Starting /dee2/code/volunteer_pipeline.sh SRR6941572 current disk space = 1551377711104 free memory = 1606576556 SRR6941572 SRAfilesize e9f1a6b8cf974cac1db73389d5530bad SRR6941572.sra SRR6941572.sra file validated SRR6941572 is single end SRR6941572 is conventional basespace SRR6941572 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941572_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.23275 34.0 33.0 34.0 32.0 34.0 2 33.3645 34.0 33.0 34.0 33.0 34.0 3 33.089 34.0 33.0 34.0 31.0 34.0 4 33.2645 34.0 33.0 34.0 32.0 34.0 5 33.233 34.0 33.0 34.0 33.0 34.0 6 37.0845 38.0 37.0 38.0 36.0 38.0 7 37.37575 38.0 38.0 38.0 37.0 38.0 8 37.58775 38.0 38.0 38.0 37.0 38.0 9 37.60125 38.0 38.0 38.0 38.0 38.0 10-11 37.585499999999996 38.0 38.0 38.0 38.0 38.0 12-13 37.511125 38.0 38.0 38.0 37.0 38.0 14-15 37.56075 38.0 38.0 38.0 38.0 38.0 16-17 36.22 38.0 37.5 38.0 31.5 38.0 18-19 36.9715 38.0 38.0 38.0 33.5 38.0 20-21 36.16075 38.0 38.0 38.0 31.0 38.0 22-23 37.31575 38.0 38.0 38.0 36.5 38.0 24-25 37.522999999999996 38.0 38.0 38.0 38.0 38.0 26-27 37.48175 38.0 38.0 38.0 37.5 38.0 28-29 37.476625 38.0 38.0 38.0 37.5 38.0 30-31 37.389875 38.0 38.0 38.0 37.0 38.0 32-33 37.299625 38.0 38.0 38.0 37.0 38.0 34-35 37.29775 38.0 38.0 38.0 37.0 38.0 36-37 37.266375 38.0 38.0 38.0 37.0 38.0 38-39 37.21425 38.0 38.0 38.0 37.0 38.0 40-41 37.18675 38.0 38.0 38.0 37.0 38.0 42-43 37.158874999999995 38.0 38.0 38.0 37.0 38.0 44-45 37.27725 38.0 38.0 38.0 37.0 38.0 46-47 37.067125000000004 38.0 38.0 38.0 36.5 38.0 48-49 37.16875 38.0 38.0 38.0 37.0 38.0 50-51 37.007 38.0 38.0 38.0 36.0 38.0 52-53 37.04675 38.0 38.0 38.0 36.0 38.0 54-55 37.19 38.0 38.0 38.0 37.0 38.0 56-57 37.12375 38.0 38.0 38.0 36.5 38.0 58-59 37.346125 38.0 38.0 38.0 37.0 38.0 60-61 37.310375 38.0 38.0 38.0 37.0 38.0 62-63 37.163375 38.0 38.0 38.0 37.0 38.0 64-65 37.048249999999996 38.0 38.0 38.0 36.5 38.0 66-67 36.84825 38.0 38.0 38.0 35.5 38.0 68-69 37.130875 38.0 38.0 38.0 37.0 38.0 70-71 36.682500000000005 38.0 38.0 38.0 34.5 38.0 72-73 36.465375 38.0 37.5 38.0 34.0 38.0 74-75 36.221000000000004 38.0 37.0 38.0 33.0 38.0 76-77 36.238125 38.0 37.0 38.0 33.0 38.0 78-79 36.542125 38.0 38.0 38.0 34.5 38.0 80-81 36.8065 38.0 38.0 38.0 35.5 38.0 82-83 36.798500000000004 38.0 38.0 38.0 36.0 38.0 84-85 36.726625 38.0 38.0 38.0 35.5 38.0 86-87 36.586 38.0 38.0 38.0 35.0 38.0 88-89 36.668375 38.0 38.0 38.0 35.5 38.0 90-91 36.6355 38.0 38.0 38.0 35.0 38.0 92-93 36.581875 38.0 38.0 38.0 35.0 38.0 94-95 36.316375 38.0 38.0 38.0 34.5 38.0 96-97 34.951375 38.0 37.5 38.0 30.0 38.0 98-99 32.768875 38.0 35.5 38.0 13.0 38.0 100-101 29.8985 38.0 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.0 18 0.0 19 0.0 20 0.0 21 2.0 22 0.0 23 4.0 24 2.0 25 3.0 26 11.0 27 16.0 28 22.0 29 21.0 30 35.0 31 38.0 32 69.0 33 92.0 34 149.0 35 351.0 36 715.0 37 2467.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.725 23.35 11.35 22.575 2 35.467733866933465 28.989494747373683 18.98449224612306 16.558279139569784 3 32.6 16.675 27.675 23.05 4 27.025 32.625 13.775 26.575 5 43.6 16.6 24.925 14.875 6 21.675 34.025 26.674999999999997 17.625 7 47.4 19.400000000000002 22.625 10.575 8 24.3 12.75 49.0 13.950000000000001 9 16.3 46.949999999999996 23.325000000000003 13.425 10-11 39.2625 26.337500000000002 19.112499999999997 15.287500000000001 12-13 15.6125 12.475 27.1 44.8125 14-15 19.2 42.425000000000004 26.85 11.525 16-17 28.3875 14.637500000000001 44.95 12.025 18-19 45.85 19.125 23.05 11.975 20-21 12.737499999999999 25.7375 41.0875 20.4375 22-23 32.1 30.837500000000002 22.900000000000002 14.1625 24-25 32.2125 32.4625 19.275000000000002 16.05 26-27 37.0375 25.174999999999997 19.925 17.8625 28-29 17.45 35.8 19.400000000000002 27.35 30-31 22.7 11.4875 42.3875 23.425 32-33 28.549999999999997 13.0 29.7375 28.712500000000002 34-35 35.7375 20.7375 28.9375 14.5875 36-37 41.475 21.637500000000003 27.3125 9.575 38-39 22.85 22.575 36.412499999999994 18.1625 40-41 20.1625 14.325 28.875 36.6375 42-43 32.9125 21.712500000000002 22.75 22.625 44-45 55.2875 11.125 15.875 17.712500000000002 46-47 34.325 24.337500000000002 16.9125 24.425 48-49 24.8 22.375 18.6 34.225 50-51 27.0625 26.575 7.7125 38.65 52-53 30.775000000000002 44.9625 5.1625 19.1 54-55 21.837500000000002 31.7875 18.6125 27.762500000000003 56-57 10.8 34.425 12.425 42.35 58-59 13.6375 29.975 17.3375 39.050000000000004 60-61 18.3 23.3625 25.937500000000004 32.4 62-63 13.9125 32.4125 25.837500000000002 27.8375 64-65 7.512499999999999 33.45 25.8625 33.175 66-67 12.675 25.2875 25.9625 36.075 68-69 17.75 26.437500000000004 27.325 28.487499999999997 70-71 16.825000000000003 31.112499999999997 36.725 15.3375 72-73 17.2875 22.1 39.725 20.8875 74-75 13.362499999999999 13.212499999999999 33.4875 39.9375 76-77 18.975 12.174999999999999 43.525000000000006 25.324999999999996 78-79 21.5375 10.2625 40.65 27.55 80-81 20.025000000000002 12.6 35.75 31.624999999999996 82-83 28.675 6.8875 36.625 27.8125 84-85 21.425 4.9625 36.0375 37.574999999999996 86-87 19.175 10.05 42.5875 28.1875 88-89 13.4125 26.85 38.95 20.7875 90-91 11.0875 29.762499999999996 36.199999999999996 22.95 92-93 19.6 34.8125 27.8125 17.775 94-95 13.212499999999999 51.1375 25.937500000000004 9.7125 96-97 11.75 68.86250000000001 15.15 4.237500000000001 98-99 6.0249999999999995 85.8875 5.5875 2.5 100-101 2.1125000000000003 91.85 3.7375 2.3 >>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 0.0 30 0.0 31 1.0 32 1.5 33 1.0 34 2.5 35 3.5 36 2.0 37 1.0 38 2.5 39 6.5 40 16.5 41 66.5 42 156.5 43 434.5 44 569.5 45 375.5 46 316.5 47 296.0 48 208.5 49 295.5 50 404.0 51 358.0 52 221.0 53 89.0 54 57.5 55 44.5 56 22.5 57 24.0 58 16.0 59 2.5 60 2.5 61 0.5 62 0.0 63 0.5 64 0.5 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 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 0.0 2 0.05 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 44.324999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 86.29441624365482 38.25 2 4.963338973491258 4.3999999999999995 3 2.3124647490129724 3.075 4 0.9588268471517203 1.7000000000000002 5 0.8460236886632826 1.875 6 0.8460236886632826 2.25 7 0.338409475465313 1.05 8 0.338409475465313 1.2 9 0.5076142131979695 2.025 >10 1.9176536943034406 18.675 >50 0.5076142131979695 14.7 >100 0.1692047377326565 10.8 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 192 4.8 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 128 3.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 112 2.8000000000000003 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 87 2.175 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 76 1.9 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 71 1.775 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 67 1.675 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 62 1.55 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 58 1.4500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 58 1.4500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 57 1.425 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 52 1.3 Illumina Small RNA Adapter 2 (100% over 21bp) CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 44 1.0999999999999999 RNA PCR Primer, Index 1 (100% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 43 1.075 Illumina Small RNA Adapter 2 (100% over 21bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 42 1.05 RNA PCR Primer, Index 1 (100% over 29bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 42 1.05 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 41 1.0250000000000001 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 38 0.95 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 35 0.8750000000000001 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 34 0.8500000000000001 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 34 0.8500000000000001 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 26bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 26 0.65 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 25 0.625 No Hit GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 23 0.575 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 22 0.5499999999999999 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 28bp) GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 16 0.4 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 16 0.4 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 22bp) TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 12 0.3 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 12 0.3 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 12 0.3 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGGAATTCTCGGGT 11 0.27499999999999997 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGTGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 10 0.25 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 10 0.25 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 10 0.25 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 9 0.22499999999999998 No Hit TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) TTTCGTGCTTATCCTAGTTGTTGGTTTAGTTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 8 0.2 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGC 8 0.2 RNA PCR Primer, Index 25 (100% over 50bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 8 0.2 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 8 0.2 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTAGTGTGAGAATTCTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 6 0.15 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 6 0.15 No Hit TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GGGCCTGTAGCTCAGAGGATTAGAGCACGTGGCTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 6 0.15 No Hit TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTTGGAATTCTCGGG 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGATATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTAATGTGAGAATTCTGGAATTCTCGGGTGCCAA 5 0.125 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCA 5 0.125 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGGAATTCTCGGGTGCC 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATGGAATTCTCGGGTG 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTA 5 0.125 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TATTCTGGTGTCCTAGGCGTATGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.2 0.0 0.0 0.0 2 0.0 0.2 0.0 0.0 0.0 3 0.0 0.2 0.0 0.0 0.0 4 0.0 0.2 0.0 0.0 0.0 5 0.0 0.2 0.0 0.0 0.0 6 0.0 0.225 0.0 0.0 0.0 7 0.0 0.225 0.0 0.0 0.0 8 0.0 0.225 0.0 0.0 0.0 9 0.0 0.225 0.0 0.0 0.0 10-11 0.0 0.25 0.0 0.0 0.0 12-13 0.0 0.25 0.0 0.0 0.0 14-15 0.0 0.325 0.0 0.0 0.0 16-17 0.0 0.45 0.0 0.0 0.0 18-19 0.0 0.6625 0.0 0.0 0.0 20-21 0.0 1.4874999999999998 0.0 0.0 0.0 22-23 0.0 6.575 0.0 0.0 0.0 24-25 0.0 17.0625 0.0 0.0 0.0 26-27 0.0 27.475 0.0 0.0 0.0 28-29 0.0 30.5875 0.0 0.0 0.0 30-31 0.0 41.975 0.0 0.0 0.0 32-33 0.0 57.625 0.0 0.0 0.0 34-35 0.0 78.125 0.0 0.0 0.0 36-37 0.0 90.0625 0.0 0.0 0.0 38-39 0.0 93.3625 0.0 0.0 0.0 40-41 0.0 94.7875 0.0 0.0 0.0 42-43 0.0 96.57499999999999 0.0 0.0 0.0 44-45 0.0 97.17500000000001 0.0 0.0 0.0 46-47 0.0 97.5 0.0 0.0 0.0 48-49 0.0 97.65 0.0 0.0 0.0 50-51 0.0 97.675 0.0 0.0 0.0 52-53 0.0 97.675 0.0 0.0 0.0 54-55 0.0 97.675 0.0 0.0 0.0 56-57 0.0 97.675 0.0 0.0 0.0 58-59 0.0 97.675 0.0 0.0 0.0 60-61 0.0 97.675 0.0 0.0 0.0 62-63 0.0 97.675 0.0 0.0 0.0 64-65 0.0 97.675 0.0 0.0 0.0 66-67 0.0 97.675 0.0 0.0 0.0 68-69 0.0 97.675 0.0 0.0 0.0 70-71 0.0 97.675 0.0 0.0 0.0 72-73 0.0 97.675 0.0 0.0 0.0 74-75 0.0 97.675 0.0 0.0 0.0 76-77 0.0 97.675 0.0 0.0 0.0 78-79 0.0 97.7 0.0 0.0 0.0 80-81 0.0 97.7125 0.0 0.0 0.0 82-83 0.0 97.7375 0.0 0.0 0.0 84-85 0.0 97.775 0.0 0.0 0.0 86-87 0.0 97.7875 0.0 0.0 0.0 88-89 0.0 97.8 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATGTA 20 1.5392321E-5 95.00001 4 GAGCGTA 20 1.5392321E-5 95.00001 3 AGCTCAG 20 1.5392321E-5 95.00001 9 TTGTAGT 40 5.456968E-12 95.00001 5 AGGATAG 20 1.5392321E-5 95.00001 4 TCAGGAT 20 1.5392321E-5 95.00001 2 GATGTAG 20 1.5392321E-5 95.00001 5 TAGCTCA 20 1.5392321E-5 95.00001 8 TAGCCAA 20 1.5392321E-5 95.00001 9 CGTAGTT 20 1.5392321E-5 95.00001 6 CGGATGT 20 1.5392321E-5 95.00001 3 GCGGATG 20 1.5392321E-5 95.00001 2 GGATAGC 20 1.5392321E-5 95.00001 5 ATAGCTC 20 1.5392321E-5 95.00001 7 TGTAGCC 20 1.5392321E-5 95.00001 7 CGAGCGT 20 1.5392321E-5 95.00001 2 GCGTAGT 20 1.5392321E-5 95.00001 5 ATGTAGC 20 1.5392321E-5 95.00001 6 AGCGTAG 20 1.5392321E-5 95.00001 4 CAGGATA 20 1.5392321E-5 95.00001 3 >>END_MODULE Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274901 READS because READLEN < 1 Read 274901 spots for SRR6941572.sra Written 274901 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra Rejected 274888 READS because READLEN < 1 Read 274888 spots for SRR6941572.sra Written 274888 spots for SRR6941572.sra SRR ids: ['SRR6941572.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yrgfu6op SRR6941572.sra spots: 5497773 blocks: [[1, 274888], [274889, 549776], [549777, 824664], [824665, 1099552], [1099553, 1374440], [1374441, 1649328], [1649329, 1924216], [1924217, 2199104], [2199105, 2473992], [2473993, 2748880], [2748881, 3023768], [3023769, 3298656], [3298657, 3573544], [3573545, 3848432], [3848433, 4123320], [4123321, 4398208], [4398209, 4673096], [4673097, 4947984], [4947985, 5222872], [5222873, 5497773]] SRR6941572 file size 1313216 SRR6941572 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 SRR6941572 SRR6941572_1.fastq Input file: SRR6941572_1.fastq trimmed: SRR6941572-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 11:43:31 2024 >> started Fri Dec 6 11:43:34 2024 >> done (2.932s) 5497773 reads processed; of these: 68 ( 0.00%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 5497696 (100.00%) reads available; of these: 713730 (12.98%) trimmed reads available after processing 4783966 (87.02%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 5 0.00% 20 4 0.00% 21 13 0.00% 22 11 0.00% 23 13 0.00% 24 15 0.00% 25 17 0.00% 26 13 0.00% 27 21 0.00% 28 28 0.00% 29 41 0.00% 30 45 0.00% 31 29 0.00% 32 44 0.00% 33 32 0.00% 34 31 0.00% 35 39 0.00% 36 44 0.00% 37 53 0.00% 38 55 0.00% 39 51 0.00% 40 66 0.00% 41 56 0.00% 42 60 0.00% 43 65 0.00% 44 59 0.00% 45 96 0.00% 46 117 0.00% 47 90 0.00% 48 76 0.00% 49 69 0.00% 50 87 0.00% 51 66 0.00% 52 67 0.00% 53 52 0.00% 54 55 0.00% 55 36 0.00% 56 51 0.00% 57 36 0.00% 58 44 0.00% 59 59 0.00% 60 73 0.00% 61 67 0.00% 62 62 0.00% 63 46 0.00% 64 47 0.00% 65 59 0.00% 66 66 0.00% 67 75 0.00% 68 123 0.00% 69 144 0.00% 70 190 0.00% 71 193 0.00% 72 317 0.01% 73 767 0.01% 74 4462 0.08% 75 3130 0.06% 76 1117 0.02% 77 423 0.01% 78 561 0.01% 79 562 0.01% 80 622 0.01% 81 593 0.01% 82 712 0.01% 83 893 0.02% 84 1201 0.02% 85 1369 0.02% 86 1473 0.03% 87 1617 0.03% 88 1823 0.03% 89 2475 0.05% 90 4055 0.07% 91 5806 0.11% 92 7467 0.14% 93 13416 0.24% 94 23790 0.43% 95 70301 1.28% 96 79751 1.45% 97 85591 1.56% 98 160339 2.92% 99 174541 3.17% 100 61494 1.12% 101 4783966 87.02% 5497696 reads passed initial QC criterion=sequence-density sequence-density=97.35 sequence-density-rank=1 fanout-score=25.54 fanout-score-rank=2 prefix-density=97.54 prefix-fanout=25.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=14 fanout-score=38.45 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=1.0 sequence=CCATCGAGTAGACCTTGTTATTGTGAGAATT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR6941572 - Input file: STDIN trimmed: SRR6941572-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:43:47 2024 >> started Fri Dec 6 11:43:53 2024 >> done (5.612s) 5385498 reads processed; of these: 23263 ( 0.43%) short reads filtered out after trimming by size control 17044 ( 0.32%) empty reads filtered out after trimming by size control 5345191 (99.25%) reads available; of these: 5300144 (99.16%) trimmed reads available after processing 45047 ( 0.84%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7536 0.14% 19 20006 0.37% 20 28240 0.53% 21 172371 3.22% 22 140009 2.62% 23 105749 1.98% 24 794501 14.86% 25 101971 1.91% 26 90030 1.68% 27 75164 1.41% 28 88856 1.66% 29 317751 5.94% 30 528404 9.89% 31 367713 6.88% 32 481272 9.00% 33 661757 12.38% 34 445552 8.34% 35 365351 6.84% 36 175634 3.29% 37 82159 1.54% 38 38655 0.72% 39 28256 0.53% 40 52499 0.98% 41 52465 0.98% 42 38528 0.72% 43 9221 0.17% 44 11483 0.21% 45 9205 0.17% 46 2481 0.05% 47 2903 0.05% 48 940 0.02% 49 482 0.01% 50 212 0.00% 51 301 0.01% 52 148 0.00% 53 118 0.00% 54 78 0.00% 55 53 0.00% 56 42 0.00% 57 40 0.00% 58 25 0.00% 59 28 0.00% 60 33 0.00% 61 21 0.00% 62 28 0.00% 63 18 0.00% 64 22 0.00% 65 21 0.00% 66 18 0.00% 67 23 0.00% 68 46 0.00% 69 53 0.00% 70 62 0.00% 71 61 0.00% 72 44 0.00% 73 55 0.00% 74 54 0.00% 75 97 0.00% 76 98 0.00% 77 400 0.01% 78 83 0.00% 79 125 0.00% 80 532 0.01% 81 188 0.00% 82 312 0.01% 83 265 0.00% 84 110 0.00% 85 94 0.00% 86 151 0.00% 87 245 0.00% 88 145 0.00% 89 142 0.00% 90 155 0.00% 91 217 0.00% 92 224 0.00% 93 275 0.01% 94 373 0.01% 95 465 0.01% 96 502 0.01% 97 622 0.01% 98 1000 0.02% 99 697 0.01% 100 644 0.01% 101 38282 0.72% criterion=sequence-density sequence-density=4.05 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGA criterion=fanout-score sequence-density=0.13 sequence-density-rank=29 fanout-score=112.19 fanout-score-rank=1 prefix-density=14.02 prefix-fanout=1.0 sequence=TATTGTGAGAAAAAA Started job on | Dec 06 11:44:21 Started mapping on | Dec 06 11:44:21 Finished on | Dec 06 11:44:41 Mapping speed, Million of reads per hour | 982.33 Number of input reads | 5457389 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 784213 Uniquely mapped reads % | 14.37% Average mapped length | 26.83 Number of splices: Total | 18274 Number of splices: Annotated (sjdb) | 1497 Number of splices: GT/AG | 17566 Number of splices: GC/AG | 592 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 116 Mismatch rate per base, % | 0.94% Deletion rate per base | 0.01% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3730853 % of reads mapped to multiple loci | 68.36% Number of reads mapped to too many loci | 686706 % of reads mapped to too many loci | 12.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.14% % of reads unmapped: other | 0.54% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 942323 942323 942323 N_multimapping 3730853 3730853 3730853 N_noFeature 486648 639156 627788 N_ambiguous 9246 4903 510 UnstrandedReadsAssigned:288319 PositiveStrandReadsAssigned:140154 NegativeStrandReadsAssigned:155915 Dataset is classified unstranded MeadianReadLen=31 20thPercentileLength=24 echo kmer=19 SRR6941572 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: SRR6941572-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,457,389 reads, 2,734,098 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 922 rounds 52973 SRR6941572.ke.tsv 35125 SRR6941572.se.tsv 88098 total ==> SRR6941572.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 1 0.0755661 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 1 0.712425 KQK14069 1603 1504 18.394 1.69032 KQK14071 474 375 0 0 ==> SRR6941572.se.tsv <== BRADI_1g14170v3 46 BRADI_1g53295v3 3 BRADI_1g59795v3 1 BRADI_1g07683v3 1 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 9 BRADI_1g09890v3 26 BRADI_1g77505v3 2 BRADI_1g48960v3 0 SRR6941572 completed mapping pipeline successfully