Starting /dee2/code/volunteer_pipeline.sh ERR9452009 current disk space = 1548580999168 free memory = 1395611508 ERR9452009 SRAfilesize b4ea0af6480d6f1209644b6dde7d5994 ERR9452009.sra ERR9452009.sra file validated ERR9452009 is single end ERR9452009 is conventional basespace ERR9452009 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452009_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 36.1775 37.0 37.0 37.0 37.0 37.0 2 36.561 37.0 37.0 37.0 37.0 37.0 3 36.62425 37.0 37.0 37.0 37.0 37.0 4 36.685 37.0 37.0 37.0 37.0 37.0 5 36.587 37.0 37.0 37.0 37.0 37.0 6 36.6195 37.0 37.0 37.0 37.0 37.0 7 36.604 37.0 37.0 37.0 37.0 37.0 8 36.63 37.0 37.0 37.0 37.0 37.0 9 36.6205 37.0 37.0 37.0 37.0 37.0 10 36.631 37.0 37.0 37.0 37.0 37.0 11 36.6815 37.0 37.0 37.0 37.0 37.0 12 36.648 37.0 37.0 37.0 37.0 37.0 13 36.715 37.0 37.0 37.0 37.0 37.0 14 36.676 37.0 37.0 37.0 37.0 37.0 15 36.676 37.0 37.0 37.0 37.0 37.0 16 36.5675 37.0 37.0 37.0 37.0 37.0 17 36.621 37.0 37.0 37.0 37.0 37.0 18 36.6445 37.0 37.0 37.0 37.0 37.0 19 36.645 37.0 37.0 37.0 37.0 37.0 20 36.619 37.0 37.0 37.0 37.0 37.0 21 36.626 37.0 37.0 37.0 37.0 37.0 22 36.698 37.0 37.0 37.0 37.0 37.0 23 36.6345 37.0 37.0 37.0 37.0 37.0 24 36.7055 37.0 37.0 37.0 37.0 37.0 25 36.6925 37.0 37.0 37.0 37.0 37.0 26 36.6595 37.0 37.0 37.0 37.0 37.0 27 36.6865 37.0 37.0 37.0 37.0 37.0 28 36.6975 37.0 37.0 37.0 37.0 37.0 29 36.6565 37.0 37.0 37.0 37.0 37.0 30 36.7285 37.0 37.0 37.0 37.0 37.0 31 36.6935 37.0 37.0 37.0 37.0 37.0 32 36.656 37.0 37.0 37.0 37.0 37.0 33 36.655 37.0 37.0 37.0 37.0 37.0 34 36.6115 37.0 37.0 37.0 37.0 37.0 35 36.7295 37.0 37.0 37.0 37.0 37.0 36 36.7635 37.0 37.0 37.0 37.0 37.0 37 36.7165 37.0 37.0 37.0 37.0 37.0 38 36.7375 37.0 37.0 37.0 37.0 37.0 39 36.685 37.0 37.0 37.0 37.0 37.0 40 36.672 37.0 37.0 37.0 37.0 37.0 41 36.6485 37.0 37.0 37.0 37.0 37.0 42 36.6725 37.0 37.0 37.0 37.0 37.0 43 36.617 37.0 37.0 37.0 37.0 37.0 44 36.6885 37.0 37.0 37.0 37.0 37.0 45 36.634 37.0 37.0 37.0 37.0 37.0 46 36.621 37.0 37.0 37.0 37.0 37.0 47 36.6055 37.0 37.0 37.0 37.0 37.0 48 36.671 37.0 37.0 37.0 37.0 37.0 49 36.595 37.0 37.0 37.0 37.0 37.0 50 36.6175 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 3.0 26 1.0 27 5.0 28 3.0 29 8.0 30 16.0 31 25.0 32 42.0 33 41.0 34 45.0 35 100.0 36 1078.0 37 2633.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 20.864756158873806 27.65208647561589 23.479135243841124 28.00402212166918 2 26.275 30.049999999999997 24.125 19.55 3 29.732433108277068 26.981745436359088 19.154788697174293 24.131032758189548 4 31.35 33.775 17.1 17.775 5 22.275 29.525000000000002 20.375 27.825 6 29.725 22.375 26.575 21.325 7 28.825 31.55 21.45 18.175 8 21.85 27.625 27.625 22.900000000000002 9 22.05 30.0 24.224999999999998 23.724999999999998 10 36.375 23.549999999999997 19.15 20.925 11 22.425 25.874999999999996 29.525000000000002 22.175 12 23.9 24.85 28.7 22.55 13 25.95 21.325 20.275000000000002 32.45 14 29.2 33.25 21.975 15.575 15 25.974999999999998 31.225 23.325000000000003 19.475 16 21.925 29.049999999999997 29.549999999999997 19.475 17 25.25 28.1 32.15 14.499999999999998 18 28.4 25.424999999999997 24.925 21.25 19 35.425000000000004 29.549999999999997 20.225 14.799999999999999 20 28.050000000000004 30.775000000000002 26.8 14.374999999999998 21 22.725 41.349999999999994 17.0 18.925 22 26.575 35.075 20.849999999999998 17.5 23 33.5 34.2 17.025000000000002 15.275 24 28.625 35.5 19.85 16.025 25 31.025000000000002 37.125 13.825000000000001 18.025 26 36.225 25.575 17.8 20.4 27 30.525000000000002 40.925 11.15 17.4 28 35.425000000000004 30.275000000000002 15.825 18.475 29 32.875 35.475 9.5 22.15 30 37.375 38.425 7.35 16.85 31 40.75 36.025 6.525 16.7 32 33.875 40.125 9.425 16.575 33 27.900000000000002 42.4 5.775 23.925 34 38.25 31.775 9.325 20.65 35 28.599999999999998 38.9 6.950000000000001 25.55 36 29.175 38.975 6.4750000000000005 25.374999999999996 37 23.549999999999997 32.925 8.924999999999999 34.599999999999994 38 24.725 37.075 8.975 29.225 39 22.425 26.875 15.675 35.025 40 23.549999999999997 31.8 14.274999999999999 30.375000000000004 41 19.35 24.6 18.725 37.325 42 26.125 26.275 17.9 29.7 43 21.65 26.075 24.975 27.3 44 20.200000000000003 25.874999999999996 20.1 33.825 45 14.625 29.15 23.200000000000003 33.025 46 20.875 30.125 18.9 30.099999999999998 47 13.750000000000002 26.974999999999998 20.599999999999998 38.675 48 12.325 32.300000000000004 21.7 33.675 49 12.575 25.124999999999996 21.525 40.775 50 14.6 22.25 27.700000000000003 35.449999999999996 >>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 0.0 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 0.5 34 1.0 35 4.5 36 8.0 37 24.0 38 40.0 39 78.0 40 116.0 41 145.0 42 174.0 43 192.5 44 211.0 45 336.0 46 461.0 47 587.0 48 713.0 49 622.5 50 532.0 51 517.5 52 503.0 53 504.5 54 506.0 55 404.5 56 303.0 57 265.0 58 227.0 59 156.5 60 86.0 61 70.5 62 55.0 63 40.0 64 25.0 65 19.0 66 13.0 67 16.0 68 19.0 69 12.5 70 6.0 71 3.5 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 0.025 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 62.375 #Duplication Level Percentage of deduplicated Percentage of total 1 82.92585170340682 51.725 2 10.941883767535069 13.65 3 2.0841683366733466 3.9 4 0.8416833667334669 2.1 5 0.7615230460921844 2.375 6 0.36072144288577157 1.35 7 0.280561122244489 1.225 8 0.4008016032064128 2.0 9 0.12024048096192384 0.675 >10 1.1623246492985972 12.875 >50 0.08016032064128256 3.65 >100 0.04008016032064128 4.475 >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 179 4.475 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATT 95 2.375 TruSeq Adapter, Index 8 (97% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 51 1.275 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATT 40 1.0 TruSeq Adapter, Index 8 (97% over 36bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 37 0.9249999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 29 0.7250000000000001 No Hit TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 15 0.375 No Hit CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 13 0.325 No Hit CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TTCATGGACGTTGATAAGATCCTTCCAGATCGGAAGAGCACACGTCTGAA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TTCATGGACGTTGATAAGATCAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AAGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TGCCAAGGATGTTTTCATTAATCAAGAACAGATCGGAAGAGCACACGTCT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 6 0.15 No Hit AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) AAGTATGAACTAATTTGAACTGTGAAACAGATCGGAAGAGCACACGTCTG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC 6 0.15 No Hit CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TCGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCTGA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT 5 0.125 TruSeq Adapter, Index 1 (100% over 35bp) ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TGTCGTGCCAATTCAACATAAACCCCTAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) AGTATGAACTAATTTGAACTGTGAAACTAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 5 0.125 No Hit TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GCCCCTATCGTCTAGTGGTTCAGGACAAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ACTCTAGTCCGACTTTGTGAAATGACAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) >>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 0.05 0.0 0.0 0.0 0.0 10 0.05 0.0 0.0 0.0 0.0 11 0.075 0.0 0.0 0.0 0.0 12 0.3 0.0 0.0 0.0 0.0 13 0.725 0.0 0.0 0.0 0.0 14 4.675 0.0 0.0 0.0 0.0 15 5.55 0.0 0.0 0.0 0.0 16 6.725 0.0 0.0 0.0 0.0 17 10.35 0.0 0.0 0.0 0.0 18 12.7 0.0 0.0 0.0 0.0 19 16.3 0.0 0.0 0.0 0.0 20 21.5 0.0 0.0 0.0 0.0 21 28.275 0.0 0.0 0.0 0.0 22 35.875 0.0 0.0 0.0 0.0 23 46.125 0.0 0.0 0.0 0.0 24 52.3 0.0 0.0 0.0 0.0 25 63.95 0.0 0.0 0.0 0.0 26 70.025 0.0 0.0 0.0 0.0 27 74.95 0.0 0.0 0.0 0.0 28 79.55 0.0 0.0 0.0 0.0 29 83.7 0.0 0.0 0.0 0.0 30 87.35 0.0 0.0 0.0 0.0 31 90.4 0.0 0.0 0.0 0.0 32 92.375 0.0 0.0 0.0 0.0 33 94.95 0.0 0.0 0.0 0.0 34 96.225 0.0 0.0 0.0 0.0 35 97.05 0.0 0.0 0.0 0.0 36 98.025 0.0 0.0 0.0 0.0 37 98.325 0.0 0.0 0.0 0.0 38 98.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACGA 20 6.952051E-4 44.000004 1 ACACGAC 25 0.002084305 35.2 2 TCGGCAA 30 0.005095276 29.333332 11 CTCTCGG 30 0.005095276 29.333332 8 ACTCTCG 30 0.005095276 29.333332 7 TCTCGGC 30 0.005095276 29.333332 9 CTCGGCA 30 0.005095276 29.333332 10 ACGACTC 30 0.005095276 29.333332 4 CGACTCT 30 0.005095276 29.333332 5 CTCCAGT 55 0.0037613558 20.0 44 AACTCCA 130 3.8385951E-7 16.923079 44 GAACTCC 160 3.381545E-6 13.750001 43 TGAACTC 175 8.584213E-6 12.571429 42 CTGAACT 210 5.6207668E-5 10.476191 41 TCTGAAC 240 0.0025129043 8.25 40 CGTCTGA 300 0.0020527702 7.3333335 38 GTCTGAA 270 0.0073174513 7.333333 39 ACGTCTG 310 0.0028396088 7.0967746 37 CACGTCT 325 0.004522727 6.7692313 36 GCACACG 370 0.0019513554 6.54054 33 >>END_MODULE Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928559 READS because READLEN < 1 Read 928559 spots for ERR9452009.sra Written 928559 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra Rejected 928556 READS because READLEN < 1 Read 928556 spots for ERR9452009.sra Written 928556 spots for ERR9452009.sra SRR ids: ['ERR9452009.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wczprvxb ERR9452009.sra spots: 18571123 blocks: [[1, 928556], [928557, 1857112], [1857113, 2785668], [2785669, 3714224], [3714225, 4642780], [4642781, 5571336], [5571337, 6499892], [6499893, 7428448], [7428449, 8357004], [8357005, 9285560], [9285561, 10214116], [10214117, 11142672], [11142673, 12071228], [12071229, 12999784], [12999785, 13928340], [13928341, 14856896], [14856897, 15785452], [15785453, 16714008], [16714009, 17642564], [17642565, 18571123]] ERR9452009 file size 2589863 ERR9452009 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 ERR9452009 ERR9452009_1.fastq Input file: ERR9452009_1.fastq trimmed: ERR9452009-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 22:39:09 2024 >> started Fri Dec 6 22:39:19 2024 >> done (10.245s) 18571123 reads processed; of these: 2298873 (12.38%) short reads filtered out after trimming by size control 1193 ( 0.01%) empty reads filtered out after trimming by size control 16271057 (87.61%) reads available; of these: 642277 ( 3.95%) trimmed reads available after processing 15628780 (96.05%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 642277 3.95% 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 15628780 96.05% 16271057 reads passed initial QC criterion=sequence-density sequence-density=94.46 sequence-density-rank=1 fanout-score=29.38 fanout-score-rank=1 prefix-density=94.97 prefix-fanout=29.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTGGCTCATC criterion=fanout-score sequence-density=94.46 sequence-density-rank=1 fanout-score=29.38 fanout-score-rank=1 prefix-density=94.97 prefix-fanout=29.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTGGCTCATC 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTGGCTCATC -o ERR9452009 - Input file: STDIN trimmed: ERR9452009-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTGGCTCATC -- 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 22:39:44 2024 >> started Fri Dec 6 22:40:01 2024 >> done (16.927s) 15928509 reads processed; of these: 10871 ( 0.07%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 15917622 (99.93%) reads available; of these: 15253855 (95.83%) trimmed reads available after processing 663767 ( 4.17%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 635028 3.99% 19 923472 5.80% 20 1196414 7.52% 21 1387877 8.72% 22 1750805 11.00% 23 1201860 7.55% 24 2212940 13.90% 25 1189780 7.47% 26 979648 6.15% 27 812625 5.11% 28 723709 4.55% 29 729979 4.59% 30 517898 3.25% 31 382852 2.41% 32 405388 2.55% 33 275076 1.73% 34 179994 1.13% 35 156685 0.98% 36 75024 0.47% 37 48934 0.31% 38 26940 0.17% 39 18559 0.12% 40 11942 0.08% 41 17494 0.11% 42 5375 0.03% 43 3340 0.02% 44 2410 0.02% 45 1830 0.01% 46 1171 0.01% 47 1165 0.01% 48 0 0.00% 49 0 0.00% 50 41408 0.26% criterion=sequence-density sequence-density=2.49 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=19.55 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=1.0 sequence=GTGAAGTGTTTGGGGGAACTCC Started job on | Dec 06 22:40:24 Started mapping on | Dec 06 22:40:24 Finished on | Dec 06 22:41:18 Mapping speed, Million of reads per hour | 1084.01 Number of input reads | 16260170 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 2432370 Uniquely mapped reads % | 14.96% Average mapped length | 24.12 Number of splices: Total | 56609 Number of splices: Annotated (sjdb) | 35874 Number of splices: GT/AG | 55096 Number of splices: GC/AG | 1032 Number of splices: AT/AC | 23 Number of splices: Non-canonical | 458 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.43 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5881445 % of reads mapped to multiple loci | 36.17% Number of reads mapped to too many loci | 7448169 % of reads mapped to too many loci | 45.81% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.64% % of reads unmapped: other | 0.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7946355 7946355 7946355 N_multimapping 5881445 5881445 5881445 N_noFeature 1488636 1609937 2291638 N_ambiguous 30972 11056 762 UnstrandedReadsAssigned:912762 PositiveStrandReadsAssigned:811377 NegativeStrandReadsAssigned:139970 Dataset is classified positive stranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 ERR9452009 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: ERR9452009-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,260,170 reads, 2,166,602 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 969 rounds 52973 ERR9452009.ke.tsv 35125 ERR9452009.se.tsv 88098 total ==> ERR9452009.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 2.91458 PNS24243 293 194 0 0 KQK14069 1603 1504 604.211 178.496 KQK14071 474 375 23.8463 28.2538 ==> ERR9452009.se.tsv <== BRADI_1g14170v3 741 BRADI_1g53295v3 2 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 27 BRADI_1g74790v3 28 BRADI_1g09890v3 0 BRADI_1g77505v3 13 BRADI_1g48960v3 0 ERR9452009 completed mapping pipeline successfully