Starting /dee2/code/volunteer_pipeline.sh ERR9451997 current disk space = 1548876214272 free memory = 1385795512 ERR9451997 SRAfilesize 682e8536df987c21dad372b1730c9372 ERR9451997.sra ERR9451997.sra file validated ERR9451997 is single end ERR9451997 is conventional basespace ERR9451997 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9451997_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 35.9135 37.0 37.0 37.0 37.0 37.0 2 36.515 37.0 37.0 37.0 37.0 37.0 3 36.55675 37.0 37.0 37.0 37.0 37.0 4 36.6705 37.0 37.0 37.0 37.0 37.0 5 36.6025 37.0 37.0 37.0 37.0 37.0 6 36.618 37.0 37.0 37.0 37.0 37.0 7 36.592 37.0 37.0 37.0 37.0 37.0 8 36.617 37.0 37.0 37.0 37.0 37.0 9 36.5865 37.0 37.0 37.0 37.0 37.0 10 36.685 37.0 37.0 37.0 37.0 37.0 11 36.6705 37.0 37.0 37.0 37.0 37.0 12 36.644 37.0 37.0 37.0 37.0 37.0 13 36.5355 37.0 37.0 37.0 37.0 37.0 14 36.52 37.0 37.0 37.0 37.0 37.0 15 36.517 37.0 37.0 37.0 37.0 37.0 16 36.4285 37.0 37.0 37.0 37.0 37.0 17 36.448 37.0 37.0 37.0 37.0 37.0 18 36.6525 37.0 37.0 37.0 37.0 37.0 19 36.5515 37.0 37.0 37.0 37.0 37.0 20 36.55 37.0 37.0 37.0 37.0 37.0 21 36.571 37.0 37.0 37.0 37.0 37.0 22 36.475 37.0 37.0 37.0 37.0 37.0 23 36.522 37.0 37.0 37.0 37.0 37.0 24 36.571 37.0 37.0 37.0 37.0 37.0 25 36.644 37.0 37.0 37.0 37.0 37.0 26 36.575 37.0 37.0 37.0 37.0 37.0 27 36.5245 37.0 37.0 37.0 37.0 37.0 28 36.658 37.0 37.0 37.0 37.0 37.0 29 36.7205 37.0 37.0 37.0 37.0 37.0 30 36.5995 37.0 37.0 37.0 37.0 37.0 31 36.6715 37.0 37.0 37.0 37.0 37.0 32 36.645 37.0 37.0 37.0 37.0 37.0 33 36.6405 37.0 37.0 37.0 37.0 37.0 34 36.558 37.0 37.0 37.0 37.0 37.0 35 36.6555 37.0 37.0 37.0 37.0 37.0 36 36.63 37.0 37.0 37.0 37.0 37.0 37 36.719 37.0 37.0 37.0 37.0 37.0 38 36.645 37.0 37.0 37.0 37.0 37.0 39 36.6215 37.0 37.0 37.0 37.0 37.0 40 36.6315 37.0 37.0 37.0 37.0 37.0 41 36.628 37.0 37.0 37.0 37.0 37.0 42 36.638 37.0 37.0 37.0 37.0 37.0 43 36.503 37.0 37.0 37.0 37.0 37.0 44 36.6245 37.0 37.0 37.0 37.0 37.0 45 36.583 37.0 37.0 37.0 37.0 37.0 46 36.61 37.0 37.0 37.0 37.0 37.0 47 36.6415 37.0 37.0 37.0 37.0 37.0 48 36.5745 37.0 37.0 37.0 37.0 37.0 49 36.585 37.0 37.0 37.0 37.0 37.0 50 36.6855 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 0.0 26 4.0 27 6.0 28 8.0 29 5.0 30 14.0 31 23.0 32 36.0 33 52.0 34 46.0 35 147.0 36 1386.0 37 2272.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 22.626262626262626 28.28282828282828 23.282828282828284 25.808080808080806 2 24.675 28.875 26.900000000000002 19.55 3 28.08202050512628 27.38184546136534 21.50537634408602 23.030757689422355 4 27.900000000000002 36.95 17.8 17.349999999999998 5 23.375 27.625 22.1 26.900000000000002 6 29.599999999999998 23.5 27.05 19.85 7 29.849999999999998 30.45 21.6 18.099999999999998 8 22.400000000000002 27.250000000000004 26.075 24.275 9 21.65 27.325 26.200000000000003 24.825 10 35.475 21.875 21.099999999999998 21.55 11 22.3 27.950000000000003 30.5 19.25 12 23.549999999999997 27.6 26.900000000000002 21.95 13 26.950000000000003 23.575 18.75 30.725 14 29.95 31.424999999999997 22.45 16.175 15 23.5 33.975 22.2 20.325 16 21.725 27.275 32.15 18.85 17 23.875 26.275 32.675 17.175 18 30.5 23.200000000000003 27.625 18.675 19 36.525 25.95 22.125 15.4 20 26.075 29.549999999999997 29.299999999999997 15.075 21 21.525 38.125 20.674999999999997 19.675 22 23.674999999999997 34.575 22.125 19.625 23 30.075000000000003 35.35 19.1 15.475 24 28.249999999999996 32.425 22.7 16.625 25 28.449999999999996 36.5 15.975 19.075 26 32.775 26.125 20.9 20.200000000000003 27 27.575 38.525 15.0 18.9 28 32.35 28.575 20.175 18.9 29 31.825 29.049999999999997 14.075 25.05 30 39.300000000000004 34.075 11.225 15.4 31 41.05 33.95 9.425 15.575 32 35.525 40.0 9.15 15.325 33 29.5 45.625 8.649999999999999 16.225 34 41.125 33.85 8.4 16.625 35 32.45 41.525 5.35 20.674999999999997 36 36.35 38.625 6.0249999999999995 19.0 37 27.474999999999998 34.449999999999996 5.45 32.625 38 26.125 42.75 5.949999999999999 25.174999999999997 39 25.874999999999996 31.1 8.1 34.925 40 26.825 37.3 9.225 26.650000000000002 41 22.900000000000002 28.925 13.65 34.525 42 30.25 26.724999999999998 12.325 30.7 43 22.725 26.8 24.099999999999998 26.375 44 23.0 26.174999999999997 17.1 33.725 45 17.299999999999997 28.475 23.65 30.575000000000003 46 24.349999999999998 28.9 17.775 28.975 47 18.025 30.5 18.2 33.275 48 14.674999999999999 33.85 21.375 30.099999999999998 49 12.825000000000001 25.674999999999997 18.675 42.825 50 15.625 22.075 26.5 35.8 >>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 0.5 30 1.0 31 1.5 32 2.0 33 1.5 34 1.0 35 10.0 36 19.0 37 36.5 38 54.0 39 107.0 40 160.0 41 183.5 42 207.0 43 227.5 44 248.0 45 387.0 46 526.0 47 595.0 48 664.0 49 532.5 50 401.0 51 445.5 52 490.0 53 483.5 54 477.0 55 394.5 56 312.0 57 260.5 58 209.0 59 155.5 60 102.0 61 70.5 62 39.0 63 32.0 64 25.0 65 18.5 66 12.0 67 21.0 68 30.0 69 24.5 70 19.0 71 10.5 72 2.0 73 1.0 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 1.0 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 67.525 #Duplication Level Percentage of deduplicated Percentage of total 1 84.07997038134025 56.775 2 10.292484265087005 13.900000000000002 3 2.7767493520918176 5.625 4 0.9996297667530544 2.7 5 0.22213994816734545 0.75 6 0.33320992225101814 1.35 7 0.1480932987782303 0.7000000000000001 8 0.259163272861903 1.4000000000000001 9 0.037023324694557574 0.22499999999999998 >10 0.8145131432802665 11.799999999999999 >50 0.0 0.0 >100 0.037023324694557574 4.775 >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 191 4.775 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 45 1.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 34 0.8500000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 34 0.8500000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 30 0.75 No Hit AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 27 0.675 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 24 0.6 No Hit GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 19 0.475 No Hit AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAG 17 0.42500000000000004 TruSeq Adapter, Index 7 (97% over 36bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAG 12 0.3 TruSeq Adapter, Index 7 (97% over 36bp) GATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) ATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) AGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCTGA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) AACAGTCGACTCAGAACTGGTACGGAGATCGGAAGAGCACACGTCTGAAC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC 7 0.17500000000000002 No Hit CACTGAGATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACA 7 0.17500000000000002 No Hit CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 6 0.15 No Hit ACAGGTCTGTGATGCCCTTAGATGTTCTGAGATCGGAAGAGCACACGTCT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAGATCGGAAGAGCACACGTC 6 0.15 No Hit AAGTATGAACTAATTTGAACTGTGAAACTAGATCGGAAGAGCACACGTCT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA 5 0.125 No Hit GTGACGGAGAATTAGGGTTCGATTAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TGTTGAGCTTGACTCTAGTCCGACTTTGTGAGATCGGAAGAGCACACGTC 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA 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 0.075 0.0 0.0 0.0 0.0 9 0.125 0.0 0.0 0.0 0.0 10 0.15 0.0 0.0 0.0 0.0 11 0.15 0.0 0.0 0.0 0.0 12 0.225 0.0 0.0 0.0 0.0 13 0.35 0.0 0.0 0.0 0.0 14 1.3 0.0 0.0 0.0 0.0 15 1.4 0.0 0.0 0.0 0.0 16 1.625 0.0 0.0 0.0 0.0 17 2.225 0.0 0.0 0.0 0.0 18 2.825 0.0 0.0 0.0 0.0 19 4.3 0.0 0.0 0.0 0.0 20 6.975 0.0 0.0 0.0 0.0 21 10.625 0.0 0.0 0.0 0.0 22 15.6 0.0 0.0 0.0 0.0 23 24.375 0.0 0.0 0.0 0.0 24 30.475 0.0 0.0 0.0 0.0 25 44.5 0.0 0.0 0.0 0.0 26 52.625 0.0 0.0 0.0 0.0 27 58.95 0.0 0.0 0.0 0.0 28 64.425 0.0 0.0 0.0 0.0 29 70.325 0.0 0.0 0.0 0.0 30 76.55 0.0 0.0 0.0 0.0 31 81.425 0.0 0.0 0.0 0.0 32 84.9 0.0 0.0 0.0 0.0 33 89.25 0.0 0.0 0.0 0.0 34 92.2 0.0 0.0 0.0 0.0 35 94.225 0.0 0.0 0.0 0.0 36 95.9 0.0 0.0 0.0 0.0 37 96.9 0.0 0.0 0.0 0.0 38 97.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACACGA 25 3.6958358E-5 44.0 1 ACACGAC 30 1.083877E-4 36.666664 2 CGGATAT 35 2.6843656E-4 31.428572 18 GGATATC 35 2.6843656E-4 31.428572 19 AACGGAT 35 2.6843656E-4 31.428572 16 ACGGATA 35 2.6843656E-4 31.428572 17 CACGACT 40 5.87456E-4 27.500002 3 GCAACGG 40 5.87456E-4 27.500002 14 CAACGGA 40 5.87456E-4 27.500002 15 GGCAACG 45 0.0011696975 24.444447 13 TCGGCAA 45 0.0011696975 24.444447 11 CTCTCGG 45 0.0011696975 24.444447 8 ACTCTCG 45 0.0011696975 24.444447 7 ACGACTC 45 0.0011696975 24.444447 4 CGGCAAC 45 0.0011696975 24.444447 12 GACTCTC 45 0.0011696975 24.444447 6 CGACTCT 45 0.0011696975 24.444447 5 GAACTCC 90 2.3813118E-7 22.000002 44 TCTCGGC 50 0.0021617375 22.0 9 CTCGGCA 50 0.0021617375 22.0 10 >>END_MODULE Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857756 READS because READLEN < 1 Read 857756 spots for ERR9451997.sra Written 857756 spots for ERR9451997.sra Rejected 857760 READS because READLEN < 1 Read 857760 spots for ERR9451997.sra Written 857760 spots for ERR9451997.sra SRR ids: ['ERR9451997.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_n3lqeugr ERR9451997.sra spots: 17155124 blocks: [[1, 857756], [857757, 1715512], [1715513, 2573268], [2573269, 3431024], [3431025, 4288780], [4288781, 5146536], [5146537, 6004292], [6004293, 6862048], [6862049, 7719804], [7719805, 8577560], [8577561, 9435316], [9435317, 10293072], [10293073, 11150828], [11150829, 12008584], [12008585, 12866340], [12866341, 13724096], [13724097, 14581852], [14581853, 15439608], [15439609, 16297364], [16297365, 17155124]] ERR9451997 file size 2390738 ERR9451997 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 ERR9451997 ERR9451997_1.fastq Input file: ERR9451997_1.fastq trimmed: ERR9451997-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 22:04:32 2024 >> started Fri Dec 6 22:04:41 2024 >> done (9.010s) 17155124 reads processed; of these: 555043 ( 3.24%) short reads filtered out after trimming by size control 1093 ( 0.01%) empty reads filtered out after trimming by size control 16598988 (96.76%) reads available; of these: 235835 ( 1.42%) trimmed reads available after processing 16363153 (98.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 235835 1.42% 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 16363153 98.58% 16598988 reads passed initial QC criterion=sequence-density sequence-density=95.80 sequence-density-rank=1 fanout-score=31.49 fanout-score-rank=1 prefix-density=96.85 prefix-fanout=31.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGAGATCATCTCGTATGCCG criterion=fanout-score sequence-density=95.80 sequence-density-rank=1 fanout-score=31.49 fanout-score-rank=1 prefix-density=96.85 prefix-fanout=31.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGAGATCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGAGATCATCTCGTATGCCG -o ERR9451997 - Input file: STDIN trimmed: ERR9451997-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGAGATCATCTCGTATGCCG -- 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 22:05:24 2024 >> started Fri Dec 6 22:05:42 2024 >> done (18.189s) 16253176 reads processed; of these: 6227 ( 0.04%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 16246934 (99.96%) reads available; of these: 15927916 (98.04%) trimmed reads available after processing 319018 ( 1.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 235541 1.45% 19 434958 2.68% 20 669494 4.12% 21 940598 5.79% 22 1455198 8.96% 23 1078243 6.64% 24 2338971 14.40% 25 1315530 8.10% 26 1164017 7.16% 27 1013476 6.24% 28 963333 5.93% 29 1013956 6.24% 30 753437 4.64% 31 583326 3.59% 32 643676 3.96% 33 480577 2.96% 34 328547 2.02% 35 289039 1.78% 36 144644 0.89% 37 102827 0.63% 38 59053 0.36% 39 43541 0.27% 40 28220 0.17% 41 38202 0.24% 42 12888 0.08% 43 7993 0.05% 44 5910 0.04% 45 4579 0.03% 46 3175 0.02% 47 3291 0.02% 48 0 0.00% 49 0 0.00% 50 90694 0.56% criterion=sequence-density sequence-density=3.87 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=26.80 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=1.1 sequence=GTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTC Started job on | Dec 06 22:06:03 Started mapping on | Dec 06 22:06:03 Finished on | Dec 06 22:07:01 Mapping speed, Million of reads per hour | 1029.89 Number of input reads | 16592746 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 2385502 Uniquely mapped reads % | 14.38% Average mapped length | 24.99 Number of splices: Total | 58409 Number of splices: Annotated (sjdb) | 37619 Number of splices: GT/AG | 56693 Number of splices: GC/AG | 926 Number of splices: AT/AC | 25 Number of splices: Non-canonical | 765 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.43 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5538279 % of reads mapped to multiple loci | 33.38% Number of reads mapped to too many loci | 8134231 % of reads mapped to too many loci | 49.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.78% % of reads unmapped: other | 0.45% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8668965 8668965 8668965 N_multimapping 5538279 5538279 5538279 N_noFeature 1525283 1642810 2250950 N_ambiguous 28270 10878 604 UnstrandedReadsAssigned:831949 PositiveStrandReadsAssigned:731814 NegativeStrandReadsAssigned:133948 Dataset is classified positive stranded MeadianReadLen=25 20thPercentileLength=22 echo kmer=19 ERR9451997 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: ERR9451997-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,592,746 reads, 1,743,060 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 929 rounds 52973 ERR9451997.ke.tsv 35125 ERR9451997.se.tsv 88098 total ==> ERR9451997.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 6 2.73139 PNS24243 293 194 1 3.21947 KQK14069 1603 1504 702.173 291.596 KQK14071 474 375 19.5439 32.5511 ==> ERR9451997.se.tsv <== BRADI_1g14170v3 774 BRADI_1g53295v3 0 BRADI_1g59795v3 7 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 21 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR9451997 completed mapping pipeline successfully