0.0 26 89.4 0.0 0.0 0.0 0.0 27 92.175 0.0 0.0 0.0 0.0 28 94.2 0.0 0.0 0.0 0.0 29 95.675 0.0 0.0 0.0 0.0 30 96.75 0.0 0.0 0.0 0.0 31 97.475 0.0 0.0 0.0 0.0 32 97.9 0.0 0.0 0.0 0.0 33 98.325 0.0 0.0 0.0 0.0 34 98.65 0.0 0.0 0.0 0.0 35 98.8 0.0 0.0 0.0 0.0 36 98.875 0.0 0.0 0.0 0.0 37 98.975 0.0 0.0 0.0 0.0 38 98.975 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 25 3.7020465E-5 43.9875 9 TAGCTCA 25 3.7020465E-5 43.9875 8 GCTCAGA 25 3.7020465E-5 43.9875 10 CTCAGAT 35 2.688849E-4 31.419643 11 CTAACGA 30 0.004790254 29.696201 1 TCACCAC 50 6.496033E-5 26.3925 44 GTCACCA 70 6.368369E-4 18.851786 43 AGTCACC 115 2.530529E-6 17.2125 44 CAGTCAC 140 1.6524986E-5 14.13884 43 CCAGTCA 150 3.1770152E-5 13.196251 42 TCCAGTC 200 3.41721E-5 10.996875 44 CTCCAGT 245 2.7071583E-4 8.97704 43 ACTCCAG 260 4.929754E-4 8.459134 42 AACTCCA 285 0.0012362697 7.717105 41 GAACTCC 330 0.005268409 6.6647725 40 TGAACTC 340 0.0070559066 6.46875 39 >>END_MODULE Rejected 933202 READS because READLEN < 1 Read 933202 spots for ERR9452011.sra Written 933202 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra Rejected 933187 READS because READLEN < 1 Read 933187 spots for ERR9452011.sra Written 933187 spots for ERR9452011.sra SRR ids: ['ERR9452011.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ujfhh9p_ ERR9452011.sra spots: 18663755 blocks: [[1, 933187], [933188, 1866374], [1866375, 2799561], [2799562, 3732748], [3732749, 4665935], [4665936, 5599122], [5599123, 6532309], [6532310, 7465496], [7465497, 8398683], [8398684, 9331870], [9331871, 10265057], [10265058, 11198244], [11198245, 12131431], [12131432, 13064618], [13064619, 13997805], [13997806, 14930992], [14930993, 15864179], [15864180, 16797366], [16797367, 17730553], [17730554, 18663755]] ERR9452011 file size 2602890 ERR9452011 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 ERR9452011 ERR9452011_1.fastq Input file: ERR9452011_1.fastq trimmed: ERR9452011-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 Fri Dec 6 22:41:44 2024 >> started Fri Dec 6 22:41:54 2024 >> done (10.221s) 18663755 reads processed; of these: 6274322 (33.62%) short reads filtered out after trimming by size control 1476 ( 0.01%) empty reads filtered out after trimming by size control 12387957 (66.37%) reads available; of these: 1192690 ( 9.63%) trimmed reads available after processing 11195267 (90.37%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1192690 9.63% 19 0 0.00% 20 0 0.00% 21 0 0.00% 22 0 0.00% 23 0 0.00% 24 0 0.00% 25 0 0.00% 26 0 0.00% 27 0 0.00% 28 0 0.00% 29 0 0.00% 30 0 0.00% 31 0 0.00% 32 0 0.00% 33 0 0.00% 34 0 0.00% 35 0 0.00% 36 0 0.00% 37 0 0.00% 38 0 0.00% 39 0 0.00% 40 0 0.00% 41 0 0.00% 42 0 0.00% 43 0 0.00% 44 0 0.00% 45 0 0.00% 46 0 0.00% 47 0 0.00% 48 0 0.00% 49 0 0.00% 50 11195267 90.37% 12387957 reads passed initial QC criterion=sequence-density sequence-density=88.99 sequence-density-rank=1 fanout-score=19.44 fanout-score-rank=1 prefix-density=89.28 prefix-fanout=19.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTTACATCTCGTATGCCG criterion=fanout-score sequence-density=88.99 sequence-density-rank=1 fanout-score=19.44 fanout-score-rank=1 prefix-density=89.28 prefix-fanout=19.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTTACATCTCGTATGCCG 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: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTTACATCTCGTATGCCG -o ERR9452011 - Input file: STDIN trimmed: ERR9452011-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTTACATCTCGTATGCCG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Fri Dec 6 22:42:10 2024 >> started Fri Dec 6 22:42:23 2024 >> done (12.311s) 12109576 reads processed; of these: 27428 ( 0.23%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 12082134 (99.77%) reads available; of these: 10878060 (90.03%) trimmed reads available after processing 1204074 ( 9.97%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1183031 9.79% 19 1454727 12.04% 20 1545890 12.79% 21 1558711 12.90% 22 1716520 14.21% 23 942130 7.80% 24 1161792 9.62% 25 706770 5.85% 26 529034 4.38% 27 367600 3.04% 28 270481 2.24% 29 217402 1.80% 30 124339 1.03% 31 73746 0.61% 32 63680 0.53% 33 41598 0.34% 34 23484 0.19% 35 20116 0.17% 36 9171 0.08% 37 6510 0.05% 38 3902 0.03% 39 3149 0.03% 40 2269 0.02% 41 2952 0.02% 42 1013 0.01% 43 643 0.01% 44 495 0.00% 45 448 0.00% 46 321 0.00% 47 641 0.01% 48 0 0.00% 49 0 0.00% 50 49569 0.41% criterion=sequence-density sequence-density=0.82 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=14 fanout-score=9.28 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=1.0 sequence=TAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAG Started job on | Dec 06 22:42:47 Started mapping on | Dec 06 22:42:47 Finished on | Dec 06 22:43:27 Mapping speed, Million of reads per hour | 1112.45 Number of input reads | 12360515 Average input read length | 22 UNIQUE READS: Uniquely mapped reads number | 1229153 Uniquely mapped reads % | 9.94% Average mapped length | 22.40 Number of splices: Total | 46558 Number of splices: Annotated (sjdb) | 23501 Number of splices: GT/AG | 45478 Number of splices: GC/AG | 970 Number of splices: AT/AC | 8 Number of splices: Non-canonical | 102 Mismatch rate per base, % | 0.53% Deletion rate per base | 0.00% Deletion average length | 1.25 Insertion rate per base | 0.00% Insertion average length | 1.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5039010 % of reads mapped to multiple loci | 40.77% Number of reads mapped to too many loci | 5720005 % of reads mapped to too many loci | 46.28% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.77% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6092352 6092352 6092352 N_multimapping 5039010 5039010 5039010 N_noFeature 578760 644806 1150861 N_ambiguous 18552 5791 660 UnstrandedReadsAssigned:631841 PositiveStrandReadsAssigned:578556 NegativeStrandReadsAssigned:77632 Dataset is classified positive stranded MeadianReadLen=22 20thPercentileLength=19 echo kmer=19 ERR9452011 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: ERR9452011-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,360,515 reads, 1,268,904 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 926 rounds 52973 ERR9452011.ke.tsv 35125 ERR9452011.se.tsv 88098 total ==> ERR9452011.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 4.33991 1.48027 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 197.593 81.9592 KQK14071 474 375 17.2001 28.6138 ==> ERR9452011.se.tsv <== BRADI_1g14170v3 400 BRADI_1g53295v3 5 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 18 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 0 ERR9452011 completed mapping pipeline successfully