Starting /dee2/code/volunteer_pipeline.sh ERR9451996 current disk space = 1548857286656 free memory = 1603125524 ERR9451996 SRAfilesize 9b27926f264193770b0d597b1673ff7a ERR9451996.sra ERR9451996.sra file validated ERR9451996 is single end ERR9451996 is conventional basespace ERR9451996 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9451996_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.0405 37.0 37.0 37.0 37.0 37.0 2 36.58 37.0 37.0 37.0 37.0 37.0 3 36.62225 37.0 37.0 37.0 37.0 37.0 4 36.6095 37.0 37.0 37.0 37.0 37.0 5 36.563 37.0 37.0 37.0 37.0 37.0 6 36.6295 37.0 37.0 37.0 37.0 37.0 7 36.649 37.0 37.0 37.0 37.0 37.0 8 36.6365 37.0 37.0 37.0 37.0 37.0 9 36.6565 37.0 37.0 37.0 37.0 37.0 10 36.6365 37.0 37.0 37.0 37.0 37.0 11 36.63 37.0 37.0 37.0 37.0 37.0 12 36.5875 37.0 37.0 37.0 37.0 37.0 13 36.496 37.0 37.0 37.0 37.0 37.0 14 36.5695 37.0 37.0 37.0 37.0 37.0 15 36.5685 37.0 37.0 37.0 37.0 37.0 16 36.652 37.0 37.0 37.0 37.0 37.0 17 36.531 37.0 37.0 37.0 37.0 37.0 18 36.6845 37.0 37.0 37.0 37.0 37.0 19 36.5955 37.0 37.0 37.0 37.0 37.0 20 36.574 37.0 37.0 37.0 37.0 37.0 21 36.5735 37.0 37.0 37.0 37.0 37.0 22 36.5585 37.0 37.0 37.0 37.0 37.0 23 36.4035 37.0 37.0 37.0 37.0 37.0 24 36.6105 37.0 37.0 37.0 37.0 37.0 25 36.5695 37.0 37.0 37.0 37.0 37.0 26 36.5485 37.0 37.0 37.0 37.0 37.0 27 36.6265 37.0 37.0 37.0 37.0 37.0 28 36.6185 37.0 37.0 37.0 37.0 37.0 29 36.7525 37.0 37.0 37.0 37.0 37.0 30 36.732 37.0 37.0 37.0 37.0 37.0 31 36.6365 37.0 37.0 37.0 37.0 37.0 32 36.721 37.0 37.0 37.0 37.0 37.0 33 36.6045 37.0 37.0 37.0 37.0 37.0 34 36.618 37.0 37.0 37.0 37.0 37.0 35 36.6555 37.0 37.0 37.0 37.0 37.0 36 36.6685 37.0 37.0 37.0 37.0 37.0 37 36.7215 37.0 37.0 37.0 37.0 37.0 38 36.685 37.0 37.0 37.0 37.0 37.0 39 36.7275 37.0 37.0 37.0 37.0 37.0 40 36.691 37.0 37.0 37.0 37.0 37.0 41 36.6175 37.0 37.0 37.0 37.0 37.0 42 36.6115 37.0 37.0 37.0 37.0 37.0 43 36.527 37.0 37.0 37.0 37.0 37.0 44 36.57 37.0 37.0 37.0 37.0 37.0 45 36.6165 37.0 37.0 37.0 37.0 37.0 46 36.5665 37.0 37.0 37.0 37.0 37.0 47 36.6005 37.0 37.0 37.0 37.0 37.0 48 36.6975 37.0 37.0 37.0 37.0 37.0 49 36.7015 37.0 37.0 37.0 37.0 37.0 50 36.6125 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 2.0 26 1.0 27 8.0 28 10.0 29 9.0 30 18.0 31 12.0 32 29.0 33 37.0 34 71.0 35 120.0 36 1266.0 37 2416.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.800403225806452 28.78024193548387 23.336693548387096 29.08266129032258 2 22.5 30.025000000000002 29.4 18.075 3 27.33183295823956 30.03250812703176 20.030007501875467 22.605651412853213 4 26.85 38.975 16.925 17.25 5 21.575 27.1 21.175 30.15 6 32.025 22.475 25.25 20.25 7 26.825 33.6 22.1 17.474999999999998 8 21.45 30.325000000000003 25.724999999999998 22.5 9 21.65 27.525 24.349999999999998 26.474999999999998 10 36.125 23.275000000000002 19.625 20.974999999999998 11 22.075 30.7 29.375 17.849999999999998 12 23.575 28.925 26.325 21.175 13 26.700000000000003 23.1 19.225 30.975 14 32.1 31.775 21.099999999999998 15.024999999999999 15 21.775 35.949999999999996 23.225 19.05 16 21.349999999999998 27.975 33.15 17.525 17 23.025000000000002 27.474999999999998 33.6 15.9 18 27.6 24.575 29.875 17.95 19 35.6 27.474999999999998 21.349999999999998 15.575 20 24.675 33.324999999999996 28.325 13.675 21 21.8 40.075 18.675 19.45 22 24.525 33.050000000000004 19.925 22.5 23 31.175000000000004 37.25 18.175 13.4 24 29.475 32.225 21.25 17.05 25 23.9 42.575 15.5 18.025 26 36.575 25.275 19.55 18.6 27 30.349999999999998 38.85 11.425 19.375 28 35.325 28.675 21.6 14.399999999999999 29 32.675 30.599999999999998 11.0 25.724999999999998 30 41.075 37.175000000000004 8.175 13.575000000000001 31 44.9 35.4 6.4750000000000005 13.225000000000001 32 37.35 42.9 6.4 13.350000000000001 33 29.075 49.65 5.5 15.775 34 44.1 32.275 5.1 18.525 35 28.025 44.175 4.175 23.625 36 34.425 39.25 4.3 22.025 37 22.975 32.324999999999996 4.575 40.125 38 22.275 44.2 6.175 27.35 39 21.875 26.875 9.025 42.225 40 23.799999999999997 35.65 12.5 28.050000000000004 41 18.025 23.05 18.95 39.975 42 29.599999999999998 21.075 16.35 32.975 43 20.849999999999998 22.7 32.324999999999996 24.125 44 22.175 23.9 18.025 35.9 45 14.2 29.725 28.325 27.750000000000004 46 24.825 27.55 19.775000000000002 27.85 47 15.024999999999999 30.725 20.275000000000002 33.975 48 11.325000000000001 34.849999999999994 23.275000000000002 30.55 49 10.65 25.374999999999996 15.975 48.0 50 12.275 23.025000000000002 28.025 36.675000000000004 >>END_MODULE >>Per sequence GC content warn #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 0.5 16 1.0 17 0.5 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 2.0 28 3.0 29 1.5 30 0.0 31 0.5 32 1.0 33 1.0 34 1.0 35 7.5 36 14.0 37 27.5 38 41.0 39 88.0 40 135.0 41 184.0 42 233.0 43 251.5 44 270.0 45 411.0 46 552.0 47 691.0 48 830.0 49 624.5 50 419.0 51 418.5 52 418.0 53 424.0 54 430.0 55 358.0 56 286.0 57 231.0 58 176.0 59 130.5 60 85.0 61 64.0 62 43.0 63 30.0 64 17.0 65 16.0 66 15.0 67 17.5 68 20.0 69 13.5 70 7.0 71 4.0 72 1.0 73 1.0 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 0.8 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 62.949999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 82.80381254964257 52.125 2 11.675933280381255 14.7 3 1.9062748212867358 3.5999999999999996 4 1.072279586973789 2.7 5 0.5162827640984908 1.625 6 0.3177124702144559 1.2 7 0.3177124702144559 1.4000000000000001 8 0.19857029388403494 1.0 9 0.11914217633042098 0.675 >10 1.0325655281969817 13.975000000000001 >50 0.0 0.0 >100 0.03971405877680699 7.000000000000001 >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 CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 280 7.000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 41 1.0250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 37 0.9249999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 36 0.8999999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 33 0.8250000000000001 No Hit TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 32 0.8 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 27 0.675 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAC 23 0.575 TruSeq Adapter, Index 1 (97% over 36bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 16 0.4 No Hit GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 9 0.22499999999999998 No Hit AGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCTGA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TCAAAAGAGGAAAGGCTTGCGGTGGATAAGATCGGAAGAGCACACGTCTG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) ATAACCGTAGTAATTCTAGAGCTAAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAC 7 0.17500000000000002 TruSeq Adapter, Index 1 (97% over 36bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 7 0.17500000000000002 No Hit TTCATGGACGTTGATAAGATCCTTCCAGATCGGAAGAGCACACGTCTGAA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) ACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TTGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TGTCGTGCCAATTCAACATAAACCCAGATCGGAAGAGCACACGTCTGAAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 5 0.125 TruSeq Adapter, Index 7 (97% over 35bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) ATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GGTAGTTCGACCGCGGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC 5 0.125 No Hit GCCCCTATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CGACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) >>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 0.05 0.0 0.0 0.0 0.0 2 0.075 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.075 0.0 0.0 0.0 0.0 6 0.075 0.0 0.0 0.0 0.0 7 0.075 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.125 0.0 0.0 0.0 0.0 10 0.15 0.0 0.0 0.0 0.0 11 0.225 0.0 0.0 0.0 0.0 12 0.35 0.0 0.0 0.0 0.0 13 0.55 0.0 0.0 0.0 0.0 14 1.525 0.0 0.0 0.0 0.0 15 1.925 0.0 0.0 0.0 0.0 16 2.425 0.0 0.0 0.0 0.0 17 3.85 0.0 0.0 0.0 0.0 18 5.25 0.0 0.0 0.0 0.0 19 7.0 0.0 0.0 0.0 0.0 20 10.625 0.0 0.0 0.0 0.0 21 16.15 0.0 0.0 0.0 0.0 22 24.075 0.0 0.0 0.0 0.0 23 36.475 0.0 0.0 0.0 0.0 24 43.125 0.0 0.0 0.0 0.0 25 60.925 0.0 0.0 0.0 0.0 26 69.3 0.0 0.0 0.0 0.0 27 75.525 0.0 0.0 0.0 0.0 28 80.425 0.0 0.0 0.0 0.0 29 84.95 0.0 0.0 0.0 0.0 30 89.1 0.0 0.0 0.0 0.0 31 91.775 0.0 0.0 0.0 0.0 32 93.65 0.0 0.0 0.0 0.0 33 95.65 0.0 0.0 0.0 0.0 34 96.825 0.0 0.0 0.0 0.0 35 97.55 0.0 0.0 0.0 0.0 36 98.15 0.0 0.0 0.0 0.0 37 98.45 0.0 0.0 0.0 0.0 38 98.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTAACGA 40 1.4099138E-5 33.0 1 TAACGAA 50 6.483462E-5 26.4 2 GAACGAA 50 6.483462E-5 26.4 6 AACGATT 55 1.240733E-4 24.0 11 GAACGAT 55 1.240733E-4 24.0 10 GATTTGA 55 1.240733E-4 24.0 14 GAACAGA 55 1.240733E-4 24.0 19 ACGATTT 55 1.240733E-4 24.0 12 TTGAACA 55 1.240733E-4 24.0 17 CGATTTG 55 1.240733E-4 24.0 13 AACTCCA 75 1.3407134E-6 23.466667 44 TGAACAG 60 2.2403775E-4 22.0 18 GAACTCC 145 3.6379788E-12 21.24138 44 AACAGAT 70 6.3561747E-4 18.857143 20 TGAACTC 165 2.3646862E-11 18.666666 43 AACGAAC 100 1.6304873E-5 17.6 7 CGAACGA 105 2.4838535E-5 16.761906 9 ACGAACG 105 2.4838535E-5 16.761906 8 TTTGAAC 80 0.0015609474 16.5 16 ACAGATC 80 0.0015609474 16.5 21 >>END_MODULE Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682875 READS because READLEN < 1 Read 682875 spots for ERR9451996.sra Written 682875 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra Rejected 682861 READS because READLEN < 1 Read 682861 spots for ERR9451996.sra Written 682861 spots for ERR9451996.sra SRR ids: ['ERR9451996.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9ouzc44c ERR9451996.sra spots: 13657234 blocks: [[1, 682861], [682862, 1365722], [1365723, 2048583], [2048584, 2731444], [2731445, 3414305], [3414306, 4097166], [4097167, 4780027], [4780028, 5462888], [5462889, 6145749], [6145750, 6828610], [6828611, 7511471], [7511472, 8194332], [8194333, 8877193], [8877194, 9560054], [9560055, 10242915], [10242916, 10925776], [10925777, 11608637], [11608638, 12291498], [12291499, 12974359], [12974360, 13657234]] ERR9451996 file size 1898848 ERR9451996 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 ERR9451996 ERR9451996_1.fastq Input file: ERR9451996_1.fastq trimmed: ERR9451996-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 22:03:57 2024 >> started Fri Dec 6 22:04:04 2024 >> done (6.652s) 13657234 reads processed; of these: 647705 ( 4.74%) short reads filtered out after trimming by size control 980 ( 0.01%) empty reads filtered out after trimming by size control 13008549 (95.25%) reads available; of these: 261119 ( 2.01%) trimmed reads available after processing 12747430 (97.99%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 261119 2.01% 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 12747430 97.99% 13008549 reads passed initial QC criterion=sequence-density sequence-density=96.18 sequence-density-rank=1 fanout-score=23.31 fanout-score-rank=1 prefix-density=96.59 prefix-fanout=23.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTCACCATCTCGT criterion=fanout-score sequence-density=96.18 sequence-density-rank=1 fanout-score=23.31 fanout-score-rank=1 prefix-density=96.59 prefix-fanout=23.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTCACCATCTCGT 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTCACCATCTCGT -o ERR9451996 - Input file: STDIN trimmed: ERR9451996-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAACTCACCATCTCGT -- 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 22:04:21 2024 >> started Fri Dec 6 22:04:35 2024 >> done (14.310s) 12740332 reads processed; of these: 7247 ( 0.06%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 12733076 (99.94%) reads available; of these: 12412466 (97.48%) trimmed reads available after processing 320610 ( 2.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 262114 2.06% 19 474690 3.73% 20 715648 5.62% 21 976778 7.67% 22 1604867 12.60% 23 996113 7.82% 24 2397939 18.83% 25 1089722 8.56% 26 889641 6.99% 27 699509 5.49% 28 603832 4.74% 29 608313 4.78% 30 388508 3.05% 31 264613 2.08% 32 272487 2.14% 33 163404 1.28% 34 95134 0.75% 35 75403 0.59% 36 29434 0.23% 37 18585 0.15% 38 10091 0.08% 39 7380 0.06% 40 5628 0.04% 41 7624 0.06% 42 2811 0.02% 43 1573 0.01% 44 1087 0.01% 45 917 0.01% 46 616 0.00% 47 1147 0.01% 48 0 0.00% 49 0 0.00% 50 67468 0.53% criterion=sequence-density sequence-density=2.86 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=8 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=15 fanout-score=8.50 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=1.0 sequence=TAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAG Started job on | Dec 06 22:04:51 Started mapping on | Dec 06 22:04:53 Finished on | Dec 06 22:05:27 Mapping speed, Million of reads per hour | 1376.61 Number of input reads | 13001293 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 2287731 Uniquely mapped reads % | 17.60% Average mapped length | 24.03 Number of splices: Total | 41892 Number of splices: Annotated (sjdb) | 22844 Number of splices: GT/AG | 40868 Number of splices: GC/AG | 698 Number of splices: AT/AC | 21 Number of splices: Non-canonical | 305 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4782378 % of reads mapped to multiple loci | 36.78% Number of reads mapped to too many loci | 5476521 % of reads mapped to too many loci | 42.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.94% % of reads unmapped: other | 0.56% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5931184 5931184 5931184 N_multimapping 4782378 4782378 4782378 N_noFeature 1612271 1729344 2157950 N_ambiguous 21301 8165 657 UnstrandedReadsAssigned:654159 PositiveStrandReadsAssigned:550222 NegativeStrandReadsAssigned:129124 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=22 echo kmer=19 ERR9451996 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: ERR9451996-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,001,293 reads, 2,359,248 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,042 rounds 52973 ERR9451996.ke.tsv 35125 ERR9451996.se.tsv 88098 total ==> ERR9451996.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 5 1.73223 PNS24243 293 194 0 0 KQK14069 1603 1504 395.007 124.838 KQK14071 474 375 16.8142 21.3126 ==> ERR9451996.se.tsv <== BRADI_1g14170v3 471 BRADI_1g53295v3 4 BRADI_1g59795v3 6 BRADI_1g07683v3 1 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 31 BRADI_1g09890v3 0 BRADI_1g77505v3 6 BRADI_1g48960v3 0 ERR9451996 completed mapping pipeline successfully