Starting /dee2/code/volunteer_pipeline.sh ERR9452010 current disk space = 1548580999168 free memory = 1594001436 ERR9452010 SRAfilesize e68dba5923b5e62310623cde18028f57 ERR9452010.sra ERR9452010.sra file validated ERR9452010 is single end ERR9452010 is conventional basespace ERR9452010 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452010_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 36.22925 37.0 37.0 37.0 37.0 37.0 2 36.604 37.0 37.0 37.0 37.0 37.0 3 36.604 37.0 37.0 37.0 37.0 37.0 4 36.6335 37.0 37.0 37.0 37.0 37.0 5 36.644 37.0 37.0 37.0 37.0 37.0 6 36.5705 37.0 37.0 37.0 37.0 37.0 7 36.6825 37.0 37.0 37.0 37.0 37.0 8 36.6215 37.0 37.0 37.0 37.0 37.0 9 36.673 37.0 37.0 37.0 37.0 37.0 10 36.606 37.0 37.0 37.0 37.0 37.0 11 36.6005 37.0 37.0 37.0 37.0 37.0 12 36.6105 37.0 37.0 37.0 37.0 37.0 13 36.6175 37.0 37.0 37.0 37.0 37.0 14 36.604 37.0 37.0 37.0 37.0 37.0 15 36.617 37.0 37.0 37.0 37.0 37.0 16 36.6025 37.0 37.0 37.0 37.0 37.0 17 36.6165 37.0 37.0 37.0 37.0 37.0 18 36.5475 37.0 37.0 37.0 37.0 37.0 19 36.6775 37.0 37.0 37.0 37.0 37.0 20 36.674 37.0 37.0 37.0 37.0 37.0 21 36.7275 37.0 37.0 37.0 37.0 37.0 22 36.726 37.0 37.0 37.0 37.0 37.0 23 36.674 37.0 37.0 37.0 37.0 37.0 24 36.719 37.0 37.0 37.0 37.0 37.0 25 36.727 37.0 37.0 37.0 37.0 37.0 26 36.664 37.0 37.0 37.0 37.0 37.0 27 36.6995 37.0 37.0 37.0 37.0 37.0 28 36.7665 37.0 37.0 37.0 37.0 37.0 29 36.751 37.0 37.0 37.0 37.0 37.0 30 36.7555 37.0 37.0 37.0 37.0 37.0 31 36.726 37.0 37.0 37.0 37.0 37.0 32 36.7925 37.0 37.0 37.0 37.0 37.0 33 36.762 37.0 37.0 37.0 37.0 37.0 34 36.7485 37.0 37.0 37.0 37.0 37.0 35 36.7185 37.0 37.0 37.0 37.0 37.0 36 36.6745 37.0 37.0 37.0 37.0 37.0 37 36.7155 37.0 37.0 37.0 37.0 37.0 38 36.779 37.0 37.0 37.0 37.0 37.0 39 36.6965 37.0 37.0 37.0 37.0 37.0 40 36.6715 37.0 37.0 37.0 37.0 37.0 41 36.6495 37.0 37.0 37.0 37.0 37.0 42 36.694 37.0 37.0 37.0 37.0 37.0 43 36.67 37.0 37.0 37.0 37.0 37.0 44 36.7445 37.0 37.0 37.0 37.0 37.0 45 36.6955 37.0 37.0 37.0 37.0 37.0 46 36.6785 37.0 37.0 37.0 37.0 37.0 47 36.6605 37.0 37.0 37.0 37.0 37.0 48 36.734 37.0 37.0 37.0 37.0 37.0 49 36.6525 37.0 37.0 37.0 37.0 37.0 50 36.7155 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 1.0 26 4.0 27 3.0 28 7.0 29 14.0 30 19.0 31 15.0 32 23.0 33 33.0 34 48.0 35 94.0 36 960.0 37 2777.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 21.753328309469982 31.926651595076617 22.682743029389602 23.637277066063803 2 33.15 25.95 22.175 18.725 3 37.09354677338669 27.01350675337669 15.307653826913455 20.58529264632316 4 36.65 30.45 17.075000000000003 15.825 5 21.3 29.075 18.2 31.424999999999997 6 23.799999999999997 20.4 35.6 20.200000000000003 7 29.275000000000002 34.449999999999996 19.8 16.475 8 19.650000000000002 24.325 35.775 20.25 9 21.625 35.15 21.95 21.275 10 43.025000000000006 20.8 18.475 17.7 11 20.275000000000002 24.675 24.75 30.3 12 22.875 22.875 33.75 20.5 13 21.575 19.900000000000002 19.575 38.95 14 26.924999999999997 40.5 18.475 14.099999999999998 15 32.775 30.025000000000002 21.2 16.0 16 20.349999999999998 35.125 25.974999999999998 18.55 17 20.974999999999998 30.85 34.849999999999994 13.325000000000001 18 27.375 24.65 23.474999999999998 24.5 19 39.2 29.575000000000003 17.724999999999998 13.5 20 33.050000000000004 31.0 24.05 11.899999999999999 21 23.799999999999997 44.4 13.750000000000002 18.05 22 27.6 41.55 13.750000000000002 17.1 23 43.025000000000006 32.0 14.149999999999999 10.825 24 28.625 43.35 13.675 14.35 25 35.475 40.300000000000004 11.200000000000001 13.025 26 39.5 23.724999999999998 12.0 24.775 27 27.975 49.65 6.425 15.950000000000001 28 35.3 29.375 12.425 22.900000000000002 29 29.575000000000003 40.400000000000006 4.8500000000000005 25.174999999999997 30 31.574999999999996 40.375 3.55 24.5 31 44.775 31.874999999999996 3.95 19.400000000000002 32 27.1 39.975 14.674999999999999 18.25 33 21.775 38.224999999999994 5.5 34.5 34 34.5 24.3 16.525000000000002 24.675 35 28.299999999999997 33.800000000000004 11.924999999999999 25.974999999999998 36 23.5 38.05 8.4 30.049999999999997 37 16.55 34.35 13.700000000000001 35.4 38 20.65 30.975 13.25 35.125 39 17.275 22.375 24.725 35.625 40 17.474999999999998 29.775000000000002 18.875 33.875 41 14.575 17.375 20.325 47.725 42 21.45 29.625 22.05 26.875 43 25.6 21.65 27.150000000000002 25.6 44 15.925 21.975 25.3 36.8 45 9.975000000000001 30.349999999999998 23.9 35.775 46 21.325 34.025 15.0 29.65 47 9.375 25.724999999999998 20.75 44.15 48 8.450000000000001 27.150000000000002 17.525 46.875 49 10.525 35.85 11.525 42.1 50 10.875 33.650000000000006 20.4 35.075 >>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 0.5 22 1.0 23 0.5 24 0.0 25 0.0 26 0.0 27 1.0 28 2.0 29 1.0 30 0.0 31 1.5 32 3.0 33 3.0 34 3.0 35 7.0 36 11.0 37 19.5 38 28.0 39 39.0 40 50.0 41 75.5 42 101.0 43 146.0 44 191.0 45 277.5 46 364.0 47 605.5 48 847.0 49 615.5 50 384.0 51 564.5 52 745.0 53 704.0 54 663.0 55 483.0 56 303.0 57 237.0 58 171.0 59 115.5 60 60.0 61 53.0 62 46.0 63 31.5 64 17.0 65 11.0 66 5.0 67 5.0 68 5.0 69 2.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.475 2 0.0 3 0.05 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 55.325 #Duplication Level Percentage of deduplicated Percentage of total 1 84.31992769995482 46.650000000000006 2 9.715318572074109 10.75 3 1.8978761861726163 3.15 4 0.7681879801174876 1.7000000000000002 5 0.6778129236330772 1.875 6 0.587437867148667 1.95 7 0.27112516945323095 1.05 8 0.09037505648441031 0.4 9 0.13556258472661548 0.675 >10 1.3104383190239492 12.55 >50 0.09037505648441031 3.25 >100 0.13556258472661548 16.0 >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 AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA 286 7.1499999999999995 TruSeq Adapter, Index 2 (97% over 36bp) CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 211 5.2749999999999995 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA 143 3.5749999999999997 TruSeq Adapter, Index 2 (97% over 36bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 78 1.95 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 52 1.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 36 0.8999999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 35 0.8750000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 31 0.775 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 30 0.75 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGGGTGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 27 0.675 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA 16 0.4 TruSeq Adapter, Index 7 (100% over 35bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAG 12 0.3 TruSeq Adapter, Index 2 (97% over 36bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GCGTCTGTAGTCCAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGGATGTAGCTCAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GCGTCTGTAGTCCAACGGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA 7 0.17500000000000002 TruSeq Adapter, Index 7 (100% over 35bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CGACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 6 0.15 No Hit ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) 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) AGCGGAGTAGAGCAGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA 5 0.125 TruSeq Adapter, Index 7 (100% over 35bp) ACTGGTTGGATCATGCTTCTAAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAGG 5 0.125 TruSeq Adapter, Index 2 (97% over 36bp) AAATCATGTGGGCTCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GGCGGATGTAGCCAAGTGGAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCTCGTGTTGCATTCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TCGTGACCCTGACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCA 5 0.125 TruSeq Adapter, Index 7 (100% over 35bp) TCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) >>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 0.025 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10 0.15 0.0 0.0 0.0 0.0 11 0.525 0.0 0.0 0.0 0.0 12 0.925 0.0 0.0 0.0 0.0 13 1.975 0.0 0.0 0.0 0.0 14 14.625 0.0 0.0 0.0 0.0 15 17.35 0.0 0.0 0.0 0.0 16 20.075 0.0 0.0 0.0 0.0 17 28.275 0.0 0.0 0.0 0.0 18 32.775 0.0 0.0 0.0 0.0 19 37.35 0.0 0.0 0.0 0.0 20 44.525 0.0 0.0 0.0 0.0 21 51.6 0.0 0.0 0.0 0.0 22 60.1 0.0 0.0 0.0 0.0 23 69.85 0.0 0.0 0.0 0.0 24 74.575 0.0 0.0 0.0 0.0 25 85.9 0.0 0.0 0.0 0.0 26 89.025 0.0 0.0 0.0 0.0 27 91.45 0.0 0.0 0.0 0.0 28 93.2 0.0 0.0 0.0 0.0 29 94.475 0.0 0.0 0.0 0.0 30 95.7 0.0 0.0 0.0 0.0 31 96.425 0.0 0.0 0.0 0.0 32 97.05 0.0 0.0 0.0 0.0 33 97.525 0.0 0.0 0.0 0.0 34 97.9 0.0 0.0 0.0 0.0 35 98.025 0.0 0.0 0.0 0.0 36 98.15 0.0 0.0 0.0 0.0 37 98.25 0.0 0.0 0.0 0.0 38 98.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGCTC 20 6.952051E-4 44.000004 7 CTAACGA 35 1.02281774E-7 44.0 1 TAGCTCA 55 3.8198777E-11 40.0 8 AGCTCAG 50 7.712515E-10 39.6 9 GCTCAGA 45 1.506669E-8 39.111115 10 CTATAGC 35 5.6380304E-6 37.714287 5 AGGGCTA 35 5.6380304E-6 37.714287 1 GCTATAG 35 5.6380304E-6 37.714287 4 ATAGCTC 35 5.6380304E-6 37.714287 7 GGCTATA 35 5.6380304E-6 37.714287 3 TATAGCT 35 5.6380304E-6 37.714287 6 GGGCTAT 35 5.6380304E-6 37.714287 2 TGTAGCT 25 0.002084305 35.2 6 TAACGAA 45 7.364706E-7 34.222225 2 TCACCAA 50 1.6800313E-6 30.8 44 CTCAGAT 60 1.9002982E-7 29.333332 11 GTCACCA 55 3.5363937E-6 28.0 43 AGTCACC 60 6.9657926E-6 25.666666 42 TCAGATC 65 1.2976836E-5 23.692308 12 AACGATT 75 3.931468E-5 20.533333 11 >>END_MODULE Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891866 READS because READLEN < 1 Read 891866 spots for ERR9452010.sra Written 891866 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra Rejected 891862 READS because READLEN < 1 Read 891862 spots for ERR9452010.sra Written 891862 spots for ERR9452010.sra SRR ids: ['ERR9452010.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cc54dj81 ERR9452010.sra spots: 17837244 blocks: [[1, 891862], [891863, 1783724], [1783725, 2675586], [2675587, 3567448], [3567449, 4459310], [4459311, 5351172], [5351173, 6243034], [6243035, 7134896], [7134897, 8026758], [8026759, 8918620], [8918621, 9810482], [9810483, 10702344], [10702345, 11594206], [11594207, 12486068], [12486069, 13377930], [13377931, 14269792], [14269793, 15161654], [15161655, 16053516], [16053517, 16945378], [16945379, 17837244]] ERR9452010 file size 2486662 ERR9452010 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 ERR9452010 ERR9452010_1.fastq Input file: ERR9452010_1.fastq trimmed: ERR9452010-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 22:39:05 2024 >> started Fri Dec 6 22:39:11 2024 >> done (5.865s) 17837244 reads processed; of these: 5817460 (32.61%) short reads filtered out after trimming by size control 1733 ( 0.01%) empty reads filtered out after trimming by size control 12018051 (67.38%) reads available; of these: 869551 ( 7.24%) trimmed reads available after processing 11148500 (92.76%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 869551 7.24% 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 11148500 92.76% 12018051 reads passed initial QC criterion=sequence-density sequence-density=91.40 sequence-density-rank=1 fanout-score=23.43 fanout-score-rank=1 prefix-density=91.65 prefix-fanout=23.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAGGAGCATCTCGTATGCCG criterion=fanout-score sequence-density=91.40 sequence-density-rank=1 fanout-score=23.43 fanout-score-rank=1 prefix-density=91.65 prefix-fanout=23.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAGGAGCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAGGAGCATCTCGTATGCCG -o ERR9452010 - Input file: STDIN trimmed: ERR9452010-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAGGAGCATCTCGTATGCCG -- 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 22:39:29 2024 >> started Fri Dec 6 22:39:45 2024 >> done (15.495s) 11756789 reads processed; of these: 14368 ( 0.12%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 11742401 (99.88%) reads available; of these: 10857115 (92.46%) trimmed reads available after processing 885286 ( 7.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 856611 7.30% 19 1172006 9.98% 20 1358812 11.57% 21 1449395 12.34% 22 1626103 13.85% 23 912241 7.77% 24 2037670 17.35% 25 639290 5.44% 26 443125 3.77% 27 302855 2.58% 28 234233 1.99% 29 219873 1.87% 30 122492 1.04% 31 77668 0.66% 32 86370 0.74% 33 54123 0.46% 34 30586 0.26% 35 30510 0.26% 36 13437 0.11% 37 8343 0.07% 38 5071 0.04% 39 4099 0.03% 40 2765 0.02% 41 7145 0.06% 42 1380 0.01% 43 825 0.01% 44 646 0.01% 45 571 0.00% 46 416 0.00% 47 625 0.01% 48 0 0.00% 49 0 0.00% 50 43115 0.37% criterion=sequence-density sequence-density=1.34 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=10 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=13.66 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=1.0 sequence=GTGAAGTGTTTGGGGGAACTCC Started job on | Dec 06 22:40:01 Started mapping on | Dec 06 22:40:01 Finished on | Dec 06 22:40:39 Mapping speed, Million of reads per hour | 1137.19 Number of input reads | 12003663 Average input read length | 23 UNIQUE READS: Uniquely mapped reads number | 2451074 Uniquely mapped reads % | 20.42% Average mapped length | 22.93 Number of splices: Total | 45428 Number of splices: Annotated (sjdb) | 17382 Number of splices: GT/AG | 44693 Number of splices: GC/AG | 646 Number of splices: AT/AC | 4 Number of splices: Non-canonical | 85 Mismatch rate per base, % | 0.15% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4649596 % of reads mapped to multiple loci | 38.73% Number of reads mapped to too many loci | 4474235 % of reads mapped to too many loci | 37.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.87% % of reads unmapped: other | 0.70% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4902993 4902993 4902993 N_multimapping 4649596 4649596 4649596 N_noFeature 1714601 1849755 2301784 N_ambiguous 25407 10380 1184 UnstrandedReadsAssigned:711066 PositiveStrandReadsAssigned:590939 NegativeStrandReadsAssigned:148106 Dataset is classified unstranded MeadianReadLen=22 20thPercentileLength=20 echo kmer=19 ERR9452010 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: ERR9452010-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,003,663 reads, 2,177,681 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,061 rounds 52973 ERR9452010.ke.tsv 35125 ERR9452010.se.tsv 88098 total ==> ERR9452010.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 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 244.978 67.3942 KQK14071 474 375 16.1305 17.7975 ==> ERR9452010.se.tsv <== BRADI_1g14170v3 351 BRADI_1g53295v3 2 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 34 BRADI_1g09890v3 1 BRADI_1g77505v3 2 BRADI_1g48960v3 0 ERR9452010 completed mapping pipeline successfully