Starting /dee2/code/volunteer_pipeline.sh ERR9452002 current disk space = 1548555755520 free memory = 1600245912 ERR9452002 SRAfilesize 93ef7428c50be39d6ab9d089ccbdcf52 ERR9452002.sra ERR9452002.sra file validated ERR9452002 is single end ERR9452002 is conventional basespace ERR9452002 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452002_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 36.264 37.0 37.0 37.0 37.0 37.0 2 36.5505 37.0 37.0 37.0 37.0 37.0 3 36.61075 37.0 37.0 37.0 37.0 37.0 4 36.597 37.0 37.0 37.0 37.0 37.0 5 36.6335 37.0 37.0 37.0 37.0 37.0 6 36.6005 37.0 37.0 37.0 37.0 37.0 7 36.6935 37.0 37.0 37.0 37.0 37.0 8 36.648 37.0 37.0 37.0 37.0 37.0 9 36.665 37.0 37.0 37.0 37.0 37.0 10 36.7145 37.0 37.0 37.0 37.0 37.0 11 36.6665 37.0 37.0 37.0 37.0 37.0 12 36.676 37.0 37.0 37.0 37.0 37.0 13 36.7165 37.0 37.0 37.0 37.0 37.0 14 36.683 37.0 37.0 37.0 37.0 37.0 15 36.6545 37.0 37.0 37.0 37.0 37.0 16 36.5965 37.0 37.0 37.0 37.0 37.0 17 36.5815 37.0 37.0 37.0 37.0 37.0 18 36.6525 37.0 37.0 37.0 37.0 37.0 19 36.7085 37.0 37.0 37.0 37.0 37.0 20 36.698 37.0 37.0 37.0 37.0 37.0 21 36.6925 37.0 37.0 37.0 37.0 37.0 22 36.6405 37.0 37.0 37.0 37.0 37.0 23 36.706 37.0 37.0 37.0 37.0 37.0 24 36.7415 37.0 37.0 37.0 37.0 37.0 25 36.7495 37.0 37.0 37.0 37.0 37.0 26 36.6945 37.0 37.0 37.0 37.0 37.0 27 36.6695 37.0 37.0 37.0 37.0 37.0 28 36.748 37.0 37.0 37.0 37.0 37.0 29 36.7255 37.0 37.0 37.0 37.0 37.0 30 36.6905 37.0 37.0 37.0 37.0 37.0 31 36.7435 37.0 37.0 37.0 37.0 37.0 32 36.6575 37.0 37.0 37.0 37.0 37.0 33 36.724 37.0 37.0 37.0 37.0 37.0 34 36.7175 37.0 37.0 37.0 37.0 37.0 35 36.7255 37.0 37.0 37.0 37.0 37.0 36 36.7205 37.0 37.0 37.0 37.0 37.0 37 36.741 37.0 37.0 37.0 37.0 37.0 38 36.6445 37.0 37.0 37.0 37.0 37.0 39 36.696 37.0 37.0 37.0 37.0 37.0 40 36.7305 37.0 37.0 37.0 37.0 37.0 41 36.7395 37.0 37.0 37.0 37.0 37.0 42 36.6885 37.0 37.0 37.0 37.0 37.0 43 36.6875 37.0 37.0 37.0 37.0 37.0 44 36.711 37.0 37.0 37.0 37.0 37.0 45 36.7 37.0 37.0 37.0 37.0 37.0 46 36.7265 37.0 37.0 37.0 37.0 37.0 47 36.678 37.0 37.0 37.0 37.0 37.0 48 36.6665 37.0 37.0 37.0 37.0 37.0 49 36.725 37.0 37.0 37.0 37.0 37.0 50 36.5185 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 2.0 26 3.0 27 2.0 28 4.0 29 10.0 30 10.0 31 12.0 32 31.0 33 40.0 34 64.0 35 95.0 36 1090.0 37 2636.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 19.81891348088531 30.935613682092555 22.61066398390342 26.634808853118713 2 27.500000000000004 28.825 21.925 21.75 3 33.383345836459114 27.306826706676667 16.35408852213053 22.95573893473368 4 34.75 31.924999999999997 14.975 18.35 5 24.349999999999998 29.45 17.075000000000003 29.125 6 26.375 25.2 28.849999999999998 19.575 7 26.85 33.0 21.325 18.825 8 22.525000000000002 24.425 31.35 21.7 9 25.025 33.15 22.025 19.8 10 37.05 22.35 20.424999999999997 20.175 11 22.625 23.95 27.200000000000003 26.224999999999998 12 23.325000000000003 23.974999999999998 30.625000000000004 22.075 13 25.424999999999997 22.675 19.275000000000002 32.625 14 27.900000000000002 35.949999999999996 20.075000000000003 16.075 15 27.700000000000003 30.7 22.8 18.8 16 20.525 33.425 27.05 19.0 17 24.4 27.675 31.924999999999997 16.0 18 27.875 25.775 22.6 23.75 19 38.875 29.849999999999998 16.8 14.475 20 33.175 32.15 21.325 13.350000000000001 21 23.799999999999997 43.075 16.8 16.325 22 28.075 38.0 17.349999999999998 16.575 23 37.525 33.725 15.0 13.750000000000002 24 32.2 38.025 15.375 14.399999999999999 25 36.025 36.375 11.95 15.65 26 35.625 29.2 13.375 21.8 27 31.65 43.5 8.625 16.225 28 34.525 33.0 11.375 21.099999999999998 29 32.550000000000004 39.675 7.074999999999999 20.7 30 33.675 37.525 5.45 23.35 31 39.825 34.9 5.7250000000000005 19.55 32 30.25 37.1 12.325 20.325 33 25.25 37.925 6.3 30.525000000000002 34 31.775 30.75 13.475000000000001 24.0 35 30.049999999999997 33.625 8.95 27.375 36 24.95 38.85 9.275 26.924999999999997 37 20.575 32.775 12.85 33.800000000000004 38 20.775 31.324999999999996 13.325000000000001 34.575 39 20.375 23.674999999999997 22.7 33.25 40 20.349999999999998 28.299999999999997 16.650000000000002 34.699999999999996 41 17.175 24.0 20.075000000000003 38.75 42 21.05 29.325000000000003 19.1 30.525000000000002 43 23.375 24.55 24.725 27.35 44 17.025000000000002 24.125 24.975 33.875 45 13.200000000000001 27.525 21.575 37.7 46 17.175 32.5 18.825 31.5 47 13.175 26.85 18.425 41.55 48 11.200000000000001 34.75 19.825 34.225 49 12.1 26.75 15.2 45.95 50 12.225 32.4 19.25 36.125 >>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 1.0 10 2.0 11 1.0 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 1.0 32 2.0 33 1.0 34 0.0 35 3.0 36 6.0 37 17.0 38 28.0 39 44.5 40 61.0 41 90.0 42 119.0 43 140.0 44 161.0 45 295.0 46 429.0 47 607.5 48 786.0 49 602.0 50 418.0 51 561.0 52 704.0 53 635.0 54 566.0 55 446.0 56 326.0 57 262.5 58 199.0 59 143.5 60 88.0 61 67.5 62 47.0 63 38.0 64 29.0 65 20.0 66 11.0 67 11.5 68 12.0 69 8.5 70 5.0 71 3.0 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 0.6 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 61.175000000000004 #Duplication Level Percentage of deduplicated Percentage of total 1 85.20637515324889 52.125 2 8.78626890069473 10.75 3 2.0841847159787497 3.8249999999999997 4 1.0625255414793624 2.6 5 0.5312627707396812 1.625 6 0.36779730281977935 1.35 7 0.36779730281977935 1.575 8 0.2451982018798529 1.2 9 0.1634654679199019 0.8999999999999999 >10 1.021659174499387 12.25 >50 0.08173273395995095 3.1 >100 0.08173273395995095 8.7 >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 AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACA 198 4.95 TruSeq Adapter, Index 5 (100% over 36bp) CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 150 3.75 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACA 67 1.675 TruSeq Adapter, Index 5 (100% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 57 1.425 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 48 1.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 40 1.0 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 31 0.775 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAC 26 0.65 TruSeq Adapter, Index 5 (100% over 35bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 22 0.5499999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 22 0.5499999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAAC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAC 10 0.25 TruSeq Adapter, Index 5 (100% over 35bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 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) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAG 9 0.22499999999999998 TruSeq Adapter, Index 5 (100% over 37bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 9 0.22499999999999998 No Hit TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) TTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGA 7 0.17500000000000002 TruSeq Adapter, Index 25 (97% over 38bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 6 0.15 No Hit ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACA 6 0.15 TruSeq Adapter, Index 5 (100% over 36bp) GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACA 6 0.15 TruSeq Adapter, Index 5 (100% over 36bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGA 6 0.15 TruSeq Adapter, Index 25 (97% over 38bp) ACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACA 5 0.125 TruSeq Adapter, Index 5 (100% over 36bp) CCTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AAGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGGAATCCGACTGTTTAATTAAAACAAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGGATGTAGCTCAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CTAGTCCGACTTTGTGAAATGAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) >>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 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 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 0.15 0.0 0.0 0.0 0.0 10 0.25 0.0 0.0 0.0 0.0 11 0.5 0.0 0.0 0.0 0.0 12 1.25 0.0 0.0 0.0 0.0 13 2.4 0.0 0.0 0.0 0.0 14 11.05 0.0 0.0 0.0 0.0 15 13.3 0.0 0.0 0.0 0.0 16 16.15 0.0 0.0 0.0 0.0 17 21.225 0.0 0.0 0.0 0.0 18 26.225 0.0 0.0 0.0 0.0 19 31.925 0.0 0.0 0.0 0.0 20 38.325 0.0 0.0 0.0 0.0 21 45.875 0.0 0.0 0.0 0.0 22 53.25 0.0 0.0 0.0 0.0 23 62.275 0.0 0.0 0.0 0.0 24 67.775 0.0 0.0 0.0 0.0 25 76.875 0.0 0.0 0.0 0.0 26 81.75 0.0 0.0 0.0 0.0 27 85.225 0.0 0.0 0.0 0.0 28 88.55 0.0 0.0 0.0 0.0 29 90.775 0.0 0.0 0.0 0.0 30 92.95 0.0 0.0 0.0 0.0 31 94.3 0.0 0.0 0.0 0.0 32 95.375 0.0 0.0 0.0 0.0 33 96.375 0.0 0.0 0.0 0.0 34 97.3 0.0 0.0 0.0 0.0 35 97.75 0.0 0.0 0.0 0.0 36 98.2 0.0 0.0 0.0 0.0 37 98.325 0.0 0.0 0.0 0.0 38 98.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGCTCA 40 5.315087E-9 44.000004 8 CTATAGC 30 1.9515464E-6 44.0 5 AGCTCAG 35 1.02281774E-7 44.0 9 AGGGCTA 30 1.9515464E-6 44.0 1 GCTATAG 30 1.9515464E-6 44.0 4 ATAGCTC 30 1.9515464E-6 44.0 7 CTAACGA 30 1.9515464E-6 44.0 1 CTCAGAT 35 1.02281774E-7 44.0 11 GGCTATA 30 1.9515464E-6 44.0 3 GCTCAGA 35 1.02281774E-7 44.0 10 TATAGCT 30 1.9515464E-6 44.0 6 GGGCTAT 30 1.9515464E-6 44.0 2 TAACGAA 35 5.6380304E-6 37.714287 2 TCAGATC 45 7.364706E-7 34.222225 12 TCACACA 60 4.603862E-9 33.0 44 GAACGAA 45 3.1577816E-5 29.333336 6 GTCACAC 70 2.0741936E-8 28.285715 43 AGTCACA 70 2.0741936E-8 28.285715 42 CAGTCAC 95 4.015692E-7 20.842106 41 GAACGAT 65 3.852825E-4 20.307693 10 >>END_MODULE Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888529 READS because READLEN < 1 Read 888529 spots for ERR9452002.sra Written 888529 spots for ERR9452002.sra Rejected 888532 READS because READLEN < 1 Read 888532 spots for ERR9452002.sra Written 888532 spots for ERR9452002.sra SRR ids: ['ERR9452002.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5roppudz ERR9452002.sra spots: 17770583 blocks: [[1, 888529], [888530, 1777058], [1777059, 2665587], [2665588, 3554116], [3554117, 4442645], [4442646, 5331174], [5331175, 6219703], [6219704, 7108232], [7108233, 7996761], [7996762, 8885290], [8885291, 9773819], [9773820, 10662348], [10662349, 11550877], [11550878, 12439406], [12439407, 13327935], [13327936, 14216464], [14216465, 15104993], [15104994, 15993522], [15993523, 16882051], [16882052, 17770583]] ERR9452002 file size 2477287 ERR9452002 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 ERR9452002 ERR9452002_1.fastq Input file: ERR9452002_1.fastq trimmed: ERR9452002-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 22:28:18 2024 >> started Fri Dec 6 22:28:29 2024 >> done (10.445s) 17770583 reads processed; of these: 4558194 (25.65%) short reads filtered out after trimming by size control 1399 ( 0.01%) empty reads filtered out after trimming by size control 13210990 (74.34%) reads available; of these: 902463 ( 6.83%) trimmed reads available after processing 12308527 (93.17%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 902463 6.83% 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 12308527 93.17% 13210990 reads passed initial QC criterion=sequence-density sequence-density=91.45 sequence-density-rank=1 fanout-score=24.48 fanout-score-rank=1 prefix-density=91.89 prefix-fanout=24.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGATTCATC criterion=fanout-score sequence-density=91.45 sequence-density-rank=1 fanout-score=24.48 fanout-score-rank=1 prefix-density=91.89 prefix-fanout=24.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGATTCATC 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGATTCATC -o ERR9452002 - Input file: STDIN trimmed: ERR9452002-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGATTCATC -- 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 22:28:43 2024 >> started Fri Dec 6 22:28:55 2024 >> done (11.559s) 12923795 reads processed; of these: 24183 ( 0.19%) short reads filtered out after trimming by size control 12 ( 0.00%) empty reads filtered out after trimming by size control 12899600 (99.81%) reads available; of these: 11972620 (92.81%) trimmed reads available after processing 926980 ( 7.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 900911 6.98% 19 1141302 8.85% 20 1235884 9.58% 21 1374184 10.65% 22 1593266 12.35% 23 1007554 7.81% 24 1470921 11.40% 25 891683 6.91% 26 705520 5.47% 27 548722 4.25% 28 459675 3.56% 29 415672 3.22% 30 284919 2.21% 31 198408 1.54% 32 188303 1.46% 33 146015 1.13% 34 89847 0.70% 35 72903 0.57% 36 36115 0.28% 37 25497 0.20% 38 15287 0.12% 39 11942 0.09% 40 8566 0.07% 41 11167 0.09% 42 4205 0.03% 43 2590 0.02% 44 1853 0.01% 45 1448 0.01% 46 1119 0.01% 47 1195 0.01% 48 0 0.00% 49 0 0.00% 50 52927 0.41% criterion=sequence-density sequence-density=1.55 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=14 fanout-score=6.98 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=1.0 sequence=TAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAG Started job on | Dec 06 22:29:12 Started mapping on | Dec 06 22:29:12 Finished on | Dec 06 22:29:54 Mapping speed, Million of reads per hour | 1130.30 Number of input reads | 13186795 Average input read length | 24 UNIQUE READS: Uniquely mapped reads number | 1411423 Uniquely mapped reads % | 10.70% Average mapped length | 23.43 Number of splices: Total | 49844 Number of splices: Annotated (sjdb) | 25886 Number of splices: GT/AG | 48498 Number of splices: GC/AG | 1088 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 245 Mismatch rate per base, % | 0.57% Deletion rate per base | 0.00% Deletion average length | 1.31 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4852650 % of reads mapped to multiple loci | 36.80% Number of reads mapped to too many loci | 6527751 % of reads mapped to too many loci | 49.50% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.68% % of reads unmapped: other | 0.32% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6922722 6922722 6922722 N_multimapping 4852650 4852650 4852650 N_noFeature 747775 818083 1327006 N_ambiguous 22002 7449 604 UnstrandedReadsAssigned:641646 PositiveStrandReadsAssigned:585891 NegativeStrandReadsAssigned:83813 Dataset is classified positive stranded MeadianReadLen=23 20thPercentileLength=20 echo kmer=19 ERR9452002 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: ERR9452002-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,186,795 reads, 1,300,859 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 887 rounds 52973 ERR9452002.ke.tsv 35125 ERR9452002.se.tsv 88098 total ==> ERR9452002.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0.15625 0.127298 PNS24247 1044 945 0 0 PNS24249 1928 1829 1.84375 0.687409 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 440.2 199.586 KQK14071 474 375 6.10962 11.1099 ==> ERR9452002.se.tsv <== BRADI_1g14170v3 586 BRADI_1g53295v3 3 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 22 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 10 BRADI_1g48960v3 0 ERR9452002 completed mapping pipeline successfully