Starting /dee2/code/volunteer_pipeline.sh ERR9452012 current disk space = 1548596420608 free memory = 1455317440 ERR9452012 SRAfilesize 18153e91312b46329ab855f44a096428 ERR9452012.sra ERR9452012.sra file validated ERR9452012 is single end ERR9452012 is conventional basespace ERR9452012 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452012_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 36.149 37.0 37.0 37.0 37.0 37.0 2 36.3755 37.0 37.0 37.0 37.0 37.0 3 36.4545 37.0 37.0 37.0 37.0 37.0 4 36.4765 37.0 37.0 37.0 37.0 37.0 5 36.383 37.0 37.0 37.0 37.0 37.0 6 36.4085 37.0 37.0 37.0 37.0 37.0 7 36.503 37.0 37.0 37.0 37.0 37.0 8 36.4275 37.0 37.0 37.0 37.0 37.0 9 36.433 37.0 37.0 37.0 37.0 37.0 10 36.4875 37.0 37.0 37.0 37.0 37.0 11 36.5475 37.0 37.0 37.0 37.0 37.0 12 36.4155 37.0 37.0 37.0 37.0 37.0 13 36.4055 37.0 37.0 37.0 37.0 37.0 14 36.3215 37.0 37.0 37.0 37.0 37.0 15 36.4685 37.0 37.0 37.0 37.0 37.0 16 36.3975 37.0 37.0 37.0 37.0 37.0 17 36.3745 37.0 37.0 37.0 37.0 37.0 18 36.3875 37.0 37.0 37.0 37.0 37.0 19 36.329 37.0 37.0 37.0 37.0 37.0 20 36.35 37.0 37.0 37.0 37.0 37.0 21 36.4105 37.0 37.0 37.0 37.0 37.0 22 36.37 37.0 37.0 37.0 37.0 37.0 23 36.4555 37.0 37.0 37.0 37.0 37.0 24 36.414 37.0 37.0 37.0 37.0 37.0 25 36.5805 37.0 37.0 37.0 37.0 37.0 26 36.384 37.0 37.0 37.0 37.0 37.0 27 36.412 37.0 37.0 37.0 37.0 37.0 28 36.5015 37.0 37.0 37.0 37.0 37.0 29 36.488 37.0 37.0 37.0 37.0 37.0 30 36.484 37.0 37.0 37.0 37.0 37.0 31 36.6135 37.0 37.0 37.0 37.0 37.0 32 36.4145 37.0 37.0 37.0 37.0 37.0 33 36.5685 37.0 37.0 37.0 37.0 37.0 34 36.4925 37.0 37.0 37.0 37.0 37.0 35 36.5105 37.0 37.0 37.0 37.0 37.0 36 36.6035 37.0 37.0 37.0 37.0 37.0 37 36.5065 37.0 37.0 37.0 37.0 37.0 38 36.5395 37.0 37.0 37.0 37.0 37.0 39 36.4995 37.0 37.0 37.0 37.0 37.0 40 36.5255 37.0 37.0 37.0 37.0 37.0 41 36.649 37.0 37.0 37.0 37.0 37.0 42 36.438 37.0 37.0 37.0 37.0 37.0 43 36.4975 37.0 37.0 37.0 37.0 37.0 44 36.4605 37.0 37.0 37.0 37.0 37.0 45 36.4255 37.0 37.0 37.0 37.0 37.0 46 36.4785 37.0 37.0 37.0 37.0 37.0 47 36.513 37.0 37.0 37.0 37.0 37.0 48 36.4185 37.0 37.0 37.0 37.0 37.0 49 36.472 37.0 37.0 37.0 37.0 37.0 50 36.208 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 1.0 24 3.0 25 1.0 26 7.0 27 7.0 28 14.0 29 18.0 30 18.0 31 28.0 32 37.0 33 64.0 34 91.0 35 157.0 36 1459.0 37 2093.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 17.477432296890672 26.028084252758276 23.8716148445336 32.62286860581745 2 25.425425425425423 29.054054054054053 24.74974974974975 20.77077077077077 3 28.925 31.6 16.925 22.55 4 31.25 34.75 16.0 18.0 5 23.3 28.825 16.900000000000002 30.975 6 29.025000000000002 23.35 26.35 21.275 7 27.6 34.325 20.125 17.95 8 22.925 28.775000000000002 25.874999999999996 22.425 9 23.599999999999998 31.424999999999997 20.575 24.4 10 36.0 23.25 19.950000000000003 20.8 11 24.525 27.375 24.975 23.125 12 24.8 27.1 27.1 21.0 13 23.575 22.45 21.675 32.300000000000004 14 30.825000000000003 31.424999999999997 22.1 15.65 15 26.55 32.475 22.8 18.175 16 22.5 28.075 29.825000000000003 19.6 17 24.025 28.249999999999996 31.125000000000004 16.6 18 26.3 26.6 26.450000000000003 20.65 19 37.05 28.4 19.075 15.475 20 28.325 34.825 22.650000000000002 14.2 21 23.400000000000002 43.525000000000006 17.025000000000002 16.05 22 26.950000000000003 34.425 18.099999999999998 20.525 23 32.975 36.05 16.625 14.35 24 32.925 34.699999999999996 16.675 15.7 25 32.4 36.8 13.850000000000001 16.950000000000003 26 34.4 28.325 18.099999999999998 19.175 27 32.275 39.074999999999996 10.100000000000001 18.55 28 39.300000000000004 33.5 10.475 16.725 29 37.475 38.425 7.3 16.8 30 34.075 41.55 6.7 17.675 31 37.625 38.475 5.775 18.125 32 35.05 37.824999999999996 7.7 19.425 33 28.7 40.849999999999994 4.775 25.674999999999997 34 33.4 34.449999999999996 7.875 24.275 35 26.875 35.925000000000004 7.025 30.175 36 24.725 39.300000000000004 7.5 28.475 37 21.65 31.825 11.0 35.525 38 22.625 32.574999999999996 12.575 32.225 39 21.4 23.674999999999997 18.625 36.3 40 23.375 27.400000000000002 17.474999999999998 31.75 41 18.625 23.125 23.549999999999997 34.699999999999996 42 19.875 27.725 19.725 32.675 43 21.2 25.174999999999997 26.075 27.55 44 21.05 24.3 22.3 32.35 45 14.025000000000002 30.575000000000003 22.25 33.15 46 15.575 30.85 19.85 33.725 47 12.8 24.95 20.4 41.85 48 12.575 25.15 23.525 38.75 49 13.0 25.275 16.05 45.675 50 12.0 27.425 19.950000000000003 40.625 >>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 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 0.5 26 0.0 27 0.0 28 0.0 29 0.5 30 1.0 31 1.0 32 1.0 33 1.5 34 2.0 35 4.0 36 6.0 37 14.0 38 22.0 39 48.5 40 75.0 41 91.5 42 108.0 43 141.0 44 174.0 45 296.5 46 419.0 47 636.0 48 853.0 49 646.5 50 440.0 51 462.0 52 484.0 53 565.5 54 647.0 55 502.5 56 358.0 57 295.0 58 232.0 59 155.5 60 79.0 61 65.5 62 52.0 63 31.0 64 10.0 65 12.5 66 15.0 67 14.0 68 13.0 69 9.0 70 5.0 71 3.5 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 0.3 2 0.1 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 58.650000000000006 #Duplication Level Percentage of deduplicated Percentage of total 1 82.6086956521739 48.449999999999996 2 10.656436487638533 12.5 3 2.3444160272804773 4.125 4 1.3640238704177323 3.2 5 0.5967604433077579 1.7500000000000002 6 0.4262574595055414 1.5 7 0.29838022165387895 1.225 8 0.17050298380221654 0.8 9 0.1278772378516624 0.675 >10 1.23614663256607 13.375 >50 0.08525149190110827 2.9250000000000003 >100 0.08525149190110827 9.475 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 259 6.4750000000000005 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCA 120 3.0 TruSeq Adapter, Index 2 (97% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 65 1.625 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 52 1.3 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 39 0.975 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 33 0.8250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 33 0.8250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCA 26 0.65 TruSeq Adapter, Index 2 (97% over 36bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCC 15 0.375 TruSeq Adapter, Index 5 (97% over 35bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAT 10 0.25 TruSeq Adapter, Index 2 (97% over 37bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 8 0.2 No Hit TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AAGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TCCTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 6 0.15 No Hit CCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TTTAGATCTTCGGAGTTTGAAGCAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CACGTCGCACGGATTCGCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) AGACTAATCGAACCATCTAGTAGCAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) ACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) >>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 0.025 0.0 0.0 0.0 0.0 2 0.025 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 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10 0.125 0.0 0.0 0.0 0.0 11 0.225 0.0 0.0 0.0 0.0 12 0.55 0.0 0.0 0.0 0.0 13 1.05 0.0 0.0 0.0 0.0 14 5.425 0.0 0.0 0.0 0.0 15 6.725 0.0 0.0 0.0 0.0 16 8.6 0.0 0.0 0.0 0.0 17 12.65 0.0 0.0 0.0 0.0 18 16.9 0.0 0.0 0.0 0.0 19 22.475 0.0 0.0 0.0 0.0 20 29.575 0.0 0.0 0.0 0.0 21 37.8 0.0 0.0 0.0 0.0 22 46.325 0.0 0.0 0.0 0.0 23 58.875 0.0 0.0 0.0 0.0 24 65.425 0.0 0.0 0.0 0.0 25 73.7 0.0 0.0 0.0 0.0 26 79.175 0.0 0.0 0.0 0.0 27 84.425 0.0 0.0 0.0 0.0 28 88.4 0.0 0.0 0.0 0.0 29 90.725 0.0 0.0 0.0 0.0 30 93.075 0.0 0.0 0.0 0.0 31 94.125 0.0 0.0 0.0 0.0 32 95.5 0.0 0.0 0.0 0.0 33 96.4 0.0 0.0 0.0 0.0 34 97.275 0.0 0.0 0.0 0.0 35 97.65 0.0 0.0 0.0 0.0 36 97.9 0.0 0.0 0.0 0.0 37 98.15 0.0 0.0 0.0 0.0 38 98.375 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 3.6958358E-5 44.0 2 GACACGA 25 3.6958358E-5 44.0 1 CGGATAT 30 1.083877E-4 36.666664 18 GGATATC 30 1.083877E-4 36.666664 19 GGCAACG 35 2.6843656E-4 31.428572 13 CTCTCGG 35 2.6843656E-4 31.428572 8 ACTCTCG 35 2.6843656E-4 31.428572 7 CACGACT 35 2.6843656E-4 31.428572 3 GCAACGG 35 2.6843656E-4 31.428572 14 TCTCGGC 35 2.6843656E-4 31.428572 9 CTCGGCA 35 2.6843656E-4 31.428572 10 ACGACTC 35 2.6843656E-4 31.428572 4 CGGCAAC 35 2.6843656E-4 31.428572 12 AACGGAT 35 2.6843656E-4 31.428572 16 GACTCTC 35 2.6843656E-4 31.428572 6 ACGGATA 35 2.6843656E-4 31.428572 17 CGACTCT 35 2.6843656E-4 31.428572 5 CAACGGA 35 2.6843656E-4 31.428572 15 TCGGCAA 40 5.87456E-4 27.500002 11 CTAACGA 50 6.483462E-5 26.4 1 >>END_MODULE Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769498 READS because READLEN < 1 Read 769498 spots for ERR9452012.sra Written 769498 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra Rejected 769480 READS because READLEN < 1 Read 769480 spots for ERR9452012.sra Written 769480 spots for ERR9452012.sra SRR ids: ['ERR9452012.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xdhk55wb ERR9452012.sra spots: 15389618 blocks: [[1, 769480], [769481, 1538960], [1538961, 2308440], [2308441, 3077920], [3077921, 3847400], [3847401, 4616880], [4616881, 5386360], [5386361, 6155840], [6155841, 6925320], [6925321, 7694800], [7694801, 8464280], [8464281, 9233760], [9233761, 10003240], [10003241, 10772720], [10772721, 11542200], [11542201, 12311680], [12311681, 13081160], [13081161, 13850640], [13850641, 14620120], [14620121, 15389618]] ERR9452012 file size 2142464 ERR9452012 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 ERR9452012 ERR9452012_1.fastq Input file: ERR9452012_1.fastq trimmed: ERR9452012-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 22:42:29 2024 >> started Fri Dec 6 22:42:37 2024 >> done (7.940s) 15389618 reads processed; of these: 2653678 (17.24%) short reads filtered out after trimming by size control 705 ( 0.00%) empty reads filtered out after trimming by size control 12735235 (82.75%) reads available; of these: 779313 ( 6.12%) trimmed reads available after processing 11955922 (93.88%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 779313 6.12% 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 11955922 93.88% 12735235 reads passed initial QC criterion=sequence-density sequence-density=92.23 sequence-density-rank=1 fanout-score=19.48 fanout-score-rank=1 prefix-density=92.72 prefix-fanout=19.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCATCCTCATC criterion=fanout-score sequence-density=92.23 sequence-density-rank=1 fanout-score=19.48 fanout-score-rank=1 prefix-density=92.72 prefix-fanout=19.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCATCCTCATC 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCATCCTCATC -o ERR9452012 - Input file: STDIN trimmed: ERR9452012-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCATCCTCATC -- 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 22:43:15 2024 >> started Fri Dec 6 22:43:31 2024 >> done (15.393s) 12461359 reads processed; of these: 13716 ( 0.11%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 12447636 (99.89%) reads available; of these: 11657335 (93.65%) trimmed reads available after processing 790301 ( 6.35%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 771818 6.20% 19 1075736 8.64% 20 1287918 10.35% 21 1384927 11.13% 22 1818708 14.61% 23 1036281 8.33% 24 1181167 9.49% 25 894051 7.18% 26 731949 5.88% 27 549256 4.41% 28 444611 3.57% 29 372181 2.99% 30 240476 1.93% 31 156804 1.26% 32 131699 1.06% 33 94935 0.76% 34 64223 0.52% 35 61025 0.49% 36 31545 0.25% 37 25006 0.20% 38 15774 0.13% 39 12720 0.10% 40 9242 0.07% 41 8423 0.07% 42 4091 0.03% 43 2584 0.02% 44 1839 0.01% 45 1569 0.01% 46 1047 0.01% 47 1141 0.01% 48 0 0.00% 49 0 0.00% 50 34890 0.28% criterion=sequence-density sequence-density=1.15 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=10 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=22 fanout-score=12.47 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=1.0 sequence=TAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATC Started job on | Dec 06 22:43:50 Started mapping on | Dec 06 22:43:50 Finished on | Dec 06 22:44:45 Mapping speed, Million of reads per hour | 832.68 Number of input reads | 12721512 Average input read length | 23 UNIQUE READS: Uniquely mapped reads number | 1091933 Uniquely mapped reads % | 8.58% Average mapped length | 23.25 Number of splices: Total | 48963 Number of splices: Annotated (sjdb) | 26010 Number of splices: GT/AG | 47715 Number of splices: GC/AG | 1030 Number of splices: AT/AC | 19 Number of splices: Non-canonical | 199 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.00% Deletion average length | 1.33 Insertion rate per base | 0.00% Insertion average length | 1.10 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5296624 % of reads mapped to multiple loci | 41.64% Number of reads mapped to too many loci | 5975345 % of reads mapped to too many loci | 46.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.63% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6332955 6332955 6332955 N_multimapping 5296624 5296624 5296624 N_noFeature 476027 536794 1018963 N_ambiguous 18290 5689 555 UnstrandedReadsAssigned:597616 PositiveStrandReadsAssigned:549450 NegativeStrandReadsAssigned:72415 Dataset is classified positive stranded MeadianReadLen=22 20thPercentileLength=20 echo kmer=19 ERR9452012 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: ERR9452012-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,721,512 reads, 1,270,044 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 925 rounds 52973 ERR9452012.ke.tsv 35125 ERR9452012.se.tsv 88098 total ==> ERR9452012.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 1.43551 1.0964 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.56449 1.19491 PNS24243 293 194 0 0 KQK14069 1603 1504 483.936 205.697 KQK14071 474 375 38.1982 65.1177 ==> ERR9452012.se.tsv <== BRADI_1g14170v3 675 BRADI_1g53295v3 4 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 0 ERR9452012 completed mapping pipeline successfully