Starting /dee2/code/volunteer_pipeline.sh ERR9452006 current disk space = 1548605382656 free memory = 1357987764 ERR9452006 SRAfilesize 3451f44ba86d76bec20528096296aef5 ERR9452006.sra ERR9452006.sra file validated ERR9452006 is single end ERR9452006 is conventional basespace ERR9452006 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452006_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 36.2855 37.0 37.0 37.0 37.0 37.0 2 36.5985 37.0 37.0 37.0 37.0 37.0 3 36.658 37.0 37.0 37.0 37.0 37.0 4 36.6505 37.0 37.0 37.0 37.0 37.0 5 36.6745 37.0 37.0 37.0 37.0 37.0 6 36.6665 37.0 37.0 37.0 37.0 37.0 7 36.7435 37.0 37.0 37.0 37.0 37.0 8 36.6505 37.0 37.0 37.0 37.0 37.0 9 36.69 37.0 37.0 37.0 37.0 37.0 10 36.7475 37.0 37.0 37.0 37.0 37.0 11 36.6545 37.0 37.0 37.0 37.0 37.0 12 36.681 37.0 37.0 37.0 37.0 37.0 13 36.7005 37.0 37.0 37.0 37.0 37.0 14 36.6815 37.0 37.0 37.0 37.0 37.0 15 36.631 37.0 37.0 37.0 37.0 37.0 16 36.683 37.0 37.0 37.0 37.0 37.0 17 36.6585 37.0 37.0 37.0 37.0 37.0 18 36.707 37.0 37.0 37.0 37.0 37.0 19 36.7215 37.0 37.0 37.0 37.0 37.0 20 36.674 37.0 37.0 37.0 37.0 37.0 21 36.7265 37.0 37.0 37.0 37.0 37.0 22 36.6985 37.0 37.0 37.0 37.0 37.0 23 36.7175 37.0 37.0 37.0 37.0 37.0 24 36.7725 37.0 37.0 37.0 37.0 37.0 25 36.714 37.0 37.0 37.0 37.0 37.0 26 36.7195 37.0 37.0 37.0 37.0 37.0 27 36.7405 37.0 37.0 37.0 37.0 37.0 28 36.8315 37.0 37.0 37.0 37.0 37.0 29 36.769 37.0 37.0 37.0 37.0 37.0 30 36.6725 37.0 37.0 37.0 37.0 37.0 31 36.8015 37.0 37.0 37.0 37.0 37.0 32 36.75 37.0 37.0 37.0 37.0 37.0 33 36.7435 37.0 37.0 37.0 37.0 37.0 34 36.682 37.0 37.0 37.0 37.0 37.0 35 36.6455 37.0 37.0 37.0 37.0 37.0 36 36.79 37.0 37.0 37.0 37.0 37.0 37 36.7805 37.0 37.0 37.0 37.0 37.0 38 36.7405 37.0 37.0 37.0 37.0 37.0 39 36.7325 37.0 37.0 37.0 37.0 37.0 40 36.7235 37.0 37.0 37.0 37.0 37.0 41 36.748 37.0 37.0 37.0 37.0 37.0 42 36.6835 37.0 37.0 37.0 37.0 37.0 43 36.6535 37.0 37.0 37.0 37.0 37.0 44 36.7 37.0 37.0 37.0 37.0 37.0 45 36.684 37.0 37.0 37.0 37.0 37.0 46 36.7075 37.0 37.0 37.0 37.0 37.0 47 36.717 37.0 37.0 37.0 37.0 37.0 48 36.7655 37.0 37.0 37.0 37.0 37.0 49 36.7295 37.0 37.0 37.0 37.0 37.0 50 36.6665 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 1.0 26 1.0 27 1.0 28 4.0 29 8.0 30 12.0 31 23.0 32 33.0 33 34.0 34 51.0 35 82.0 36 940.0 37 2810.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.117765475591344 31.202818319073984 21.187720181177657 29.491696024157022 2 29.925 28.4 20.8 20.875 3 35.225 26.275 16.225 22.275 4 37.35 30.975 14.6 17.075000000000003 5 23.3 29.525000000000002 16.825000000000003 30.349999999999998 6 26.125 22.725 30.3 20.849999999999998 7 28.025 33.7 20.875 17.4 8 22.75 23.325000000000003 32.75 21.175 9 24.099999999999998 32.625 22.475 20.8 10 39.525 21.4 20.175 18.9 11 23.45 25.4 25.224999999999998 25.924999999999997 12 23.9 24.95 31.15 20.0 13 24.65 24.05 18.224999999999998 33.074999999999996 14 26.224999999999998 38.05 19.275000000000002 16.45 15 31.025000000000002 30.475 20.424999999999997 18.075 16 21.875 36.5 23.3 18.325 17 24.6 28.999999999999996 31.775 14.625 18 26.35 27.875 21.675 24.099999999999998 19 36.65 30.55 18.3 14.499999999999998 20 34.25 31.3 19.975 14.475 21 27.3 42.025 14.45 16.225 22 28.825 40.275 15.4 15.5 23 39.35 33.85 13.900000000000002 12.9 24 31.25 42.675000000000004 12.15 13.925 25 40.975 34.25 10.975 13.8 26 34.875 31.574999999999996 10.549999999999999 23.0 27 31.900000000000002 44.275 6.8500000000000005 16.975 28 35.15 33.800000000000004 6.775 24.275 29 31.4 43.175000000000004 5.65 19.775000000000002 30 28.675 39.85 4.375 27.1 31 38.550000000000004 33.6 5.075 22.775000000000002 32 27.250000000000004 35.05 13.8 23.9 33 25.074999999999996 33.35 7.6 33.975 34 27.0 27.950000000000003 17.424999999999997 27.625 35 28.725 30.425 11.924999999999999 28.925 36 21.825 35.75 11.875 30.55 37 21.85 33.95 15.625 28.575 38 19.45 27.700000000000003 16.125 36.725 39 17.825 25.575 24.775 31.825 40 18.975 24.3 20.599999999999998 36.125 41 16.85 22.575 20.65 39.925 42 15.675 31.85 21.125 31.35 43 23.674999999999997 24.275 20.9 31.15 44 16.125 24.325 26.674999999999997 32.875 45 13.3 28.000000000000004 20.75 37.95 46 15.275 31.95 18.2 34.575 47 12.925 24.6 19.6 42.875 48 13.825000000000001 34.8 17.175 34.2 49 23.575 25.424999999999997 15.325 35.675000000000004 50 23.474999999999998 24.8 16.775000000000002 34.949999999999996 >>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 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 2.0 36 4.0 37 9.0 38 14.0 39 38.0 40 62.0 41 72.0 42 82.0 43 111.5 44 141.0 45 238.0 46 335.0 47 531.5 48 728.0 49 619.5 50 511.0 51 504.0 52 497.0 53 652.0 54 807.0 55 634.5 56 462.0 57 330.0 58 198.0 59 140.0 60 82.0 61 58.0 62 34.0 63 28.0 64 22.0 65 16.5 66 11.0 67 8.0 68 5.0 69 4.0 70 3.0 71 2.5 72 2.0 73 1.0 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 0.65 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 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 58.599999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 82.2098976109215 48.175000000000004 2 11.945392491467576 14.000000000000002 3 2.04778156996587 3.5999999999999996 4 1.151877133105802 2.7 5 0.5546075085324232 1.625 6 0.25597269624573377 0.8999999999999999 7 0.3412969283276451 1.4000000000000001 8 0.08532423208191127 0.4 9 0.2986348122866894 1.575 >10 0.9812286689419796 14.524999999999999 >50 0.042662116040955635 1.425 >100 0.08532423208191127 9.675 >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 AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGG 253 6.325 TruSeq Adapter, Index 15 (97% over 36bp) CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 134 3.35 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGG 57 1.425 TruSeq Adapter, Index 15 (97% over 36bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 45 1.125 TruSeq Adapter, Index 2 (97% over 35bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 45 1.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 41 1.0250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 37 0.9249999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 37 0.9249999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 36 0.8999999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 22 0.5499999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGC 21 0.525 TruSeq Adapter, Index 13 (97% over 37bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCT 14 0.35000000000000003 TruSeq Adapter, Index 13 (97% over 37bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 9 0.22499999999999998 TruSeq Adapter, Index 2 (97% over 35bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGGATATGGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGC 7 0.17500000000000002 TruSeq Adapter, Index 13 (97% over 37bp) CGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGG 6 0.15 TruSeq Adapter, Index 15 (97% over 36bp) TGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGC 6 0.15 TruSeq Adapter, Index 13 (97% over 37bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CTCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCT 5 0.125 TruSeq Adapter, Index 13 (97% over 37bp) CCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGGATTGTAGTTCAATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGC 5 0.125 TruSeq Adapter, Index 13 (97% over 35bp) AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TCAAAAGAGGAAAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 5 0.125 No Hit TCGATGCCAGAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGG 5 0.125 TruSeq Adapter, Index 15 (97% over 36bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TCCGACTTTGTGAAATGACTAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) >>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 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.175 0.0 0.0 0.0 0.0 10 0.25 0.0 0.0 0.0 0.0 11 0.725 0.0 0.0 0.0 0.0 12 1.75 0.0 0.0 0.0 0.0 13 3.35 0.0 0.0 0.0 0.0 14 14.15 0.0 0.0 0.0 0.0 15 18.05 0.0 0.0 0.0 0.0 16 23.375 0.0 0.0 0.0 0.0 17 30.475 0.0 0.0 0.0 0.0 18 35.9 0.0 0.0 0.0 0.0 19 42.875 0.0 0.0 0.0 0.0 20 51.1 0.0 0.0 0.0 0.0 21 57.725 0.0 0.0 0.0 0.0 22 65.675 0.0 0.0 0.0 0.0 23 73.525 0.0 0.0 0.0 0.0 24 78.375 0.0 0.0 0.0 0.0 25 83.675 0.0 0.0 0.0 0.0 26 87.75 0.0 0.0 0.0 0.0 27 90.375 0.0 0.0 0.0 0.0 28 92.5 0.0 0.0 0.0 0.0 29 94.2 0.0 0.0 0.0 0.0 30 95.475 0.0 0.0 0.0 0.0 31 96.4 0.0 0.0 0.0 0.0 32 96.975 0.0 0.0 0.0 0.0 33 97.45 0.0 0.0 0.0 0.0 34 97.75 0.0 0.0 0.0 0.0 35 98.075 0.0 0.0 0.0 0.0 36 98.25 0.0 0.0 0.0 0.0 37 98.3 0.0 0.0 0.0 0.0 38 98.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTATAGC 30 1.9515464E-6 44.0 5 AGGGCTA 30 1.9515464E-6 44.0 1 TAGCTCA 35 1.02281774E-7 44.0 8 GCTATAG 30 1.9515464E-6 44.0 4 ATAGCTC 30 1.9515464E-6 44.0 7 GGCTATA 30 1.9515464E-6 44.0 3 TATAGCT 30 1.9515464E-6 44.0 6 GGGCTAT 30 1.9515464E-6 44.0 2 AGCTCAG 40 2.923025E-7 38.500004 9 GCTCAGA 45 7.364706E-7 34.222225 10 TCACAGG 60 1.9002982E-7 29.333332 44 CTCAGAT 60 6.9657926E-6 25.666666 11 GTCACAG 75 1.3407134E-6 23.466667 43 AGTCACA 95 1.0464639E-5 18.526316 42 TCAGATC 90 1.6006906E-4 17.111113 12 CAGTCAC 125 1.10924615E-4 14.08 41 CCAGTCA 150 5.2259833E-4 11.733334 40 TCCAGTC 165 0.0011668158 10.666667 39 CTCCAGT 200 0.0058023334 8.8 38 CAGATCG 200 0.0058023334 8.8 13 >>END_MODULE Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861638 READS because READLEN < 1 Read 861638 spots for ERR9452006.sra Written 861638 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra Rejected 861633 READS because READLEN < 1 Read 861633 spots for ERR9452006.sra Written 861633 spots for ERR9452006.sra SRR ids: ['ERR9452006.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vlyrbeot ERR9452006.sra spots: 17232665 blocks: [[1, 861633], [861634, 1723266], [1723267, 2584899], [2584900, 3446532], [3446533, 4308165], [4308166, 5169798], [5169799, 6031431], [6031432, 6893064], [6893065, 7754697], [7754698, 8616330], [8616331, 9477963], [9477964, 10339596], [10339597, 11201229], [11201230, 12062862], [12062863, 12924495], [12924496, 13786128], [13786129, 14647761], [14647762, 15509394], [15509395, 16371027], [16371028, 17232665]] ERR9452006 file size 2401643 ERR9452006 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 ERR9452006 ERR9452006_1.fastq Input file: ERR9452006_1.fastq trimmed: ERR9452006-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 22:30:41 2024 >> started Fri Dec 6 22:30:49 2024 >> done (8.625s) 17232665 reads processed; of these: 6255249 (36.30%) short reads filtered out after trimming by size control 1450 ( 0.01%) empty reads filtered out after trimming by size control 10975966 (63.69%) reads available; of these: 1136568 (10.36%) trimmed reads available after processing 9839398 (89.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1136568 10.36% 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 9839398 89.64% 10975966 reads passed initial QC criterion=sequence-density sequence-density=88.12 sequence-density-rank=1 fanout-score=21.77 fanout-score-rank=1 prefix-density=88.50 prefix-fanout=21.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCTAACATCTCGTATGCCG criterion=fanout-score sequence-density=88.12 sequence-density-rank=1 fanout-score=21.77 fanout-score-rank=1 prefix-density=88.50 prefix-fanout=21.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCTAACATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCTAACATCTCGTATGCCG -o ERR9452006 - Input file: STDIN trimmed: ERR9452006-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCTAACATCTCGTATGCCG -- 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 22:31:07 2024 >> started Fri Dec 6 22:31:20 2024 >> done (13.123s) 10729315 reads processed; of these: 33177 ( 0.31%) short reads filtered out after trimming by size control 25 ( 0.00%) empty reads filtered out after trimming by size control 10696113 (99.69%) reads available; of these: 9544018 (89.23%) trimmed reads available after processing 1152095 (10.77%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1145371 10.71% 19 1313924 12.28% 20 1310983 12.26% 21 1298519 12.14% 22 1381172 12.91% 23 836617 7.82% 24 1011774 9.46% 25 624369 5.84% 26 468135 4.38% 27 337667 3.16% 28 256419 2.40% 29 207873 1.94% 30 131168 1.23% 31 83838 0.78% 32 72282 0.68% 33 53054 0.50% 34 32885 0.31% 35 26489 0.25% 36 14280 0.13% 37 10318 0.10% 38 6830 0.06% 39 5535 0.05% 40 4022 0.04% 41 4667 0.04% 42 1841 0.02% 43 1033 0.01% 44 793 0.01% 45 677 0.01% 46 461 0.00% 47 728 0.01% 48 0 0.00% 49 0 0.00% 50 52389 0.49% criterion=sequence-density sequence-density=0.80 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=46 fanout-score=9.43 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=1.5 sequence=TCTGTGAAGGGTTCGAGTTGGAGCACGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGCG Started job on | Dec 06 22:31:39 Started mapping on | Dec 06 22:31:40 Finished on | Dec 06 22:32:25 Mapping speed, Million of reads per hour | 875.42 Number of input reads | 10942764 Average input read length | 23 UNIQUE READS: Uniquely mapped reads number | 975624 Uniquely mapped reads % | 8.92% Average mapped length | 22.65 Number of splices: Total | 36464 Number of splices: Annotated (sjdb) | 19186 Number of splices: GT/AG | 35593 Number of splices: GC/AG | 745 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 120 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.00% Deletion average length | 1.23 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4403870 % of reads mapped to multiple loci | 40.24% Number of reads mapped to too many loci | 5241724 % of reads mapped to too many loci | 47.90% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.71% % of reads unmapped: other | 0.23% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5563270 5563270 5563270 N_multimapping 4403870 4403870 4403870 N_noFeature 479569 529587 914997 N_ambiguous 15543 4599 439 UnstrandedReadsAssigned:480512 PositiveStrandReadsAssigned:441438 NegativeStrandReadsAssigned:60188 Dataset is classified positive stranded MeadianReadLen=22 20thPercentileLength=19 echo kmer=19 ERR9452006 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: ERR9452006-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,942,764 reads, 995,257 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 975 rounds 52973 ERR9452006.ke.tsv 35125 ERR9452006.se.tsv 88098 total ==> ERR9452006.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 9 5.15027 PNS24243 293 194 0 0 KQK14069 1603 1504 362.815 189.4 KQK14071 474 375 5.2042e-05 0.000108959 ==> ERR9452006.se.tsv <== BRADI_1g14170v3 430 BRADI_1g53295v3 5 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR9452006 completed mapping pipeline successfully