Starting /dee2/code/volunteer_pipeline.sh ERR9451998 current disk space = 1548125360128 free memory = 1599852080 ERR9451998 SRAfilesize cc9b958c7358984d22449f5f8f83b0a2 ERR9451998.sra ERR9451998.sra file validated ERR9451998 is single end ERR9451998 is conventional basespace ERR9451998 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9451998_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 35.85525 37.0 37.0 37.0 37.0 37.0 2 36.5885 37.0 37.0 37.0 37.0 37.0 3 36.596 37.0 37.0 37.0 37.0 37.0 4 36.6355 37.0 37.0 37.0 37.0 37.0 5 36.674 37.0 37.0 37.0 37.0 37.0 6 36.668 37.0 37.0 37.0 37.0 37.0 7 36.68 37.0 37.0 37.0 37.0 37.0 8 36.571 37.0 37.0 37.0 37.0 37.0 9 36.5835 37.0 37.0 37.0 37.0 37.0 10 36.652 37.0 37.0 37.0 37.0 37.0 11 36.621 37.0 37.0 37.0 37.0 37.0 12 36.609 37.0 37.0 37.0 37.0 37.0 13 36.638 37.0 37.0 37.0 37.0 37.0 14 36.6065 37.0 37.0 37.0 37.0 37.0 15 36.599 37.0 37.0 37.0 37.0 37.0 16 36.5795 37.0 37.0 37.0 37.0 37.0 17 36.4955 37.0 37.0 37.0 37.0 37.0 18 36.656 37.0 37.0 37.0 37.0 37.0 19 36.561 37.0 37.0 37.0 37.0 37.0 20 36.637 37.0 37.0 37.0 37.0 37.0 21 36.5835 37.0 37.0 37.0 37.0 37.0 22 36.6265 37.0 37.0 37.0 37.0 37.0 23 36.6475 37.0 37.0 37.0 37.0 37.0 24 36.673 37.0 37.0 37.0 37.0 37.0 25 36.709 37.0 37.0 37.0 37.0 37.0 26 36.692 37.0 37.0 37.0 37.0 37.0 27 36.6795 37.0 37.0 37.0 37.0 37.0 28 36.7475 37.0 37.0 37.0 37.0 37.0 29 36.78 37.0 37.0 37.0 37.0 37.0 30 36.776 37.0 37.0 37.0 37.0 37.0 31 36.702 37.0 37.0 37.0 37.0 37.0 32 36.6165 37.0 37.0 37.0 37.0 37.0 33 36.718 37.0 37.0 37.0 37.0 37.0 34 36.7 37.0 37.0 37.0 37.0 37.0 35 36.6765 37.0 37.0 37.0 37.0 37.0 36 36.733 37.0 37.0 37.0 37.0 37.0 37 36.626 37.0 37.0 37.0 37.0 37.0 38 36.633 37.0 37.0 37.0 37.0 37.0 39 36.6235 37.0 37.0 37.0 37.0 37.0 40 36.649 37.0 37.0 37.0 37.0 37.0 41 36.637 37.0 37.0 37.0 37.0 37.0 42 36.572 37.0 37.0 37.0 37.0 37.0 43 36.474 37.0 37.0 37.0 37.0 37.0 44 36.6115 37.0 37.0 37.0 37.0 37.0 45 36.588 37.0 37.0 37.0 37.0 37.0 46 36.616 37.0 37.0 37.0 37.0 37.0 47 36.5895 37.0 37.0 37.0 37.0 37.0 48 36.619 37.0 37.0 37.0 37.0 37.0 49 36.557 37.0 37.0 37.0 37.0 37.0 50 36.6705 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 1.0 26 2.0 27 5.0 28 5.0 29 10.0 30 16.0 31 29.0 32 37.0 33 39.0 34 47.0 35 112.0 36 1208.0 37 2489.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 15.529053539710732 33.214920071047956 22.380106571936057 28.875919817305252 2 28.075 29.349999999999998 22.55 20.025000000000002 3 33.616808404202104 28.8144072036018 15.857928964482241 21.710855427713856 4 35.9 30.625000000000004 16.6 16.875 5 22.275 29.025000000000002 17.875 30.825000000000003 6 25.25 23.35 30.575000000000003 20.825 7 25.424999999999997 36.325 19.675 18.575 8 22.225 26.35 30.75 20.674999999999997 9 22.475 33.75 23.075000000000003 20.7 10 37.775 22.525000000000002 21.349999999999998 18.35 11 22.475 24.775 26.400000000000002 26.35 12 23.75 24.2 31.574999999999996 20.474999999999998 13 23.025000000000002 23.474999999999998 20.25 33.25 14 27.900000000000002 36.925000000000004 20.775 14.399999999999999 15 29.25 31.374999999999996 22.5 16.875 16 21.575 34.2 26.625 17.599999999999998 17 22.900000000000002 29.225 32.25 15.625 18 25.6 26.325 23.95 24.125 19 39.15 28.65 16.900000000000002 15.299999999999999 20 32.9 33.25 20.225 13.625000000000002 21 24.65 43.8 15.35 16.2 22 26.974999999999998 39.725 16.225 17.075000000000003 23 39.975 33.425 14.025000000000002 12.575 24 32.300000000000004 39.324999999999996 14.475 13.900000000000002 25 36.8 37.625 11.575000000000001 14.000000000000002 26 37.275000000000006 28.675 11.0 23.05 27 32.45 44.85 7.074999999999999 15.625 28 34.8 33.650000000000006 10.325 21.224999999999998 29 31.974999999999998 41.949999999999996 5.1499999999999995 20.925 30 32.15 38.85 3.975 25.025 31 42.0 34.65 3.55 19.8 32 28.425 37.925 12.174999999999999 21.475 33 23.549999999999997 38.275 6.075 32.1 34 29.299999999999997 27.725 14.774999999999999 28.199999999999996 35 27.925 33.475 10.100000000000001 28.499999999999996 36 24.025 35.775 10.85 29.349999999999998 37 18.475 33.225 13.100000000000001 35.199999999999996 38 19.05 29.425 15.975 35.55 39 19.175 21.075 24.95 34.8 40 17.775 27.3 20.65 34.275 41 15.375 21.2 21.375 42.05 42 20.325 29.049999999999997 20.674999999999997 29.95 43 23.825 23.575 26.474999999999998 26.125 44 16.35 23.625 25.3 34.725 45 11.05 27.925 23.9 37.125 46 16.7 32.574999999999996 17.349999999999998 33.375 47 11.675 27.725 19.05 41.55 48 10.75 36.5 18.475 34.275 49 12.15 35.05 13.450000000000001 39.35 50 21.025 28.075 19.05 31.85 >>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 0.5 26 1.0 27 0.5 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 1.5 34 3.0 35 3.5 36 4.0 37 13.0 38 22.0 39 46.0 40 70.0 41 89.5 42 109.0 43 153.0 44 197.0 45 317.0 46 437.0 47 653.0 48 869.0 49 645.5 50 422.0 51 590.0 52 758.0 53 633.5 54 509.0 55 412.5 56 316.0 57 244.0 58 172.0 59 112.5 60 53.0 61 43.0 62 33.0 63 22.5 64 12.0 65 8.0 66 4.0 67 5.5 68 7.0 69 4.5 70 2.0 71 1.0 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 1.4749999999999999 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 57.599999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 82.85590277777779 47.725 2 10.980902777777777 12.65 3 2.430555555555556 4.2 4 0.9548611111111112 2.1999999999999997 5 0.564236111111111 1.625 6 0.2170138888888889 0.75 7 0.3472222222222222 1.4000000000000001 8 0.08680555555555555 0.4 9 0.13020833333333331 0.675 >10 1.2586805555555556 14.924999999999999 >50 0.08680555555555555 3.0 >100 0.08680555555555555 10.45 >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 AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAG 244 6.1 TruSeq Adapter, Index 7 (97% over 36bp) CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 174 4.35 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 67 1.675 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAG 53 1.325 TruSeq Adapter, Index 7 (97% over 36bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 45 1.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 44 1.0999999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 44 1.0999999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 38 0.95 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 34 0.8500000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 26 0.65 TruSeq Adapter, Index 7 (97% over 35bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 22 0.5499999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGG 17 0.42500000000000004 TruSeq Adapter, Index 7 (97% over 36bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 15 0.375 TruSeq Adapter, Index 7 (97% over 35bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAG 12 0.3 TruSeq Adapter, Index 7 (97% over 36bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAA 9 0.22499999999999998 TruSeq Adapter, Index 7 (97% over 35bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGA 7 0.17500000000000002 TruSeq Adapter, Index 7 (97% over 36bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AAAAGGACTTTGAAAAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 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) TGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TTCCATAACTGTTGTTGCTCAAGAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) AAGTATGAACTAATTTGAACTAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCCAGTCACAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (96% over 28bp) AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TAATTCATGATCTGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) AGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) AAAGGACTTTGAAAAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) >>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 0.05 0.0 0.0 0.0 0.0 8 0.075 0.0 0.0 0.0 0.0 9 0.175 0.0 0.0 0.0 0.0 10 0.2 0.0 0.0 0.0 0.0 11 0.4 0.0 0.0 0.0 0.0 12 0.85 0.0 0.0 0.0 0.0 13 2.125 0.0 0.0 0.0 0.0 14 12.4 0.0 0.0 0.0 0.0 15 15.575 0.0 0.0 0.0 0.0 16 19.025 0.0 0.0 0.0 0.0 17 24.85 0.0 0.0 0.0 0.0 18 31.2 0.0 0.0 0.0 0.0 19 37.575 0.0 0.0 0.0 0.0 20 45.275 0.0 0.0 0.0 0.0 21 53.225 0.0 0.0 0.0 0.0 22 62.2 0.0 0.0 0.0 0.0 23 71.325 0.0 0.0 0.0 0.0 24 76.5 0.0 0.0 0.0 0.0 25 85.825 0.0 0.0 0.0 0.0 26 89.475 0.0 0.0 0.0 0.0 27 92.275 0.0 0.0 0.0 0.0 28 94.025 0.0 0.0 0.0 0.0 29 94.975 0.0 0.0 0.0 0.0 30 96.05 0.0 0.0 0.0 0.0 31 96.675 0.0 0.0 0.0 0.0 32 97.225 0.0 0.0 0.0 0.0 33 97.6 0.0 0.0 0.0 0.0 34 97.775 0.0 0.0 0.0 0.0 35 97.85 0.0 0.0 0.0 0.0 36 97.875 0.0 0.0 0.0 0.0 37 97.975 0.0 0.0 0.0 0.0 38 98.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGGGCTA 50 1.2732926E-11 44.544304 1 CTATAGC 55 0.0 43.9875 5 AGCTCAG 55 0.0 43.9875 9 TAGCTCA 55 0.0 43.9875 8 GCTATAG 55 0.0 43.9875 4 ATAGCTC 45 2.746674E-10 43.9875 7 GGCTATA 50 1.4551915E-11 43.9875 3 GCTCAGA 55 0.0 43.9875 10 TATAGCT 45 2.746674E-10 43.9875 6 GGGCTAT 50 1.4551915E-11 43.9875 2 TCACAAG 55 4.0017767E-11 39.988636 44 GTCACAA 70 5.275069E-10 31.419643 43 AGTCACA 70 5.275069E-10 31.419643 42 CTAACGA 30 0.004790254 29.696201 1 TCAGATC 90 2.2919266E-10 26.88125 12 CTCAGAT 90 2.2919266E-10 26.88125 11 CAGTCAC 100 2.39379E-8 21.99375 41 CCAGTCA 130 3.8501094E-7 16.918268 40 TCCAGTC 150 1.7288639E-6 14.6625 39 CTCCAGT 175 8.609539E-6 12.567858 38 >>END_MODULE Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105529 READS because READLEN < 1 Read 1105529 spots for ERR9451998.sra Written 1105529 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra Rejected 1105524 READS because READLEN < 1 Read 1105524 spots for ERR9451998.sra Written 1105524 spots for ERR9451998.sra SRR ids: ['ERR9451998.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8v_99gd8 ERR9451998.sra spots: 22110485 blocks: [[1, 1105524], [1105525, 2211048], [2211049, 3316572], [3316573, 4422096], [4422097, 5527620], [5527621, 6633144], [6633145, 7738668], [7738669, 8844192], [8844193, 9949716], [9949717, 11055240], [11055241, 12160764], [12160765, 13266288], [13266289, 14371812], [14371813, 15477336], [15477337, 16582860], [16582861, 17688384], [17688385, 18793908], [18793909, 19899432], [19899433, 21004956], [21004957, 22110485]] ERR9451998 file size 3087586 ERR9451998 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 ERR9451998 ERR9451998_1.fastq Input file: ERR9451998_1.fastq trimmed: ERR9451998-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 22:16:39 2024 >> started Fri Dec 6 22:16:55 2024 >> done (16.477s) 22110485 reads processed; of these: 7031611 (31.80%) short reads filtered out after trimming by size control 1827 ( 0.01%) empty reads filtered out after trimming by size control 15077047 (68.19%) reads available; of these: 1306628 ( 8.67%) trimmed reads available after processing 13770419 (91.33%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1306628 8.67% 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 13770419 91.33% 15077047 reads passed initial QC criterion=sequence-density sequence-density=89.34 sequence-density-rank=1 fanout-score=19.38 fanout-score-rank=1 prefix-density=89.66 prefix-fanout=19.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGACACATCTCGTATGCCG criterion=fanout-score sequence-density=89.34 sequence-density-rank=1 fanout-score=19.38 fanout-score-rank=1 prefix-density=89.66 prefix-fanout=19.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGACACATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGACACATCTCGTATGCCG -o ERR9451998 - Input file: STDIN trimmed: ERR9451998-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGACACATCTCGTATGCCG -- 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 22:17:14 2024 >> started Fri Dec 6 22:17:32 2024 >> done (18.161s) 14742002 reads processed; of these: 38057 ( 0.26%) short reads filtered out after trimming by size control 25 ( 0.00%) empty reads filtered out after trimming by size control 14703920 (99.74%) reads available; of these: 13343251 (90.75%) trimmed reads available after processing 1360669 ( 9.25%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1316094 8.95% 19 1628542 11.08% 20 1751143 11.91% 21 1777590 12.09% 22 2110137 14.35% 23 1156183 7.86% 24 2141894 14.57% 25 800615 5.44% 26 540015 3.67% 27 368009 2.50% 28 276336 1.88% 29 241533 1.64% 30 146288 0.99% 31 95318 0.65% 32 86711 0.59% 33 54251 0.37% 34 33964 0.23% 35 28084 0.19% 36 14502 0.10% 37 11260 0.08% 38 6955 0.05% 39 5505 0.04% 40 4058 0.03% 41 5828 0.04% 42 2086 0.01% 43 1343 0.01% 44 1005 0.01% 45 973 0.01% 46 628 0.00% 47 1359 0.01% 48 0 0.00% 49 0 0.00% 50 95711 0.65% criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=19.27 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=1.0 sequence=GTGAAGTGTTTGGGGGAACTCC Started job on | Dec 06 22:17:48 Started mapping on | Dec 06 22:17:48 Finished on | Dec 06 22:18:42 Mapping speed, Million of reads per hour | 1002.60 Number of input reads | 15038965 Average input read length | 23 UNIQUE READS: Uniquely mapped reads number | 2349934 Uniquely mapped reads % | 15.63% Average mapped length | 22.91 Number of splices: Total | 44174 Number of splices: Annotated (sjdb) | 22162 Number of splices: GT/AG | 43429 Number of splices: GC/AG | 586 Number of splices: AT/AC | 5 Number of splices: Non-canonical | 154 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5800651 % of reads mapped to multiple loci | 38.57% Number of reads mapped to too many loci | 6364808 % of reads mapped to too many loci | 42.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.98% % of reads unmapped: other | 0.50% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6888380 6888380 6888380 N_multimapping 5800651 5800651 5800651 N_noFeature 1592753 1712085 2215282 N_ambiguous 24984 9171 703 UnstrandedReadsAssigned:732197 PositiveStrandReadsAssigned:628678 NegativeStrandReadsAssigned:133949 Dataset is classified unstranded MeadianReadLen=22 20thPercentileLength=19 echo kmer=19 ERR9451998 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: ERR9451998-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,038,965 reads, 2,323,103 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,060 rounds 52973 ERR9451998.ke.tsv 35125 ERR9451998.se.tsv 88098 total ==> ERR9451998.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 2 0.575896 PNS24243 293 194 0 0 KQK14069 1603 1504 392.359 103.063 KQK14071 474 375 14.4788 15.2535 ==> ERR9451998.se.tsv <== BRADI_1g14170v3 500 BRADI_1g53295v3 3 BRADI_1g59795v3 1 BRADI_1g07683v3 1 BRADI_1g00485v3 1 BRADI_1g20270v3 15 BRADI_1g74790v3 28 BRADI_1g09890v3 0 BRADI_1g77505v3 17 BRADI_1g48960v3 0 ERR9451998 completed mapping pipeline successfully