Starting /dee2/code/volunteer_pipeline.sh ERR9451999 current disk space = 1548356075520 free memory = 1600326396 ERR9451999 SRAfilesize 78a2c955dd36421556cee7ac0be7d3d8 ERR9451999.sra ERR9451999.sra file validated ERR9451999 is single end ERR9451999 is conventional basespace ERR9451999 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9451999_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.266 37.0 37.0 37.0 37.0 37.0 2 36.555 37.0 37.0 37.0 37.0 37.0 3 36.615 37.0 37.0 37.0 37.0 37.0 4 36.716 37.0 37.0 37.0 37.0 37.0 5 36.6005 37.0 37.0 37.0 37.0 37.0 6 36.598 37.0 37.0 37.0 37.0 37.0 7 36.7765 37.0 37.0 37.0 37.0 37.0 8 36.626 37.0 37.0 37.0 37.0 37.0 9 36.67 37.0 37.0 37.0 37.0 37.0 10 36.6615 37.0 37.0 37.0 37.0 37.0 11 36.681 37.0 37.0 37.0 37.0 37.0 12 36.7055 37.0 37.0 37.0 37.0 37.0 13 36.7565 37.0 37.0 37.0 37.0 37.0 14 36.654 37.0 37.0 37.0 37.0 37.0 15 36.614 37.0 37.0 37.0 37.0 37.0 16 36.717 37.0 37.0 37.0 37.0 37.0 17 36.6215 37.0 37.0 37.0 37.0 37.0 18 36.636 37.0 37.0 37.0 37.0 37.0 19 36.708 37.0 37.0 37.0 37.0 37.0 20 36.6705 37.0 37.0 37.0 37.0 37.0 21 36.6615 37.0 37.0 37.0 37.0 37.0 22 36.5985 37.0 37.0 37.0 37.0 37.0 23 36.6585 37.0 37.0 37.0 37.0 37.0 24 36.668 37.0 37.0 37.0 37.0 37.0 25 36.668 37.0 37.0 37.0 37.0 37.0 26 36.6575 37.0 37.0 37.0 37.0 37.0 27 36.642 37.0 37.0 37.0 37.0 37.0 28 36.6445 37.0 37.0 37.0 37.0 37.0 29 36.5985 37.0 37.0 37.0 37.0 37.0 30 36.6515 37.0 37.0 37.0 37.0 37.0 31 36.6175 37.0 37.0 37.0 37.0 37.0 32 36.5215 37.0 37.0 37.0 37.0 37.0 33 36.555 37.0 37.0 37.0 37.0 37.0 34 36.429 37.0 37.0 37.0 37.0 37.0 35 36.438 37.0 37.0 37.0 37.0 37.0 36 36.441 37.0 37.0 37.0 37.0 37.0 37 36.5655 37.0 37.0 37.0 37.0 37.0 38 36.478 37.0 37.0 37.0 37.0 37.0 39 36.3935 37.0 37.0 37.0 37.0 37.0 40 36.442 37.0 37.0 37.0 37.0 37.0 41 36.409 37.0 37.0 37.0 37.0 37.0 42 36.517 37.0 37.0 37.0 37.0 37.0 43 36.4685 37.0 37.0 37.0 37.0 37.0 44 36.518 37.0 37.0 37.0 37.0 37.0 45 36.5375 37.0 37.0 37.0 37.0 37.0 46 36.588 37.0 37.0 37.0 37.0 37.0 47 36.585 37.0 37.0 37.0 37.0 37.0 48 36.6145 37.0 37.0 37.0 37.0 37.0 49 36.6975 37.0 37.0 37.0 37.0 37.0 50 36.6595 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 1.0 24 0.0 25 1.0 26 7.0 27 2.0 28 12.0 29 12.0 30 16.0 31 19.0 32 18.0 33 37.0 34 50.0 35 120.0 36 1403.0 37 2300.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 16.23931623931624 31.975867269984914 22.574157868275517 29.21065862242333 2 27.3 29.049999999999997 22.85 20.8 3 32.59129564782391 28.31415707853927 16.23311655827914 22.861430715357677 4 34.5 32.95 15.325 17.224999999999998 5 23.225 27.700000000000003 17.849999999999998 31.225 6 26.35 22.5 30.3 20.849999999999998 7 25.85 34.975 20.925 18.25 8 22.375 26.650000000000002 30.225 20.75 9 23.075000000000003 32.0 22.650000000000002 22.275 10 37.05 23.0 20.3 19.650000000000002 11 23.200000000000003 24.175 26.900000000000002 25.724999999999998 12 24.825 24.725 29.875 20.575 13 24.675 21.525 19.575 34.225 14 28.449999999999996 36.525 20.75 14.274999999999999 15 28.95 31.424999999999997 22.175 17.45 16 20.325 32.475 28.275 18.925 17 24.425 30.275000000000002 30.775000000000002 14.524999999999999 18 27.525 27.55 23.65 21.275 19 37.974999999999994 30.15 17.549999999999997 14.325 20 30.95 33.5 21.525 14.025000000000002 21 25.2 43.3 14.674999999999999 16.825000000000003 22 28.725 38.925 14.649999999999999 17.7 23 37.225 36.125 15.049999999999999 11.600000000000001 24 31.474999999999998 38.775 15.4 14.35 25 35.55 38.15 11.25 15.049999999999999 26 38.375 27.700000000000003 12.825000000000001 21.099999999999998 27 33.775 43.25 6.1 16.875 28 36.3 34.8 8.875 20.025000000000002 29 33.1 41.525 4.95 20.424999999999997 30 31.125000000000004 41.925000000000004 3.875 23.075000000000003 31 39.4 36.8 3.8 20.0 32 30.8 36.275 10.925 22.0 33 23.775 38.224999999999994 5.6000000000000005 32.4 34 30.525000000000002 28.325 13.450000000000001 27.700000000000003 35 25.825 32.675 10.674999999999999 30.825000000000003 36 21.925 37.325 10.575 30.175 37 20.175 31.025000000000002 13.750000000000002 35.05 38 21.425 30.15 15.25 33.175 39 18.825 22.75 23.825 34.599999999999994 40 19.25 26.0 20.875 33.875 41 15.950000000000001 20.275000000000002 24.125 39.65 42 19.3 28.199999999999996 21.05 31.45 43 21.825 25.95 24.9 27.325 44 16.85 25.75 23.025000000000002 34.375 45 11.525 29.325000000000003 22.675 36.475 46 16.575 31.35 19.875 32.2 47 11.0 24.075 20.25 44.675 48 9.425 34.599999999999994 20.3 35.675000000000004 49 11.5 35.05 13.8 39.65 50 11.774999999999999 27.125 26.650000000000002 34.449999999999996 >>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 0.5 10 1.0 11 0.5 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 0.5 22 1.0 23 1.0 24 1.0 25 1.0 26 1.0 27 1.0 28 1.0 29 0.5 30 0.0 31 0.0 32 0.0 33 0.5 34 1.0 35 2.0 36 3.0 37 14.5 38 26.0 39 42.5 40 59.0 41 79.5 42 100.0 43 126.5 44 153.0 45 289.5 46 426.0 47 659.5 48 893.0 49 801.0 50 709.0 51 609.5 52 510.0 53 490.5 54 471.0 55 406.5 56 342.0 57 255.5 58 169.0 59 120.5 60 72.0 61 54.0 62 36.0 63 25.0 64 14.0 65 10.0 66 6.0 67 4.5 68 3.0 69 2.0 70 1.0 71 1.0 72 1.0 73 0.5 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 0.5499999999999999 2 0.0 3 0.05 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 55.974999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 84.14470745868692 47.099999999999994 2 9.066547565877624 10.15 3 2.3671281822242074 3.975 4 1.0719071013845467 2.4 5 0.8039303260384101 2.25 6 0.2679767753461367 0.8999999999999999 7 0.31263957123715946 1.225 8 0.13398838767306834 0.6 9 0.1786511835640911 0.8999999999999999 >10 1.4292094685127288 14.825 >50 0.13398838767306834 4.475 >100 0.08932559178204555 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 AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAT 236 5.8999999999999995 TruSeq Adapter, Index 8 (97% over 36bp) CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 212 5.3 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 75 1.875 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 53 1.325 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 51 1.275 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 48 1.2 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 45 1.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAT 37 0.9249999999999999 TruSeq Adapter, Index 8 (97% over 36bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 34 0.8500000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 27 0.675 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 25 0.625 TruSeq Adapter, Index 7 (97% over 35bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 13 0.325 TruSeq Adapter, Index 7 (97% over 35bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TCGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATC 10 0.25 TruSeq Adapter, Index 9 (97% over 37bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAGT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AGGGCTATAGCTCAGTTCGGAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CTCGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAGT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) ATAACCGTAGTAATTCTAGAGCTAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCC 7 0.17500000000000002 TruSeq Adapter, Index 27 (97% over 38bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 6 0.15 No Hit TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCCG 6 0.15 TruSeq Adapter, Index 27 (97% over 38bp) TGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAT 5 0.125 TruSeq Adapter, Index 8 (97% over 36bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) ACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TTCATGGACGTTGATAAGATCCTTCCAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCGACTTTGTGAAATGACTAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GCGTCTGTAGTCCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CGACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) >>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 0.0 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10 0.15 0.0 0.0 0.0 0.0 11 0.5 0.0 0.0 0.0 0.0 12 1.125 0.0 0.0 0.0 0.0 13 2.025 0.0 0.0 0.0 0.0 14 10.5 0.0 0.0 0.0 0.0 15 13.675 0.0 0.0 0.0 0.0 16 17.725 0.0 0.0 0.0 0.0 17 24.55 0.0 0.0 0.0 0.0 18 30.125 0.0 0.0 0.0 0.0 19 35.925 0.0 0.0 0.0 0.0 20 44.425 0.0 0.0 0.0 0.0 21 53.65 0.0 0.0 0.0 0.0 22 62.4 0.0 0.0 0.0 0.0 23 72.675 0.0 0.0 0.0 0.0 24 77.35 0.0 0.0 0.0 0.0 25 85.25 0.0 0.0 0.0 0.0 26 89.175 0.0 0.0 0.0 0.0 27 91.85 0.0 0.0 0.0 0.0 28 94.1 0.0 0.0 0.0 0.0 29 95.65 0.0 0.0 0.0 0.0 30 96.875 0.0 0.0 0.0 0.0 31 97.55 0.0 0.0 0.0 0.0 32 97.95 0.0 0.0 0.0 0.0 33 98.375 0.0 0.0 0.0 0.0 34 98.6 0.0 0.0 0.0 0.0 35 98.7 0.0 0.0 0.0 0.0 36 98.725 0.0 0.0 0.0 0.0 37 98.725 0.0 0.0 0.0 0.0 38 98.725 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTATAGC 20 6.952051E-4 44.000004 5 AGGGCTA 20 6.952051E-4 44.000004 1 GCTATAG 20 6.952051E-4 44.000004 4 ATAGCTC 20 6.952051E-4 44.000004 7 GGCTATA 20 6.952051E-4 44.000004 3 TATAGCT 20 6.952051E-4 44.000004 6 GGGCTAT 20 6.952051E-4 44.000004 2 AGCTCAG 25 3.6958358E-5 44.0 9 TAGCTCA 25 3.6958358E-5 44.0 8 GCTCAGA 25 0.002084305 35.2 10 GTCACAA 45 7.364706E-7 34.222225 43 TCACAAT 45 7.364706E-7 34.222225 44 AGTCACA 60 6.9657926E-6 25.666666 42 CAGTCAC 100 1.6304873E-5 17.6 44 CCAGTCA 125 1.10924615E-4 14.08 43 TCCAGTC 155 6.8933814E-4 11.354839 42 CTCCAGT 185 0.003037992 9.513514 41 ACTCCAG 230 0.001702617 8.608696 44 AACTCCA 265 0.0061811972 7.4716988 43 >>END_MODULE Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754057 READS because READLEN < 1 Read 754057 spots for ERR9451999.sra Written 754057 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra Rejected 754044 READS because READLEN < 1 Read 754044 spots for ERR9451999.sra Written 754044 spots for ERR9451999.sra SRR ids: ['ERR9451999.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_iclp5od1 ERR9451999.sra spots: 15080893 blocks: [[1, 754044], [754045, 1508088], [1508089, 2262132], [2262133, 3016176], [3016177, 3770220], [3770221, 4524264], [4524265, 5278308], [5278309, 6032352], [6032353, 6786396], [6786397, 7540440], [7540441, 8294484], [8294485, 9048528], [9048529, 9802572], [9802573, 10556616], [10556617, 11310660], [11310661, 12064704], [12064705, 12818748], [12818749, 13572792], [13572793, 14326836], [14326837, 15080893]] ERR9451999 file size 2099050 ERR9451999 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 ERR9451999 ERR9451999_1.fastq Input file: ERR9451999_1.fastq trimmed: ERR9451999-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 22:19:24 2024 >> started Fri Dec 6 22:19:32 2024 >> done (7.894s) 15080893 reads processed; of these: 4606261 (30.54%) short reads filtered out after trimming by size control 1307 ( 0.01%) empty reads filtered out after trimming by size control 10473325 (69.45%) reads available; of these: 941252 ( 8.99%) trimmed reads available after processing 9532073 (91.01%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 941252 8.99% 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 9532073 91.01% 10473325 reads passed initial QC criterion=sequence-density sequence-density=89.86 sequence-density-rank=1 fanout-score=19.28 fanout-score-rank=1 prefix-density=90.05 prefix-fanout=19.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCCGTCATCTCGTATGCCG criterion=fanout-score sequence-density=89.86 sequence-density-rank=1 fanout-score=19.28 fanout-score-rank=1 prefix-density=90.05 prefix-fanout=19.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCCGTCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCCGTCATCTCGTATGCCG -o ERR9451999 - Input file: STDIN trimmed: ERR9451999-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATCCGTCATCTCGTATGCCG -- 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 22:19:47 2024 >> started Fri Dec 6 22:19:58 2024 >> done (11.669s) 10240585 reads processed; of these: 15855 ( 0.15%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 10224722 (99.85%) reads available; of these: 9275841 (90.72%) trimmed reads available after processing 948881 ( 9.28%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 931759 9.11% 19 1186828 11.61% 20 1314207 12.85% 21 1298231 12.70% 22 1540376 15.07% 23 803641 7.86% 24 1214282 11.88% 25 596197 5.83% 26 395431 3.87% 27 262005 2.56% 28 191046 1.87% 29 167078 1.63% 30 92869 0.91% 31 57163 0.56% 32 54386 0.53% 33 29513 0.29% 34 16162 0.16% 35 14045 0.14% 36 6393 0.06% 37 4582 0.04% 38 2615 0.03% 39 2068 0.02% 40 1383 0.01% 41 2076 0.02% 42 656 0.01% 43 392 0.00% 44 353 0.00% 45 342 0.00% 46 290 0.00% 47 508 0.00% 48 0 0.00% 49 0 0.00% 50 37845 0.37% criterion=sequence-density sequence-density=0.98 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=10 prefix-density=0.00 prefix-fanout=1.0 sequence=TTCATGGACGTTGATAAGATCCTTCCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=21.76 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=1.0 sequence=GTGAAGTGTTTGGGGGAACTCC Started job on | Dec 06 22:20:13 Started mapping on | Dec 06 22:20:13 Finished on | Dec 06 22:20:50 Mapping speed, Million of reads per hour | 1017.48 Number of input reads | 10457462 Average input read length | 22 UNIQUE READS: Uniquely mapped reads number | 1344110 Uniquely mapped reads % | 12.85% Average mapped length | 22.69 Number of splices: Total | 29170 Number of splices: Annotated (sjdb) | 17134 Number of splices: GT/AG | 28641 Number of splices: GC/AG | 436 Number of splices: AT/AC | 12 Number of splices: Non-canonical | 81 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.26 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4142360 % of reads mapped to multiple loci | 39.61% Number of reads mapped to too many loci | 4654152 % of reads mapped to too many loci | 44.51% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.66% % of reads unmapped: other | 0.37% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4970992 4970992 4970992 N_multimapping 4142360 4142360 4142360 N_noFeature 825479 893206 1266150 N_ambiguous 16337 5850 397 UnstrandedReadsAssigned:502294 PositiveStrandReadsAssigned:445054 NegativeStrandReadsAssigned:77563 Dataset is classified positive stranded MeadianReadLen=22 20thPercentileLength=19 echo kmer=19 ERR9451999 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: ERR9451999-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,457,462 reads, 1,054,423 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 918 rounds 52973 ERR9451999.ke.tsv 35125 ERR9451999.se.tsv 88098 total ==> ERR9451999.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 2.29819e-08 2.05421e-08 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 5 2.72646 PNS24243 293 194 0 0 KQK14069 1603 1504 295.974 147.227 KQK14071 474 375 6.28865 12.5461 ==> ERR9451999.se.tsv <== BRADI_1g14170v3 352 BRADI_1g53295v3 0 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 11 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 3 BRADI_1g48960v3 0 ERR9451999 completed mapping pipeline successfully