Starting /dee2/code/volunteer_pipeline.sh ERR9452008 current disk space = 1548572700672 free memory = 1603524792 ERR9452008 SRAfilesize 2e10976ac1f0401528c9ad6eca39b590 ERR9452008.sra ERR9452008.sra file validated ERR9452008 is single end ERR9452008 is conventional basespace ERR9452008 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452008_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 36.05575 37.0 37.0 37.0 37.0 37.0 2 36.493 37.0 37.0 37.0 37.0 37.0 3 36.56175 37.0 37.0 37.0 37.0 37.0 4 36.5985 37.0 37.0 37.0 37.0 37.0 5 36.6425 37.0 37.0 37.0 37.0 37.0 6 36.56 37.0 37.0 37.0 37.0 37.0 7 36.56 37.0 37.0 37.0 37.0 37.0 8 36.6845 37.0 37.0 37.0 37.0 37.0 9 36.633 37.0 37.0 37.0 37.0 37.0 10 36.5885 37.0 37.0 37.0 37.0 37.0 11 36.6095 37.0 37.0 37.0 37.0 37.0 12 36.5935 37.0 37.0 37.0 37.0 37.0 13 36.545 37.0 37.0 37.0 37.0 37.0 14 36.5235 37.0 37.0 37.0 37.0 37.0 15 36.607 37.0 37.0 37.0 37.0 37.0 16 36.591 37.0 37.0 37.0 37.0 37.0 17 36.552 37.0 37.0 37.0 37.0 37.0 18 36.6975 37.0 37.0 37.0 37.0 37.0 19 36.655 37.0 37.0 37.0 37.0 37.0 20 36.5205 37.0 37.0 37.0 37.0 37.0 21 36.6345 37.0 37.0 37.0 37.0 37.0 22 36.5125 37.0 37.0 37.0 37.0 37.0 23 36.59 37.0 37.0 37.0 37.0 37.0 24 36.5275 37.0 37.0 37.0 37.0 37.0 25 36.597 37.0 37.0 37.0 37.0 37.0 26 36.6045 37.0 37.0 37.0 37.0 37.0 27 36.618 37.0 37.0 37.0 37.0 37.0 28 36.697 37.0 37.0 37.0 37.0 37.0 29 36.724 37.0 37.0 37.0 37.0 37.0 30 36.6595 37.0 37.0 37.0 37.0 37.0 31 36.6995 37.0 37.0 37.0 37.0 37.0 32 36.6635 37.0 37.0 37.0 37.0 37.0 33 36.597 37.0 37.0 37.0 37.0 37.0 34 36.6205 37.0 37.0 37.0 37.0 37.0 35 36.687 37.0 37.0 37.0 37.0 37.0 36 36.737 37.0 37.0 37.0 37.0 37.0 37 36.6825 37.0 37.0 37.0 37.0 37.0 38 36.701 37.0 37.0 37.0 37.0 37.0 39 36.658 37.0 37.0 37.0 37.0 37.0 40 36.742 37.0 37.0 37.0 37.0 37.0 41 36.6795 37.0 37.0 37.0 37.0 37.0 42 36.666 37.0 37.0 37.0 37.0 37.0 43 36.6755 37.0 37.0 37.0 37.0 37.0 44 36.632 37.0 37.0 37.0 37.0 37.0 45 36.5755 37.0 37.0 37.0 37.0 37.0 46 36.6575 37.0 37.0 37.0 37.0 37.0 47 36.674 37.0 37.0 37.0 37.0 37.0 48 36.645 37.0 37.0 37.0 37.0 37.0 49 36.6695 37.0 37.0 37.0 37.0 37.0 50 36.6565 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 3.0 25 4.0 26 4.0 27 6.0 28 9.0 29 10.0 30 5.0 31 20.0 32 27.0 33 43.0 34 56.0 35 124.0 36 1195.0 37 2494.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 19.293820933165197 27.28877679697352 25.498108448928118 27.919293820933166 2 23.400000000000002 31.225 24.275 21.099999999999998 3 28.232058014503625 29.957489372343087 18.579644911227806 23.23080770192548 4 29.675 36.3 16.375 17.65 5 24.4 28.925 20.025000000000002 26.650000000000002 6 27.900000000000002 22.575 27.950000000000003 21.575 7 28.299999999999997 31.1 22.25 18.35 8 21.4 27.500000000000004 28.175 22.925 9 22.45 27.750000000000004 27.6 22.2 10 33.475 23.05 21.125 22.35 11 25.124999999999996 26.125 29.599999999999998 19.15 12 24.125 26.200000000000003 25.624999999999996 24.05 13 26.8 23.474999999999998 20.225 29.5 14 29.975 32.15 21.525 16.35 15 24.6 32.275 22.975 20.150000000000002 16 21.5 30.25 28.95 19.3 17 24.55 29.799999999999997 30.775000000000002 14.875 18 27.500000000000004 24.9 26.825 20.775 19 34.25 28.375 21.525 15.85 20 27.800000000000004 31.474999999999998 25.825 14.899999999999999 21 23.325000000000003 39.875 19.400000000000002 17.4 22 25.924999999999997 35.0 20.875 18.2 23 31.125000000000004 36.0 18.375 14.499999999999998 24 29.349999999999998 34.449999999999996 20.275000000000002 15.925 25 29.5 37.4 15.125 17.974999999999998 26 36.625 27.0 16.525000000000002 19.85 27 30.925000000000004 39.65 11.65 17.775 28 34.525 32.125 16.5 16.85 29 34.150000000000006 33.925 9.325 22.6 30 37.974999999999994 38.875 7.575 15.575 31 41.05 35.25 7.5 16.2 32 34.175 41.075 7.225 17.525 33 29.875 42.6 7.175 20.349999999999998 34 37.1 33.074999999999996 7.6499999999999995 22.175 35 28.325 40.425 6.425 24.825 36 31.724999999999998 37.325 6.325 24.625 37 24.3 33.425 7.75 34.525 38 22.45 39.65 9.0 28.9 39 23.799999999999997 26.0 13.8 36.4 40 21.9 32.550000000000004 14.975 30.575000000000003 41 20.375 24.725 18.224999999999998 36.675000000000004 42 26.424999999999997 24.6 17.45 31.525 43 20.75 27.224999999999998 25.6 26.424999999999997 44 19.825 25.474999999999998 19.3 35.4 45 16.125 28.225 25.474999999999998 30.175 46 20.5 27.85 19.975 31.674999999999997 47 14.975 29.299999999999997 19.5 36.225 48 12.25 31.924999999999997 22.225 33.6 49 12.775 25.8 19.3 42.125 50 12.525 24.224999999999998 26.25 37.0 >>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 0.5 14 1.0 15 0.5 16 0.0 17 0.5 18 1.0 19 0.5 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 1.5 30 3.0 31 2.0 32 1.0 33 3.0 34 5.0 35 6.5 36 8.0 37 29.5 38 51.0 39 82.0 40 113.0 41 155.5 42 198.0 43 230.5 44 263.0 45 388.0 46 513.0 47 624.5 48 736.0 49 580.5 50 425.0 51 453.5 52 482.0 53 480.0 54 478.0 55 393.0 56 308.0 57 265.5 58 223.0 59 155.5 60 88.0 61 63.0 62 38.0 63 29.0 64 20.0 65 17.5 66 15.0 67 19.0 68 23.0 69 13.5 70 4.0 71 2.5 72 1.0 73 1.0 74 1.0 75 0.5 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 0.8750000000000001 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 63.625 #Duplication Level Percentage of deduplicated Percentage of total 1 82.55402750491159 52.525 2 10.25540275049116 13.05 3 3.3398821218074657 6.375 4 1.0609037328094302 2.7 5 0.5893909626719057 1.875 6 0.4322200392927309 1.6500000000000001 7 0.2357563850687623 1.05 8 0.0 0.0 9 0.15717092337917485 0.8999999999999999 >10 1.2966601178781925 14.424999999999999 >50 0.03929273084479371 1.35 >100 0.03929273084479371 4.1000000000000005 >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 164 4.1000000000000005 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATC 54 1.35 TruSeq Adapter, Index 1 (100% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 44 1.0999999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 39 0.975 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATC 24 0.6 TruSeq Adapter, Index 1 (100% over 36bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 19 0.475 No Hit TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 16 0.4 No Hit CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 14 0.35000000000000003 No Hit CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 13 0.325 No Hit ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT 11 0.27499999999999997 TruSeq Adapter, Index 1 (100% over 35bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TTCATGGACGTTGATAAGATCCTTCCAGATCGGAAGAGCACACGTCTGAA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCTGA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT 7 0.17500000000000002 TruSeq Adapter, Index 1 (100% over 35bp) GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT 6 0.15 TruSeq Adapter, Index 1 (100% over 35bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 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) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACAC 5 0.125 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATAAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CGACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CGGATTATGACTGAACGCCTCTAAGTCAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) AAGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TCCGACTTTGTGAAATGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) ACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) ATATTGGGTAGGTTGTGGTATTTCATTGCAGATCGGAAGAGCACACGTCT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GCGTCTGTAGTCCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGGATGTTTTCATTAATCAAGAACAGATCGGAAGAGCACACGTCTGAA 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 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.075 0.0 0.0 0.0 0.0 11 0.1 0.0 0.0 0.0 0.0 12 0.225 0.0 0.0 0.0 0.0 13 0.575 0.0 0.0 0.0 0.0 14 3.125 0.0 0.0 0.0 0.0 15 4.675 0.0 0.0 0.0 0.0 16 6.1 0.0 0.0 0.0 0.0 17 8.6 0.0 0.0 0.0 0.0 18 11.05 0.0 0.0 0.0 0.0 19 14.5 0.0 0.0 0.0 0.0 20 19.6 0.0 0.0 0.0 0.0 21 26.325 0.0 0.0 0.0 0.0 22 34.025 0.0 0.0 0.0 0.0 23 43.55 0.0 0.0 0.0 0.0 24 50.3 0.0 0.0 0.0 0.0 25 63.25 0.0 0.0 0.0 0.0 26 69.55 0.0 0.0 0.0 0.0 27 74.825 0.0 0.0 0.0 0.0 28 79.925 0.0 0.0 0.0 0.0 29 83.475 0.0 0.0 0.0 0.0 30 87.75 0.0 0.0 0.0 0.0 31 90.525 0.0 0.0 0.0 0.0 32 92.375 0.0 0.0 0.0 0.0 33 94.3 0.0 0.0 0.0 0.0 34 95.7 0.0 0.0 0.0 0.0 35 96.475 0.0 0.0 0.0 0.0 36 97.45 0.0 0.0 0.0 0.0 37 97.625 0.0 0.0 0.0 0.0 38 98.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTAACGA 45 0.0011696975 24.444447 1 TAACGAA 50 0.0021617375 22.0 2 GAACGAA 60 0.0062267617 18.333332 6 AACTCCA 115 5.4313954E-5 15.304348 44 GAACTCC 160 5.826223E-5 12.375001 44 CTGAACT 255 1.8105311E-7 11.215687 44 TGAACTC 190 2.9137218E-4 10.421053 43 TCTGAAC 290 9.684536E-7 9.862069 43 GTCTGAA 310 2.2952736E-6 9.225806 42 CGTCTGA 330 5.1310744E-6 8.666667 41 ACGTCTG 350 1.0893966E-5 8.171429 40 CACGTCT 350 1.0893966E-5 8.171429 39 ACACGTC 365 1.85881E-5 7.835616 38 CACACGT 375 2.6191878E-5 7.6266665 37 AGCACAC 380 3.097378E-5 7.5263157 35 GCACACG 380 3.097378E-5 7.5263157 36 GAGCACA 385 3.6539932E-5 7.428571 34 AAGAGCA 395 5.049637E-5 7.2405066 32 GATCGGA 395 5.049637E-5 7.2405066 26 GAAGAGC 395 5.049637E-5 7.2405066 31 >>END_MODULE Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741052 READS because READLEN < 1 Read 741052 spots for ERR9452008.sra Written 741052 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra Rejected 741033 READS because READLEN < 1 Read 741033 spots for ERR9452008.sra Written 741033 spots for ERR9452008.sra SRR ids: ['ERR9452008.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_op2n2p2a ERR9452008.sra spots: 14820679 blocks: [[1, 741033], [741034, 1482066], [1482067, 2223099], [2223100, 2964132], [2964133, 3705165], [3705166, 4446198], [4446199, 5187231], [5187232, 5928264], [5928265, 6669297], [6669298, 7410330], [7410331, 8151363], [8151364, 8892396], [8892397, 9633429], [9633430, 10374462], [10374463, 11115495], [11115496, 11856528], [11856529, 12597561], [12597562, 13338594], [13338595, 14079627], [14079628, 14820679]] ERR9452008 file size 2062457 ERR9452008 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 ERR9452008 ERR9452008_1.fastq Input file: ERR9452008_1.fastq trimmed: ERR9452008-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 22:38:24 2024 >> started Fri Dec 6 22:38:32 2024 >> done (7.973s) 14820679 reads processed; of these: 1558890 (10.52%) short reads filtered out after trimming by size control 896 ( 0.01%) empty reads filtered out after trimming by size control 13260893 (89.48%) reads available; of these: 491948 ( 3.71%) trimmed reads available after processing 12768945 (96.29%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 491948 3.71% 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 12768945 96.29% 13260893 reads passed initial QC criterion=sequence-density sequence-density=94.03 sequence-density-rank=1 fanout-score=29.00 fanout-score-rank=1 prefix-density=94.71 prefix-fanout=28.8 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCATTCCATCTCGTATGCCG criterion=fanout-score sequence-density=94.03 sequence-density-rank=1 fanout-score=29.00 fanout-score-rank=1 prefix-density=94.71 prefix-fanout=28.8 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCATTCCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCATTCCATCTCGTATGCCG -o ERR9452008 - Input file: STDIN trimmed: ERR9452008-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCATTCCATCTCGTATGCCG -- 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 22:38:48 2024 >> started Fri Dec 6 22:39:02 2024 >> done (14.343s) 12981716 reads processed; of these: 11230 ( 0.09%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 12970477 (99.91%) reads available; of these: 12423858 (95.79%) trimmed reads available after processing 546619 ( 4.21%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 490152 3.78% 19 733623 5.66% 20 974825 7.52% 21 1141342 8.80% 22 1437494 11.08% 23 1007175 7.77% 24 1915643 14.77% 25 973701 7.51% 26 788359 6.08% 27 635978 4.90% 28 559096 4.31% 29 565690 4.36% 30 389016 3.00% 31 287195 2.21% 32 306596 2.36% 33 205082 1.58% 34 137293 1.06% 35 125988 0.97% 36 63999 0.49% 37 45303 0.35% 38 27382 0.21% 39 21328 0.16% 40 15365 0.12% 41 29019 0.22% 42 8065 0.06% 43 5084 0.04% 44 3772 0.03% 45 2758 0.02% 46 1830 0.01% 47 1987 0.02% 48 0 0.00% 49 0 0.00% 50 70337 0.54% criterion=sequence-density sequence-density=2.39 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=8 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=22.37 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=1.0 sequence=GTGAAGTGTTTGGGGGAACTCC Started job on | Dec 06 22:39:21 Started mapping on | Dec 06 22:39:21 Finished on | Dec 06 22:40:11 Mapping speed, Million of reads per hour | 953.98 Number of input reads | 13249654 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 1963836 Uniquely mapped reads % | 14.82% Average mapped length | 24.05 Number of splices: Total | 42251 Number of splices: Annotated (sjdb) | 23551 Number of splices: GT/AG | 41286 Number of splices: GC/AG | 672 Number of splices: AT/AC | 24 Number of splices: Non-canonical | 269 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4400284 % of reads mapped to multiple loci | 33.21% Number of reads mapped to too many loci | 6439657 % of reads mapped to too many loci | 48.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.89% % of reads unmapped: other | 0.47% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6885534 6885534 6885534 N_multimapping 4400284 4400284 4400284 N_noFeature 1289085 1390568 1848577 N_ambiguous 22798 8643 612 UnstrandedReadsAssigned:651953 PositiveStrandReadsAssigned:564625 NegativeStrandReadsAssigned:114647 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 ERR9452008 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: ERR9452008-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,249,654 reads, 2,415,268 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,034 rounds 52973 ERR9452008.ke.tsv 35125 ERR9452008.se.tsv 88098 total ==> ERR9452008.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2.82193 0.699069 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 7.17807 2.37051 PNS24243 293 194 0 0 KQK14069 1603 1504 380.204 114.54 KQK14071 474 375 6.07741 7.34302 ==> ERR9452008.se.tsv <== BRADI_1g14170v3 506 BRADI_1g53295v3 7 BRADI_1g59795v3 5 BRADI_1g07683v3 1 BRADI_1g00485v3 0 BRADI_1g20270v3 17 BRADI_1g74790v3 23 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR9452008 completed mapping pipeline successfully