Starting /dee2/code/volunteer_pipeline.sh ERR9452000 current disk space = 1548369817600 free memory = 1397786032 ERR9452000 SRAfilesize 6325d2bae3e28debcb90023e9c2e521d ERR9452000.sra ERR9452000.sra file validated ERR9452000 is single end ERR9452000 is conventional basespace ERR9452000 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452000_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 36.3995 37.0 37.0 37.0 37.0 37.0 2 36.6515 37.0 37.0 37.0 37.0 37.0 3 36.737 37.0 37.0 37.0 37.0 37.0 4 36.6805 37.0 37.0 37.0 37.0 37.0 5 36.7125 37.0 37.0 37.0 37.0 37.0 6 36.6705 37.0 37.0 37.0 37.0 37.0 7 36.717 37.0 37.0 37.0 37.0 37.0 8 36.661 37.0 37.0 37.0 37.0 37.0 9 36.703 37.0 37.0 37.0 37.0 37.0 10 36.7245 37.0 37.0 37.0 37.0 37.0 11 36.7255 37.0 37.0 37.0 37.0 37.0 12 36.7055 37.0 37.0 37.0 37.0 37.0 13 36.693 37.0 37.0 37.0 37.0 37.0 14 36.7045 37.0 37.0 37.0 37.0 37.0 15 36.6255 37.0 37.0 37.0 37.0 37.0 16 36.679 37.0 37.0 37.0 37.0 37.0 17 36.6295 37.0 37.0 37.0 37.0 37.0 18 36.651 37.0 37.0 37.0 37.0 37.0 19 36.673 37.0 37.0 37.0 37.0 37.0 20 36.706 37.0 37.0 37.0 37.0 37.0 21 36.643 37.0 37.0 37.0 37.0 37.0 22 36.654 37.0 37.0 37.0 37.0 37.0 23 36.6375 37.0 37.0 37.0 37.0 37.0 24 36.6935 37.0 37.0 37.0 37.0 37.0 25 36.743 37.0 37.0 37.0 37.0 37.0 26 36.666 37.0 37.0 37.0 37.0 37.0 27 36.721 37.0 37.0 37.0 37.0 37.0 28 36.745 37.0 37.0 37.0 37.0 37.0 29 36.739 37.0 37.0 37.0 37.0 37.0 30 36.7355 37.0 37.0 37.0 37.0 37.0 31 36.705 37.0 37.0 37.0 37.0 37.0 32 36.7325 37.0 37.0 37.0 37.0 37.0 33 36.758 37.0 37.0 37.0 37.0 37.0 34 36.7195 37.0 37.0 37.0 37.0 37.0 35 36.7275 37.0 37.0 37.0 37.0 37.0 36 36.7615 37.0 37.0 37.0 37.0 37.0 37 36.774 37.0 37.0 37.0 37.0 37.0 38 36.761 37.0 37.0 37.0 37.0 37.0 39 36.769 37.0 37.0 37.0 37.0 37.0 40 36.72 37.0 37.0 37.0 37.0 37.0 41 36.715 37.0 37.0 37.0 37.0 37.0 42 36.678 37.0 37.0 37.0 37.0 37.0 43 36.6755 37.0 37.0 37.0 37.0 37.0 44 36.6725 37.0 37.0 37.0 37.0 37.0 45 36.6325 37.0 37.0 37.0 37.0 37.0 46 36.6705 37.0 37.0 37.0 37.0 37.0 47 36.621 37.0 37.0 37.0 37.0 37.0 48 36.6265 37.0 37.0 37.0 37.0 37.0 49 36.6435 37.0 37.0 37.0 37.0 37.0 50 36.5905 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 3.0 26 2.0 27 4.0 28 5.0 29 14.0 30 11.0 31 15.0 32 22.0 33 36.0 34 38.0 35 85.0 36 1093.0 37 2672.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.60873932697137 30.989452536413864 22.827724761426417 27.574083375188348 2 24.075 30.3 25.900000000000002 19.725 3 30.725 28.199999999999996 17.474999999999998 23.599999999999998 4 30.45 35.225 16.875 17.45 5 22.175 28.075 19.5 30.25 6 28.15 23.775 28.1 19.975 7 26.5 34.25 21.4 17.849999999999998 8 20.175 27.400000000000002 29.299999999999997 23.125 9 21.85 29.875 24.45 23.825 10 37.25 21.375 20.65 20.724999999999998 11 22.75 27.3 28.675 21.275 12 24.55 26.05 26.174999999999997 23.225 13 25.174999999999997 22.125 20.424999999999997 32.275 14 30.5 34.699999999999996 20.775 14.025000000000002 15 24.95 33.300000000000004 23.7 18.05 16 22.175 29.65 30.349999999999998 17.825 17 24.575 27.425 33.725 14.274999999999999 18 26.625 26.275 25.95 21.15 19 36.925000000000004 29.475 19.650000000000002 13.950000000000001 20 28.275 33.175 24.349999999999998 14.2 21 23.5 42.699999999999996 17.125 16.675 22 26.1 35.825 19.325 18.75 23 33.650000000000006 35.675000000000004 17.2 13.475000000000001 24 28.975 36.375 18.7 15.950000000000001 25 31.75 39.775 12.475 16.0 26 38.9 26.724999999999998 15.15 19.225 27 28.999999999999996 44.15 10.075000000000001 16.775000000000002 28 34.125 29.65 17.724999999999998 18.5 29 32.35 34.8 7.95 24.9 30 40.375 36.35 5.675 17.599999999999998 31 43.6 35.475 4.8 16.125 32 31.674999999999997 43.075 8.674999999999999 16.575 33 26.1 45.2 5.1499999999999995 23.549999999999997 34 37.55 31.6 9.35 21.5 35 27.775 39.45 6.0 26.775 36 31.1 36.625 6.6000000000000005 25.674999999999997 37 20.349999999999998 31.225 9.55 38.875 38 19.925 37.824999999999996 10.65 31.6 39 18.95 24.025 17.25 39.775 40 21.775 32.425 15.375 30.425 41 18.65 21.45 19.85 40.050000000000004 42 27.474999999999998 25.724999999999998 18.4 28.4 43 20.849999999999998 22.775000000000002 30.275000000000002 26.1 44 18.224999999999998 23.825 22.225 35.725 45 13.750000000000002 26.775 27.800000000000004 31.674999999999997 46 22.7 30.5 17.349999999999998 29.45 47 12.4 32.6 17.875 37.125 48 11.4 37.0 19.775000000000002 31.825 49 10.85 28.775000000000002 17.025000000000002 43.35 50 11.799999999999999 22.025 31.025000000000002 35.15 >>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 0.5 16 1.0 17 0.5 18 0.0 19 0.5 20 1.0 21 0.5 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 1.0 32 2.0 33 2.5 34 3.0 35 6.0 36 9.0 37 28.0 38 47.0 39 69.0 40 91.0 41 121.5 42 152.0 43 197.0 44 242.0 45 358.0 46 474.0 47 667.0 48 860.0 49 702.5 50 545.0 51 531.5 52 518.0 53 500.5 54 483.0 55 386.0 56 289.0 57 218.5 58 148.0 59 106.0 60 64.0 61 48.5 62 33.0 63 24.5 64 16.0 65 12.0 66 8.0 67 8.5 68 9.0 69 7.0 70 5.0 71 2.5 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.44999999999999996 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 59.62499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 83.9412997903564 50.05 2 9.559748427672957 11.4 3 2.851153039832285 5.1 4 0.8385744234800839 2.0 5 0.41928721174004197 1.25 6 0.29350104821802936 1.05 7 0.25157232704402516 1.05 8 0.20964360587002098 1.0 9 0.08385744234800838 0.44999999999999996 >10 1.4255765199161425 16.425 >50 0.04192872117400419 1.675 >100 0.08385744234800838 8.55 >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 228 5.7 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAT 114 2.85 TruSeq Adapter, Index 8 (97% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 67 1.675 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 46 1.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAT 44 1.0999999999999999 TruSeq Adapter, Index 8 (97% over 36bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 33 0.8250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 29 0.7250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 22 0.5499999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 18 0.44999999999999996 TruSeq Adapter, Index 7 (97% over 35bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 17 0.42500000000000004 No Hit GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 15 0.375 No Hit ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA 8 0.2 No Hit GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 8 0.2 No Hit GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CATCGAGTAGACCTTGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 6 0.15 No Hit GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATG 6 0.15 TruSeq Adapter, Index 25 (97% over 37bp) GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC 6 0.15 No Hit GCGTCTGTAGTCCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) AGGGCTATAGCTCAGTTCGGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 5 0.125 TruSeq Adapter, Index 7 (97% over 35bp) GGGGATGTAGCTCAGATGGTAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) AGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GTATGAACTAATTTGAACTGTGAAACAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) AAGGGGAATCCGACTGTTTAATAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) >>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 0.025 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10 0.075 0.0 0.0 0.0 0.0 11 0.175 0.0 0.0 0.0 0.0 12 0.525 0.0 0.0 0.0 0.0 13 1.15 0.0 0.0 0.0 0.0 14 6.025 0.0 0.0 0.0 0.0 15 7.45 0.0 0.0 0.0 0.0 16 9.275 0.0 0.0 0.0 0.0 17 12.5 0.0 0.0 0.0 0.0 18 15.625 0.0 0.0 0.0 0.0 19 20.125 0.0 0.0 0.0 0.0 20 26.025 0.0 0.0 0.0 0.0 21 33.025 0.0 0.0 0.0 0.0 22 40.4 0.0 0.0 0.0 0.0 23 50.8 0.0 0.0 0.0 0.0 24 57.75 0.0 0.0 0.0 0.0 25 73.2 0.0 0.0 0.0 0.0 26 78.65 0.0 0.0 0.0 0.0 27 82.75 0.0 0.0 0.0 0.0 28 85.575 0.0 0.0 0.0 0.0 29 88.275 0.0 0.0 0.0 0.0 30 90.825 0.0 0.0 0.0 0.0 31 92.725 0.0 0.0 0.0 0.0 32 93.825 0.0 0.0 0.0 0.0 33 95.1 0.0 0.0 0.0 0.0 34 96.3 0.0 0.0 0.0 0.0 35 96.75 0.0 0.0 0.0 0.0 36 97.325 0.0 0.0 0.0 0.0 37 97.475 0.0 0.0 0.0 0.0 38 97.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACACGAC 25 0.002084305 35.2 2 GACACGA 25 0.002084305 35.2 1 CTAACGA 35 2.6843656E-4 31.428572 1 GGCAACG 30 0.005095276 29.333332 13 GCAACGG 30 0.005095276 29.333332 14 CAACGGA 30 0.005095276 29.333332 15 TAACGAA 40 5.87456E-4 27.500002 2 ACTCCAG 155 4.3189786E-5 12.774194 44 AACTCCA 175 1.3518654E-4 11.314286 43 GAACTCC 230 1.0750613E-5 10.52174 44 TGAACTC 240 1.7283644E-5 10.083333 43 CTGAACT 295 1.6869079E-4 8.203389 42 TCTGAAC 320 4.0921307E-4 7.5625005 41 GTCTGAA 325 4.8409586E-4 7.446154 40 CGTCTGA 330 5.710564E-4 7.3333335 39 ACGTCTG 340 7.8816287E-4 7.117647 38 CACGTCT 350 0.0010765606 6.914286 37 ACACGTC 370 0.0019513554 6.54054 36 CACACGT 385 0.0029781973 6.285714 35 GATCGGA 390 0.003414818 6.205128 26 >>END_MODULE Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685670 READS because READLEN < 1 Read 685670 spots for ERR9452000.sra Written 685670 spots for ERR9452000.sra Rejected 685673 READS because READLEN < 1 Read 685673 spots for ERR9452000.sra Written 685673 spots for ERR9452000.sra SRR ids: ['ERR9452000.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4wryf39e ERR9452000.sra spots: 13713403 blocks: [[1, 685670], [685671, 1371340], [1371341, 2057010], [2057011, 2742680], [2742681, 3428350], [3428351, 4114020], [4114021, 4799690], [4799691, 5485360], [5485361, 6171030], [6171031, 6856700], [6856701, 7542370], [7542371, 8228040], [8228041, 8913710], [8913711, 9599380], [9599381, 10285050], [10285051, 10970720], [10970721, 11656390], [11656391, 12342060], [12342061, 13027730], [13027731, 13713403]] ERR9452000 file size 1906746 ERR9452000 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 ERR9452000 ERR9452000_1.fastq Input file: ERR9452000_1.fastq trimmed: ERR9452000-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 22:19:57 2024 >> started Fri Dec 6 22:20:05 2024 >> done (8.032s) 13713403 reads processed; of these: 2049569 (14.95%) short reads filtered out after trimming by size control 1678 ( 0.01%) empty reads filtered out after trimming by size control 11662156 (85.04%) reads available; of these: 501828 ( 4.30%) trimmed reads available after processing 11160328 (95.70%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 501828 4.30% 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 11160328 95.70% 11662156 reads passed initial QC criterion=sequence-density sequence-density=93.58 sequence-density-rank=1 fanout-score=23.34 fanout-score-rank=1 prefix-density=94.18 prefix-fanout=23.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATGTTGCATCTCGTATGCCG criterion=fanout-score sequence-density=93.58 sequence-density-rank=1 fanout-score=23.34 fanout-score-rank=1 prefix-density=94.18 prefix-fanout=23.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATGTTGCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATGTTGCATCTCGTATGCCG -o ERR9452000 - Input file: STDIN trimmed: ERR9452000-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAATGTTGCATCTCGTATGCCG -- 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 22:20:19 2024 >> started Fri Dec 6 22:20:31 2024 >> done (12.173s) 11414025 reads processed; of these: 14467 ( 0.13%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 11399538 (99.87%) reads available; of these: 10868383 (95.34%) trimmed reads available after processing 531155 ( 4.66%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 504212 4.42% 19 745125 6.54% 20 951594 8.35% 21 1137949 9.98% 22 1508909 13.24% 23 884813 7.76% 24 2126699 18.66% 25 781933 6.86% 26 574340 5.04% 27 425024 3.73% 28 352363 3.09% 29 364667 3.20% 30 231885 2.03% 31 159228 1.40% 32 187887 1.65% 33 128332 1.13% 34 79175 0.69% 35 74836 0.66% 36 33227 0.29% 37 24713 0.22% 38 15211 0.13% 39 12994 0.11% 40 9892 0.09% 41 23679 0.21% 42 5316 0.05% 43 3505 0.03% 44 2513 0.02% 45 1978 0.02% 46 1384 0.01% 47 1304 0.01% 48 0 0.00% 49 0 0.00% 50 44851 0.39% criterion=sequence-density sequence-density=2.40 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=9 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTC criterion=fanout-score sequence-density=0.17 sequence-density-rank=12 fanout-score=7.08 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=3.3 sequence=TAGCTCAGTTGGTAGAGCAGAGGACTG Started job on | Dec 06 22:20:50 Started mapping on | Dec 06 22:20:50 Finished on | Dec 06 22:21:24 Mapping speed, Million of reads per hour | 1233.28 Number of input reads | 11647669 Average input read length | 24 UNIQUE READS: Uniquely mapped reads number | 2235705 Uniquely mapped reads % | 19.19% Average mapped length | 23.67 Number of splices: Total | 27591 Number of splices: Annotated (sjdb) | 16613 Number of splices: GT/AG | 26907 Number of splices: GC/AG | 496 Number of splices: AT/AC | 10 Number of splices: Non-canonical | 178 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.00% Deletion average length | 1.24 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4382467 % of reads mapped to multiple loci | 37.63% Number of reads mapped to too many loci | 4656943 % of reads mapped to too many loci | 39.98% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.53% % of reads unmapped: other | 0.67% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5029497 5029497 5029497 N_multimapping 4382467 4382467 4382467 N_noFeature 1624211 1736783 2111540 N_ambiguous 20090 8134 539 UnstrandedReadsAssigned:591404 PositiveStrandReadsAssigned:490788 NegativeStrandReadsAssigned:123626 Dataset is classified unstranded MeadianReadLen=23 20thPercentileLength=21 echo kmer=19 ERR9452000 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: ERR9452000-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,647,669 reads, 2,072,555 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,053 rounds 52973 ERR9452000.ke.tsv 35125 ERR9452000.se.tsv 88098 total ==> ERR9452000.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0.15625 0.0934528 PNS24247 1044 945 0 0 PNS24249 1928 1829 1.84375 0.504645 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 388.696 129.378 KQK14071 474 375 23.8368 31.821 ==> ERR9452000.se.tsv <== BRADI_1g14170v3 484 BRADI_1g53295v3 3 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 9 BRADI_1g74790v3 27 BRADI_1g09890v3 0 BRADI_1g77505v3 3 BRADI_1g48960v3 0 ERR9452000 completed mapping pipeline successfully