Starting /dee2/code/volunteer_pipeline.sh SRR8846492 current disk space = 1501686456320 free memory = 1349346700 SRR8846492 SRAfilesize 38b991eb32457c0801fb46c3045d449a SRR8846492.sra SRR8846492.sra file validated SRR8846492 is single end SRR8846492 is conventional basespace SRR8846492 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846492_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.002 34.0 33.0 34.0 30.0 34.0 2 32.8695 34.0 33.0 34.0 30.0 34.0 3 33.02 34.0 33.0 34.0 32.0 34.0 4 33.23325 34.0 33.0 34.0 32.0 34.0 5 33.2575 34.0 33.0 34.0 33.0 34.0 6 36.872 38.0 37.0 38.0 36.0 38.0 7 37.1645 38.0 38.0 38.0 36.0 38.0 8 37.371 38.0 38.0 38.0 37.0 38.0 9 37.49975 38.0 38.0 38.0 37.0 38.0 10-11 37.511125 38.0 38.0 38.0 37.5 38.0 12-13 37.502250000000004 38.0 38.0 38.0 38.0 38.0 14-15 37.504625000000004 38.0 38.0 38.0 37.5 38.0 16-17 37.489000000000004 38.0 38.0 38.0 37.5 38.0 18-19 37.542375 38.0 38.0 38.0 38.0 38.0 20-21 37.370875 38.0 38.0 38.0 37.0 38.0 22-23 37.460499999999996 38.0 38.0 38.0 37.0 38.0 24-25 37.447374999999994 38.0 38.0 38.0 37.0 38.0 26-27 37.550625 38.0 38.0 38.0 37.5 38.0 28-29 37.394999999999996 38.0 38.0 38.0 37.5 38.0 30-31 37.357 38.0 38.0 38.0 37.0 38.0 32-33 37.405375 38.0 38.0 38.0 37.0 38.0 34-35 37.27175 38.0 38.0 38.0 37.0 38.0 36-37 37.191500000000005 38.0 38.0 38.0 36.5 38.0 38-39 37.142625 38.0 38.0 38.0 36.0 38.0 40-41 36.96425 38.0 38.0 38.0 36.0 38.0 42-43 36.98325 38.0 38.0 38.0 36.0 38.0 44-45 36.996625 38.0 38.0 38.0 36.0 38.0 46-47 36.94475 38.0 38.0 38.0 35.5 38.0 48-49 36.80925 38.0 38.0 38.0 35.0 38.0 50-51 36.96475 38.0 38.0 38.0 36.0 38.0 52-53 36.945 38.0 38.0 38.0 36.0 38.0 54-55 36.825 38.0 38.0 38.0 35.0 38.0 56-57 36.474999999999994 38.0 38.0 38.0 34.0 38.0 58-59 36.515125 38.0 38.0 38.0 34.5 38.0 60-61 36.4585 38.0 38.0 38.0 34.0 38.0 62-63 36.346000000000004 38.0 37.5 38.0 33.5 38.0 64-65 36.240750000000006 38.0 37.0 38.0 33.5 38.0 66-67 35.988125 38.0 37.0 38.0 31.0 38.0 68-69 35.875 38.0 37.0 38.0 31.0 38.0 70-71 35.489875 38.0 37.0 38.0 29.0 38.0 72-73 35.455 38.0 37.0 38.0 29.5 38.0 74-75 34.95875 38.0 36.0 38.0 28.0 38.0 76-77 34.955375000000004 38.0 36.5 38.0 28.0 38.0 78-79 34.2825 38.0 35.0 38.0 25.5 38.0 80-81 34.546 38.0 36.0 38.0 26.0 38.0 82-83 33.894375 38.0 34.0 38.0 20.0 38.0 84-85 34.195499999999996 38.0 34.5 38.0 25.0 38.0 86-87 34.5195 38.0 36.0 38.0 26.5 38.0 88-89 34.24225 38.0 35.0 38.0 25.5 38.0 90-91 34.081625 38.0 35.0 38.0 24.0 38.0 92-93 33.760374999999996 38.0 35.0 38.0 15.0 38.0 94-95 33.359375 38.0 34.5 38.0 15.0 38.0 96-97 32.641375 38.0 34.0 38.0 15.0 38.0 98-99 31.626375 38.0 33.5 38.0 2.0 38.0 100-101 29.7175 38.0 28.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 2.0 11 1.0 12 0.0 13 0.0 14 1.0 15 1.0 16 2.0 17 0.0 18 0.0 19 2.0 20 3.0 21 1.0 22 3.0 23 11.0 24 17.0 25 34.0 26 27.0 27 23.0 28 23.0 29 46.0 30 56.0 31 86.0 32 91.0 33 147.0 34 229.0 35 456.0 36 958.0 37 1780.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.05428648212846 22.816447191615158 18.677774791722655 20.451491534533726 2 30.475 25.525 14.299999999999999 29.7 3 28.749999999999996 17.825 18.45 34.975 4 25.3 34.949999999999996 18.05 21.7 5 26.424999999999997 25.124999999999996 27.125 21.325 6 25.074999999999996 23.125 28.475 23.325000000000003 7 38.574999999999996 25.924999999999997 17.575 17.925 8 19.875 19.875 41.25 19.0 9 24.775 38.25 20.674999999999997 16.3 10-11 32.275 21.8125 26.025 19.8875 12-13 23.0125 20.849999999999998 22.5875 33.550000000000004 14-15 22.912499999999998 44.1125 17.5625 15.412500000000001 16-17 25.337500000000002 24.7 31.125000000000004 18.8375 18-19 36.6375 23.3875 20.375 19.6 20-21 19.85 29.45 27.2625 23.4375 22-23 27.275 32.5375 24.337500000000002 15.85 24-25 27.55 28.175 22.475 21.8 26-27 28.9125 28.000000000000004 19.6875 23.400000000000002 28-29 22.912499999999998 23.6625 24.087500000000002 29.3375 30-31 29.7375 19.8375 29.7125 20.7125 32-33 21.762500000000003 18.987499999999997 34.55 24.7 34-35 28.0875 18.2 31.55 22.162499999999998 36-37 28.475 22.6 30.5 18.425 38-39 31.075000000000003 22.35 29.799999999999997 16.775000000000002 40-41 28.3125 17.6875 29.95 24.05 42-43 30.8125 18.5 27.712500000000002 22.975 44-45 40.612500000000004 18.2625 18.1125 23.0125 46-47 34.137499999999996 25.6125 19.950000000000003 20.3 48-49 30.3875 20.175 21.25 28.1875 50-51 24.25 25.924999999999997 17.3625 32.4625 52-53 30.9875 26.625 13.3875 28.999999999999996 54-55 26.787499999999998 29.212500000000002 15.837499999999999 28.1625 56-57 23.525 26.625 17.9125 31.937500000000004 58-59 14.637500000000001 26.2875 20.962500000000002 38.1125 60-61 17.775 29.3375 20.1125 32.775 62-63 17.3375 26.25 25.55 30.862499999999997 64-65 13.900000000000002 29.325000000000003 28.299999999999997 28.475 66-67 10.5125 22.2625 32.2625 34.9625 68-69 14.025000000000002 22.237499999999997 33.175 30.562499999999996 70-71 16.150000000000002 21.5625 38.587500000000006 23.7 72-73 17.712500000000002 22.95 35.362500000000004 23.974999999999998 74-75 12.75 20.4875 35.4125 31.35 76-77 18.0 14.000000000000002 40.35 27.650000000000002 78-79 20.0375 12.737499999999999 39.0 28.225 80-81 20.325 15.875 37.85 25.95 82-83 18.85 12.5 39.5875 29.062500000000004 84-85 21.025 8.924999999999999 38.65 31.4 86-87 21.224999999999998 11.1625 37.675 29.9375 88-89 16.537499999999998 20.05 40.325 23.0875 90-91 18.0375 24.212500000000002 35.862500000000004 21.8875 92-93 16.4875 32.725 27.775 23.0125 94-95 15.325 40.9625 29.2 14.512500000000001 96-97 10.65 53.387499999999996 24.525 11.4375 98-99 9.1625 64.97500000000001 17.05 8.8125 100-101 7.0375 73.3 13.1375 6.525 >>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 0.5 31 1.0 32 2.5 33 6.0 34 7.0 35 9.0 36 11.0 37 9.5 38 22.5 39 35.0 40 63.5 41 101.0 42 126.5 43 204.5 44 270.5 45 333.5 46 345.5 47 299.5 48 329.5 49 423.5 50 397.0 51 236.5 52 155.5 53 172.5 54 216.0 55 138.5 56 34.5 57 18.0 58 10.5 59 9.5 60 6.5 61 1.5 62 0.5 63 0.5 64 0.0 65 0.0 66 0.0 67 0.5 68 0.5 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 warn #Base N-Count 1 6.9750000000000005 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 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 warn #Total Deduplicated Percentage 50.375 #Duplication Level Percentage of deduplicated Percentage of total 1 81.48883374689827 41.05 2 8.883374689826303 8.95 3 2.2332506203473943 3.375 4 1.8858560794044668 3.8 5 1.0421836228287842 2.625 6 0.8933002481389578 2.7 7 0.5955334987593052 2.1 8 0.2977667493796526 1.2 9 0.34739454094292804 1.575 >10 1.9851116625310175 17.775 >50 0.24813895781637718 9.025 >100 0.09925558312655086 5.825 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 132 3.3000000000000003 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 101 2.5250000000000004 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 83 2.075 RNA PCR Primer, Index 1 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 81 2.025 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 71 1.775 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 70 1.7500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 56 1.4000000000000001 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 42 1.05 RNA PCR Primer, Index 1 (100% over 23bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 38 0.95 RNA PCR Primer, Index 1 (100% over 29bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 35 0.8750000000000001 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 31 0.775 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 21 0.525 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 20 0.5 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTT 20 0.5 RNA PCR Primer, Index 12 (100% over 50bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 20 0.5 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 20 0.5 RNA PCR Primer, Index 1 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 19 0.475 RNA PCR Primer, Index 1 (100% over 24bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGT 19 0.475 RNA PCR Primer, Index 12 (100% over 50bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 19 0.475 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 19 0.475 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 18 0.44999999999999996 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 18 0.44999999999999996 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 18 0.44999999999999996 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCCTGGAATTC 17 0.42500000000000004 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 15 0.375 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 15 0.375 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 15 0.375 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 23bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 14 0.35000000000000003 No Hit CGACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAA 13 0.325 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 13 0.325 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 13 0.325 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 13 0.325 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGAGTGGAATTCT 12 0.3 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) CTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTC 12 0.3 RNA PCR Primer, Index 12 (100% over 50bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTC 11 0.27499999999999997 RNA PCR Primer, Index 12 (100% over 50bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 10 0.25 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 10 0.25 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 9 0.22499999999999998 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 9 0.22499999999999998 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 9 0.22499999999999998 No Hit CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 8 0.2 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 8 0.2 No Hit GCATCATTGGTCTAGTGGTAGAATTCGTCGTTTGGAATTCTCGGGTGCCA 8 0.2 No Hit TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 8 0.2 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 22bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATTGGAATTCTCG 7 0.17500000000000002 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 7 0.17500000000000002 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCT 7 0.17500000000000002 RNA PCR Primer, Index 12 (100% over 50bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 7 0.17500000000000002 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 7 0.17500000000000002 No Hit AACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CGACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTTGGAATTCT 6 0.15 No Hit TATTCTGGTGTCCTAGGCGTAGAGGAACCACACCTGGAATTCTCGGGTGC 6 0.15 No Hit NACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 6 0.15 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCTGGAATTCTCGGGT 6 0.15 No Hit GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 6 0.15 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) ACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATT 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 6 0.15 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 6 0.15 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACTGGAATTCTCG 5 0.125 No Hit CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAAT 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 5 0.125 No Hit GCATCATTGGTCTAGTGGTAGAATTCGTCTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTC 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 5 0.125 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CCGGATTATGACTGAACGCCTCTAAGTCATGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 5 0.125 No Hit GCCTACTTAACTCAGTGGTTAGAGTATTGCTTTCATACGGCTGGAATTCT 5 0.125 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGATGGAATTCTCGGGTG 5 0.125 No Hit ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) TCGTGCTGAAGAGCGTGGAGGTTCGAGTCCTCTTCAAGGCACCATGGAAT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATT 5 0.125 No Hit >>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 0.1 0.0 0.0 0.0 2 0.0 0.1 0.0 0.0 0.0 3 0.0 0.1 0.0 0.0 0.0 4 0.0 0.125 0.0 0.0 0.0 5 0.0 0.125 0.0 0.0 0.0 6 0.0 0.125 0.0 0.0 0.0 7 0.0 0.125 0.0 0.0 0.0 8 0.0 0.125 0.0 0.0 0.0 9 0.0 0.2 0.0 0.0 0.0 10-11 0.0 0.2875 0.0 0.0 0.0 12-13 0.0 0.35 0.0 0.0 0.0 14-15 0.0 0.4 0.0 0.0 0.0 16-17 0.0 0.65 0.0 0.0 0.0 18-19 0.0 1.2 0.0 0.0 0.0 20-21 0.0 2.2625 0.0 0.0 0.0 22-23 0.0 5.6125 0.0 0.0 0.0 24-25 0.0 11.175 0.0 0.0 0.0 26-27 0.0 18.15 0.0 0.0 0.0 28-29 0.0 26.4625 0.0 0.0 0.0 30-31 0.0 35.5 0.0 0.0 0.0 32-33 0.0 45.0625 0.0 0.0 0.0 34-35 0.0 58.4875 0.0 0.0 0.0 36-37 0.0 69.15 0.0 0.0 0.0 38-39 0.0 75.125 0.0 0.0 0.0 40-41 0.0 79.9625 0.0 0.0 0.0 42-43 0.0 87.175 0.0 0.0 0.0 44-45 0.0 91.5125 0.0 0.0 0.0 46-47 0.0 93.3375 0.0 0.0 0.0 48-49 0.0 93.95 0.0 0.0 0.0 50-51 0.0 94.1875 0.0 0.0 0.0 52-53 0.0 94.325 0.0 0.0 0.0 54-55 0.0 94.36250000000001 0.0 0.0 0.0 56-57 0.0 94.425 0.0 0.0 0.0 58-59 0.0 94.425 0.0 0.0 0.0 60-61 0.0 94.425 0.0 0.0 0.0 62-63 0.0 94.425 0.0 0.0 0.0 64-65 0.0 94.45 0.0 0.0 0.0 66-67 0.0 94.45 0.0 0.0 0.0 68-69 0.0 94.45 0.0 0.0 0.0 70-71 0.0 94.45 0.0 0.0 0.0 72-73 0.0 94.45 0.0 0.0 0.0 74-75 0.0 94.45 0.0 0.0 0.0 76-77 0.0 94.45 0.0 0.0 0.0 78-79 0.0 94.5 0.0 0.0 0.0 80-81 0.0 94.5 0.0 0.0 0.0 82-83 0.0 94.5 0.0 0.0 0.0 84-85 0.0 94.5 0.0 0.0 0.0 86-87 0.0 94.5 0.0 0.0 0.0 88-89 0.0 94.5 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGATTG 30 5.4096745E-9 102.62162 1 GCGAGCG 15 4.4910912E-4 102.62162 1 GCCTTGA 20 1.038194E-5 102.62161 1 TCCACTG 20 1.038194E-5 102.62161 1 GATTGTA 35 2.3283064E-10 94.925 3 ATTGTAG 35 2.3283064E-10 94.925 4 TGTAGTT 35 2.3283064E-10 94.925 6 TGATGGT 20 1.545283E-5 94.924995 5 GAGCGTA 15 6.1614934E-4 94.924995 3 GGTGAAA 20 1.545283E-5 94.924995 9 CTGAGAT 20 1.545283E-5 94.924995 5 AGCTCAG 15 6.1614934E-4 94.924995 9 TTGTAGT 40 5.456968E-12 94.924995 5 TAGCTCA 15 6.1614934E-4 94.924995 8 ATGGTGA 20 1.545283E-5 94.924995 7 CGTAGTT 15 6.1614934E-4 94.924995 6 CCTTGAT 20 1.545283E-5 94.924995 2 CACTGAG 20 1.545283E-5 94.924995 3 TAGTTCA 50 0.0 94.924995 8 CCACTGA 20 1.545283E-5 94.924995 2 >>END_MODULE Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra Rejected 838444 READS because READLEN < 1 Read 838444 spots for SRR8846492.sra Written 838444 spots for SRR8846492.sra Rejected 838431 READS because READLEN < 1 Read 838431 spots for SRR8846492.sra Written 838431 spots for SRR8846492.sra SRR ids: ['SRR8846492.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ty4d6986 SRR8846492.sra spots: 16768633 blocks: [[1, 838431], [838432, 1676862], [1676863, 2515293], [2515294, 3353724], [3353725, 4192155], [4192156, 5030586], [5030587, 5869017], [5869018, 6707448], [6707449, 7545879], [7545880, 8384310], [8384311, 9222741], [9222742, 10061172], [10061173, 10899603], [10899604, 11738034], [11738035, 12576465], [12576466, 13414896], [13414897, 14253327], [14253328, 15091758], [15091759, 15930189], [15930190, 16768633]] SRR8846492 file size 4023077 SRR8846492 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 SRR8846492 SRR8846492_1.fastq Input file: SRR8846492_1.fastq trimmed: SRR8846492-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 Sun Dec 8 21:22:42 2024 >> started Sun Dec 8 21:23:27 2024 >> done (45.157s) 16768633 reads processed; of these: 311 ( 0.00%) short reads filtered out after trimming by size control 54 ( 0.00%) empty reads filtered out after trimming by size control 16768268 (100.00%) reads available; of these: 2198569 (13.11%) trimmed reads available after processing 14569699 (86.89%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 41 0.00% 19 29 0.00% 20 38 0.00% 21 43 0.00% 22 40 0.00% 23 52 0.00% 24 56 0.00% 25 76 0.00% 26 122 0.00% 27 139 0.00% 28 194 0.00% 29 256 0.00% 30 254 0.00% 31 226 0.00% 32 234 0.00% 33 219 0.00% 34 297 0.00% 35 260 0.00% 36 215 0.00% 37 203 0.00% 38 189 0.00% 39 196 0.00% 40 211 0.00% 41 237 0.00% 42 278 0.00% 43 285 0.00% 44 286 0.00% 45 341 0.00% 46 322 0.00% 47 327 0.00% 48 300 0.00% 49 346 0.00% 50 339 0.00% 51 293 0.00% 52 274 0.00% 53 271 0.00% 54 217 0.00% 55 203 0.00% 56 233 0.00% 57 277 0.00% 58 330 0.00% 59 540 0.00% 60 672 0.00% 61 1175 0.01% 62 1545 0.01% 63 1780 0.01% 64 2665 0.02% 65 3771 0.02% 66 9013 0.05% 67 46320 0.28% 68 55362 0.33% 69 36603 0.22% 70 30844 0.18% 71 36602 0.22% 72 14676 0.09% 73 4277 0.03% 74 5889 0.04% 75 3449 0.02% 76 2886 0.02% 77 2947 0.02% 78 3193 0.02% 79 3371 0.02% 80 3749 0.02% 81 4625 0.03% 82 6615 0.04% 83 6301 0.04% 84 6553 0.04% 85 7394 0.04% 86 8575 0.05% 87 11151 0.07% 88 16210 0.10% 89 23706 0.14% 90 31040 0.19% 91 33160 0.20% 92 41183 0.25% 93 66575 0.40% 94 84483 0.50% 95 183715 1.10% 96 218112 1.30% 97 236024 1.41% 98 349042 2.08% 99 377058 2.25% 100 206969 1.23% 101 14569699 86.89% 16768268 reads passed initial QC criterion=sequence-density sequence-density=94.04 sequence-density-rank=1 fanout-score=30.58 fanout-score-rank=2 prefix-density=94.40 prefix-fanout=30.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.64 sequence-density-rank=5 fanout-score=60.57 fanout-score-rank=1 prefix-density=98.39 prefix-fanout=1.0 sequence=CACCTTGTAATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846492 - Input file: STDIN trimmed: SRR8846492-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTGA -- 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 Sun Dec 8 21:26:21 2024 >> started Sun Dec 8 21:27:39 2024 >> done (77.703s) 16415252 reads processed; of these: 147318 ( 0.90%) short reads filtered out after trimming by size control 9560 ( 0.06%) empty reads filtered out after trimming by size control 16258374 (99.04%) reads available; of these: 15771311 (97.00%) trimmed reads available after processing 487063 ( 3.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 42534 0.26% 19 80719 0.50% 20 92492 0.57% 21 374757 2.31% 22 225323 1.39% 23 323977 1.99% 24 1057543 6.50% 25 441883 2.72% 26 600887 3.70% 27 627862 3.86% 28 795996 4.90% 29 654154 4.02% 30 705381 4.34% 31 533980 3.28% 32 1268333 7.80% 33 1065551 6.55% 34 999849 6.15% 35 861885 5.30% 36 980059 6.03% 37 459988 2.83% 38 421126 2.59% 39 420728 2.59% 40 456939 2.81% 41 664503 4.09% 42 670087 4.12% 43 281184 1.73% 44 277907 1.71% 45 153398 0.94% 46 80335 0.49% 47 43639 0.27% 48 36678 0.23% 49 21634 0.13% 50 14568 0.09% 51 12583 0.08% 52 6653 0.04% 53 4677 0.03% 54 5937 0.04% 55 1533 0.01% 56 1667 0.01% 57 901 0.01% 58 706 0.00% 59 776 0.00% 60 754 0.00% 61 1251 0.01% 62 1465 0.01% 63 1683 0.01% 64 2518 0.02% 65 3535 0.02% 66 8633 0.05% 67 45172 0.28% 68 53874 0.33% 69 35496 0.22% 70 29833 0.18% 71 35310 0.22% 72 12935 0.08% 73 2698 0.02% 74 1919 0.01% 75 1279 0.01% 76 1357 0.01% 77 1876 0.01% 78 1440 0.01% 79 1375 0.01% 80 1680 0.01% 81 1421 0.01% 82 1292 0.01% 83 1514 0.01% 84 1044 0.01% 85 971 0.01% 86 975 0.01% 87 916 0.01% 88 830 0.01% 89 923 0.01% 90 946 0.01% 91 973 0.01% 92 994 0.01% 93 1198 0.01% 94 1336 0.01% 95 1823 0.01% 96 2817 0.02% 97 3566 0.02% 98 5468 0.03% 99 6794 0.04% 100 8771 0.05% 101 196407 1.21% criterion=sequence-density sequence-density=4.15 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGT criterion=fanout-score sequence-density=0.04 sequence-density-rank=27 fanout-score=18.19 fanout-score-rank=1 prefix-density=0.70 prefix-fanout=1.1 sequence=GGCGGATTGCTCGAGCTGCTCACGCGGCGAGAGCGGGTCGCCGCGTGCCGGCCGGGGGACGGACCGGGAGTCGCCCCTTCGGGGGCTTTCCCCGAGCGCTGAACAGTCGACTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGAT Started job on | Dec 08 21:29:58 Started mapping on | Dec 08 21:29:59 Finished on | Dec 08 21:36:25 Mapping speed, Million of reads per hour | 154.92 Number of input reads | 16611390 Average input read length | 35 UNIQUE READS: Uniquely mapped reads number | 2178368 Uniquely mapped reads % | 13.11% Average mapped length | 29.90 Number of splices: Total | 33172 Number of splices: Annotated (sjdb) | 22858 Number of splices: GT/AG | 30639 Number of splices: GC/AG | 1727 Number of splices: AT/AC | 24 Number of splices: Non-canonical | 782 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.31 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6950738 % of reads mapped to multiple loci | 41.84% Number of reads mapped to too many loci | 6342463 % of reads mapped to too many loci | 38.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.50% % of reads unmapped: other | 0.36% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7482284 7482284 7482284 N_multimapping 6950738 6950738 6950738 N_noFeature 1097904 1325866 1937315 N_ambiguous 44175 30887 350 UnstrandedReadsAssigned:1036289 PositiveStrandReadsAssigned:821615 NegativeStrandReadsAssigned:240703 Dataset is classified unstranded MeadianReadLen=33 20thPercentileLength=27 echo kmer=23 SRR8846492 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=23 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 23 [index] number of targets: 52,972 [index] number of k-mers: 66,237,239 [index] number of equivalence classes: 154,277 [quant] running in single-end mode [quant] will process file 1: SRR8846492-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,611,390 reads, 3,281,837 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 906 rounds 52973 SRR8846492.ke.tsv 35125 SRR8846492.se.tsv 88098 total ==> SRR8846492.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 4 0.714073 PNS24243 293 194 0 0 KQK14069 1603 1504 57.8376 9.41888 KQK14071 474 375 0 0 ==> SRR8846492.se.tsv <== BRADI_1g14170v3 63 BRADI_1g53295v3 0 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 36 BRADI_1g74790v3 26 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846492 completed mapping pipeline successfully