Starting /dee2/code/volunteer_pipeline.sh SRR8846524 current disk space = 2792276963328 free memory = 1544578348 SRR8846524 SRAfilesize 74df545af165982e6618200431a1b944 SRR8846524.sra SRR8846524.sra file validated SRR8846524 is single end SRR8846524 is conventional basespace SRR8846524 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846524_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 31.5405 34.0 33.0 34.0 32.0 34.0 2 32.915 34.0 33.0 34.0 31.0 34.0 3 33.08425 34.0 33.0 34.0 32.0 34.0 4 33.1295 34.0 33.0 34.0 32.0 34.0 5 33.17525 34.0 33.0 34.0 33.0 34.0 6 36.8715 38.0 37.0 38.0 36.0 38.0 7 37.299 38.0 38.0 38.0 36.0 38.0 8 37.4745 38.0 38.0 38.0 37.0 38.0 9 37.42125 38.0 38.0 38.0 37.0 38.0 10-11 37.489625000000004 38.0 38.0 38.0 37.5 38.0 12-13 37.532375 38.0 38.0 38.0 38.0 38.0 14-15 37.4885 38.0 38.0 38.0 38.0 38.0 16-17 37.460750000000004 38.0 38.0 38.0 37.5 38.0 18-19 37.5135 38.0 38.0 38.0 37.5 38.0 20-21 37.439125000000004 38.0 38.0 38.0 37.5 38.0 22-23 37.487375 38.0 38.0 38.0 37.5 38.0 24-25 37.524625 38.0 38.0 38.0 38.0 38.0 26-27 37.485 38.0 38.0 38.0 37.5 38.0 28-29 37.48725 38.0 38.0 38.0 38.0 38.0 30-31 37.482 38.0 38.0 38.0 37.0 38.0 32-33 37.460375 38.0 38.0 38.0 37.0 38.0 34-35 37.2915 38.0 38.0 38.0 37.0 38.0 36-37 37.221000000000004 38.0 38.0 38.0 37.0 38.0 38-39 37.09375 38.0 38.0 38.0 36.0 38.0 40-41 37.09875 38.0 38.0 38.0 36.5 38.0 42-43 36.99675 38.0 38.0 38.0 35.5 38.0 44-45 37.059625 38.0 38.0 38.0 36.0 38.0 46-47 37.021 38.0 38.0 38.0 36.0 38.0 48-49 37.020875000000004 38.0 38.0 38.0 36.0 38.0 50-51 37.025999999999996 38.0 38.0 38.0 35.5 38.0 52-53 37.05075 38.0 38.0 38.0 36.0 38.0 54-55 36.956625 38.0 38.0 38.0 36.0 38.0 56-57 36.966125000000005 38.0 38.0 38.0 36.0 38.0 58-59 36.849375 38.0 38.0 38.0 36.0 38.0 60-61 36.556875 38.0 38.0 38.0 34.5 38.0 62-63 36.397875 38.0 38.0 38.0 34.0 38.0 64-65 36.1505 38.0 37.5 38.0 32.5 38.0 66-67 35.759625 38.0 37.0 38.0 29.0 38.0 68-69 35.8615 38.0 37.0 38.0 30.0 38.0 70-71 35.67975 38.0 37.0 38.0 30.0 38.0 72-73 35.5035 38.0 37.0 38.0 29.0 38.0 74-75 35.12225 38.0 36.5 38.0 28.0 38.0 76-77 34.933 38.0 36.0 38.0 27.5 38.0 78-79 34.427499999999995 38.0 35.0 38.0 26.0 38.0 80-81 34.531625 38.0 35.0 38.0 26.0 38.0 82-83 34.533125 38.0 35.5 38.0 26.0 38.0 84-85 34.36475 38.0 35.0 38.0 25.0 38.0 86-87 34.640875 38.0 35.5 38.0 27.0 38.0 88-89 35.088499999999996 38.0 36.0 38.0 28.0 38.0 90-91 34.870875 38.0 36.0 38.0 27.5 38.0 92-93 34.767624999999995 38.0 36.5 38.0 28.0 38.0 94-95 34.039500000000004 38.0 35.0 38.0 24.0 38.0 96-97 33.06925 38.0 34.5 38.0 15.0 38.0 98-99 31.547874999999998 38.0 32.5 38.0 8.0 38.0 100-101 28.967750000000002 38.0 24.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 1.0 13 0.0 14 0.0 15 1.0 16 1.0 17 3.0 18 1.0 19 2.0 20 1.0 21 2.0 22 1.0 23 6.0 24 13.0 25 27.0 26 24.0 27 21.0 28 25.0 29 37.0 30 46.0 31 71.0 32 88.0 33 157.0 34 217.0 35 432.0 36 1001.0 37 1821.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.55962095288234 26.05948933929982 21.268754935509346 26.112134772308504 2 23.925 32.1 18.8 25.174999999999997 3 25.45 22.75 22.5 29.299999999999997 4 28.15 29.349999999999998 17.224999999999998 25.275 5 33.074999999999996 26.05 17.75 23.125 6 25.7 31.8 21.8 20.7 7 34.575 27.750000000000004 18.825 18.85 8 22.625 23.225 33.475 20.674999999999997 9 24.075 35.6 21.3 19.025 10-11 30.4625 26.700000000000003 22.675 20.1625 12-13 23.0625 24.9125 20.25 31.775 14-15 23.6875 33.5625 24.5 18.25 16-17 26.5125 27.6375 28.4375 17.4125 18-19 29.2375 27.0875 23.175 20.5 20-21 22.425 28.9 28.212500000000002 20.4625 22-23 28.1875 29.4375 25.5625 16.8125 24-25 28.000000000000004 27.6625 24.025 20.3125 26-27 32.7125 26.75 22.787499999999998 17.75 28-29 24.224999999999998 31.05 25.837500000000002 18.8875 30-31 24.2375 22.125 34.949999999999996 18.6875 32-33 25.775 19.875 32.7625 21.587500000000002 34-35 28.000000000000004 20.4625 30.6375 20.9 36-37 33.324999999999996 17.6875 31.5625 17.424999999999997 38-39 30.9875 19.0875 29.9875 19.9375 40-41 29.462500000000002 17.962500000000002 26.625 25.95 42-43 31.5 22.112499999999997 24.8 21.587500000000002 44-45 38.1875 18.9 20.2625 22.650000000000002 46-47 32.375 25.8 17.6875 24.1375 48-49 29.525000000000002 23.974999999999998 18.9625 27.537499999999998 50-51 28.1 23.3375 16.2125 32.35 52-53 26.700000000000003 31.137500000000003 13.3 28.8625 54-55 23.8375 27.200000000000003 17.775 31.1875 56-57 22.3375 30.575000000000003 14.274999999999999 32.8125 58-59 20.3875 27.787499999999998 19.25 32.574999999999996 60-61 14.7375 31.9625 16.275000000000002 37.025000000000006 62-63 15.0625 31.35 17.7 35.8875 64-65 14.887500000000001 31.125000000000004 22.05 31.937500000000004 66-67 11.95 26.875 24.1625 37.012499999999996 68-69 15.075 27.725 22.6125 34.5875 70-71 14.762500000000001 27.212500000000002 26.400000000000002 31.624999999999996 72-73 16.537499999999998 24.712500000000002 26.700000000000003 32.05 74-75 15.275 20.974999999999998 27.1125 36.6375 76-77 17.9375 18.25 34.3125 29.5 78-79 18.0 13.487499999999999 35.5 33.0125 80-81 18.025 13.337499999999999 35.375 33.2625 82-83 21.224999999999998 11.5625 38.95 28.262500000000003 84-85 20.125 9.625 38.4375 31.8125 86-87 20.8 12.812499999999998 38.1875 28.199999999999996 88-89 18.35 23.4875 35.4375 22.725 90-91 14.4625 30.5375 34.075 20.925 92-93 16.0125 38.15 27.875 17.962500000000002 94-95 12.537499999999998 49.0625 24.4125 13.9875 96-97 10.6875 58.8875 20.625 9.8 98-99 8.412500000000001 69.0 15.25 7.3374999999999995 100-101 6.2125 77.17500000000001 10.5625 6.05 >>END_MODULE >>Per sequence GC content pass #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 0.5 28 0.5 29 0.0 30 0.0 31 0.0 32 0.0 33 2.0 34 5.5 35 7.5 36 6.5 37 8.5 38 17.0 39 37.0 40 49.0 41 84.5 42 134.5 43 188.5 44 295.5 45 340.0 46 335.5 47 364.0 48 357.0 49 334.5 50 342.0 51 308.0 52 215.5 53 151.5 54 123.5 55 125.0 56 90.0 57 28.0 58 18.0 59 13.0 60 4.5 61 3.5 62 2.0 63 3.0 64 3.5 65 1.0 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 warn #Base N-Count 1 5.025 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 61.224999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 84.03429971416905 51.449999999999996 2 7.717435688035932 9.45 3 2.2458146182115146 4.125 4 1.347488770926909 3.3000000000000003 5 1.0208248264597795 3.125 6 0.6941608819926501 2.55 7 0.4899959167006942 2.1 8 0.2041649652919559 1.0 9 0.4899959167006942 2.7 >10 1.7149857084524296 18.725 >50 0.04083299305839118 1.4749999999999999 >100 0.0 0.0 >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 TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 59 1.4749999999999999 No Hit AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 45 1.125 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 43 1.075 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 36 0.8999999999999999 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 32 0.8 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 29 0.7250000000000001 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 22bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 27 0.675 Illumina Small RNA Adapter 2 (100% over 21bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 24 0.6 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 23 0.575 RNA PCR Primer, Index 1 (100% over 24bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 23 0.575 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 25bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 21 0.525 RNA PCR Primer, Index 1 (100% over 23bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 21 0.525 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 18 0.44999999999999996 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 17 0.42500000000000004 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 15 0.375 RNA PCR Primer, Index 1 (100% over 25bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 15 0.375 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 15 0.375 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 15 0.375 Illumina Small RNA Adapter 2 (100% over 21bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 15 0.375 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 14 0.35000000000000003 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 14 0.35000000000000003 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 14 0.35000000000000003 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTT 13 0.325 RNA PCR Primer, Index 4 (100% over 50bp) TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 13 0.325 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 12 0.3 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 12 0.3 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 12 0.3 No Hit CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 12 0.3 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 11 0.27499999999999997 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 11 0.27499999999999997 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGT 11 0.27499999999999997 RNA PCR Primer, Index 4 (100% over 50bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 11 0.27499999999999997 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 10 0.25 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 10 0.25 RNA PCR Primer, Index 1 (100% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 10 0.25 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 10 0.25 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 9 0.22499999999999998 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 9 0.22499999999999998 No Hit GAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) CTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTC 9 0.22499999999999998 RNA PCR Primer, Index 4 (100% over 50bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 9 0.22499999999999998 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCG 8 0.2 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGCC 8 0.2 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 8 0.2 No Hit GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 7 0.17500000000000002 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTC 7 0.17500000000000002 RNA PCR Primer, Index 4 (100% over 50bp) ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTC 6 0.15 No Hit GATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) TAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 6 0.15 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 6 0.15 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 6 0.15 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 6 0.15 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 6 0.15 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCT 6 0.15 RNA PCR Primer, Index 4 (100% over 50bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 6 0.15 No Hit ATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGG 6 0.15 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 6 0.15 No Hit CACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGC 6 0.15 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) AGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTC 5 0.125 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCGG 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTCTCGTGGAATTCTCGGGTG 5 0.125 No Hit ATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit ACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAAATGGAATTCTCGGG 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 5 0.125 No Hit TCCACAGGCTTTCTTGAACTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATT 5 0.125 No Hit GCAAGGATTGACAGACTGAGAGCTCTTTCTTGTGGAATTCTCGGGTGCCA 5 0.125 No Hit GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) CCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAAT 5 0.125 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCT 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAATGGAATTCTCGGGT 5 0.125 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 5 0.125 No Hit ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 5 0.125 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 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 0.1 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 0.15 0.0 0.0 0.0 8 0.0 0.15 0.0 0.0 0.0 9 0.0 0.25 0.0 0.0 0.0 10-11 0.0 0.275 0.0 0.0 0.0 12-13 0.0 0.35 0.0 0.0 0.0 14-15 0.0 0.5625 0.0 0.0 0.0 16-17 0.0 0.8875 0.0 0.0 0.0 18-19 0.0 1.3875 0.0 0.0 0.0 20-21 0.0 2.45 0.0 0.0 0.0 22-23 0.0 6.65 0.0 0.0 0.0 24-25 0.0 14.3875 0.0 0.0 0.0 26-27 0.0 24.200000000000003 0.0 0.0 0.0 28-29 0.0 32.0 0.0 0.0 0.0 30-31 0.0 42.3 0.0 0.0 0.0 32-33 0.0 52.075 0.0 0.0 0.0 34-35 0.0 62.8125 0.0 0.0 0.0 36-37 0.0 72.7625 0.0 0.0 0.0 38-39 0.0 79.6875 0.0 0.0 0.0 40-41 0.0 84.225 0.0 0.0 0.0 42-43 0.0 88.45 0.0 0.0 0.0 44-45 0.0 91.5875 0.0 0.0 0.0 46-47 0.0 93.05000000000001 0.0 0.0 0.0 48-49 0.0 93.80000000000001 0.0 0.0 0.0 50-51 0.0 94.1 0.0 0.0 0.0 52-53 0.0 94.25 0.0 0.0 0.0 54-55 0.0 94.3125 0.0 0.0 0.0 56-57 0.0 94.35 0.0 0.0 0.0 58-59 0.0 94.35 0.0 0.0 0.0 60-61 0.0 94.35 0.0 0.0 0.0 62-63 0.0 94.35 0.0 0.0 0.0 64-65 0.0 94.35 0.0 0.0 0.0 66-67 0.0 94.35 0.0 0.0 0.0 68-69 0.0 94.35 0.0 0.0 0.0 70-71 0.0 94.35 0.0 0.0 0.0 72-73 0.0 94.35 0.0 0.0 0.0 74-75 0.0 94.35 0.0 0.0 0.0 76-77 0.0 94.35 0.0 0.0 0.0 78-79 0.0 94.35 0.0 0.0 0.0 80-81 0.0 94.35 0.0 0.0 0.0 82-83 0.0 94.375 0.0 0.0 0.0 84-85 0.0 94.4 0.0 0.0 0.0 86-87 0.0 94.4 0.0 0.0 0.0 88-89 0.0 94.4 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCACTG 15 5.268781E-4 98.66234 1 GGGATTG 25 3.0332922E-7 98.66234 1 CATCGAG 25 3.0332922E-7 98.66234 1 GTAGACC 25 3.837995E-7 94.9625 7 TTGTAGT 25 3.837995E-7 94.9625 5 AGTAGAC 25 3.837995E-7 94.9625 6 TAGCTCA 20 1.5422538E-5 94.9625 8 GGATTGT 25 3.837995E-7 94.9625 2 GATTGTA 25 3.837995E-7 94.9625 3 GAGTAGA 25 3.837995E-7 94.9625 5 TGTAGTT 25 3.837995E-7 94.9625 6 CGAGTAG 25 3.837995E-7 94.9625 4 AGACCTT 25 3.837995E-7 94.9625 9 ATCGAGT 25 3.837995E-7 94.9625 2 TCGAGTA 25 3.837995E-7 94.9625 3 TAGACCT 25 3.837995E-7 94.9625 8 AGCTCAG 15 6.1518257E-4 94.962494 9 TAGTTCA 30 9.48603E-9 94.962494 8 CCACTGA 15 6.1518257E-4 94.962494 2 AGTTCAA 30 9.48603E-9 94.962494 9 >>END_MODULE Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666932 READS because READLEN < 1 Read 666932 spots for SRR8846524.sra Written 666932 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra Rejected 666924 READS because READLEN < 1 Read 666924 spots for SRR8846524.sra Written 666924 spots for SRR8846524.sra SRR ids: ['SRR8846524.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_o53cddk5 SRR8846524.sra spots: 13338488 blocks: [[1, 666924], [666925, 1333848], [1333849, 2000772], [2000773, 2667696], [2667697, 3334620], [3334621, 4001544], [4001545, 4668468], [4668469, 5335392], [5335393, 6002316], [6002317, 6669240], [6669241, 7336164], [7336165, 8003088], [8003089, 8670012], [8670013, 9336936], [9336937, 10003860], [10003861, 10670784], [10670785, 11337708], [11337709, 12004632], [12004633, 12671556], [12671557, 13338488]] SRR8846524 file size 3195688 SRR8846524 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 SRR8846524 SRR8846524_1.fastq Input file: SRR8846524_1.fastq trimmed: SRR8846524-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 Mon Mar 17 01:48:48 2025 >> started Mon Mar 17 01:49:00 2025 >> done (12.050s) 13338488 reads processed; of these: 216 ( 0.00%) short reads filtered out after trimming by size control 31 ( 0.00%) empty reads filtered out after trimming by size control 13338241 (100.00%) reads available; of these: 1949550 (14.62%) trimmed reads available after processing 11388691 (85.38%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 26 0.00% 19 16 0.00% 20 29 0.00% 21 24 0.00% 22 29 0.00% 23 33 0.00% 24 35 0.00% 25 53 0.00% 26 47 0.00% 27 62 0.00% 28 84 0.00% 29 97 0.00% 30 75 0.00% 31 110 0.00% 32 106 0.00% 33 118 0.00% 34 169 0.00% 35 157 0.00% 36 151 0.00% 37 199 0.00% 38 306 0.00% 39 289 0.00% 40 333 0.00% 41 332 0.00% 42 353 0.00% 43 327 0.00% 44 280 0.00% 45 235 0.00% 46 225 0.00% 47 208 0.00% 48 208 0.00% 49 249 0.00% 50 291 0.00% 51 333 0.00% 52 254 0.00% 53 267 0.00% 54 192 0.00% 55 156 0.00% 56 142 0.00% 57 137 0.00% 58 150 0.00% 59 202 0.00% 60 305 0.00% 61 344 0.00% 62 535 0.00% 63 709 0.01% 64 1190 0.01% 65 1618 0.01% 66 3492 0.03% 67 16582 0.12% 68 21500 0.16% 69 16584 0.12% 70 16535 0.12% 71 24719 0.19% 72 11221 0.08% 73 3506 0.03% 74 5525 0.04% 75 3412 0.03% 76 2222 0.02% 77 2139 0.02% 78 2477 0.02% 79 2798 0.02% 80 3111 0.02% 81 3738 0.03% 82 4932 0.04% 83 5350 0.04% 84 5688 0.04% 85 6464 0.05% 86 7383 0.06% 87 9397 0.07% 88 13451 0.10% 89 19427 0.15% 90 27234 0.20% 91 32201 0.24% 92 37472 0.28% 93 58765 0.44% 94 75757 0.57% 95 158034 1.18% 96 202303 1.52% 97 223477 1.68% 98 328393 2.46% 99 362515 2.72% 100 219956 1.65% 101 11388691 85.38% 13338241 reads passed initial QC criterion=sequence-density sequence-density=94.15 sequence-density-rank=1 fanout-score=36.67 fanout-score-rank=2 prefix-density=94.59 prefix-fanout=36.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=2.13 sequence-density-rank=5 fanout-score=46.58 fanout-score-rank=1 prefix-density=98.59 prefix-fanout=1.0 sequence=CACTGACCAATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846524 - Input file: STDIN trimmed: SRR8846524-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGA -- 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 Mon Mar 17 01:49:31 2025 >> started Mon Mar 17 01:49:44 2025 >> done (13.642s) 13057436 reads processed; of these: 151041 ( 1.16%) short reads filtered out after trimming by size control 10208 ( 0.08%) empty reads filtered out after trimming by size control 12896187 (98.77%) reads available; of these: 12632565 (97.96%) trimmed reads available after processing 263622 ( 2.04%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 47854 0.37% 19 86483 0.67% 20 99810 0.77% 21 359226 2.79% 22 233054 1.81% 23 336774 2.61% 24 1124833 8.72% 25 509974 3.95% 26 475228 3.69% 27 502212 3.89% 28 534436 4.14% 29 688952 5.34% 30 805028 6.24% 31 581806 4.51% 32 600087 4.65% 33 696118 5.40% 34 718906 5.57% 35 744224 5.77% 36 691525 5.36% 37 465148 3.61% 38 413139 3.20% 39 330834 2.57% 40 287045 2.23% 41 314704 2.44% 42 309611 2.40% 43 173624 1.35% 44 207564 1.61% 45 101392 0.79% 46 58508 0.45% 47 40520 0.31% 48 35946 0.28% 49 17617 0.14% 50 11169 0.09% 51 10051 0.08% 52 5229 0.04% 53 3966 0.03% 54 3736 0.03% 55 1404 0.01% 56 1017 0.01% 57 676 0.01% 58 517 0.00% 59 421 0.00% 60 361 0.00% 61 359 0.00% 62 502 0.00% 63 673 0.01% 64 1113 0.01% 65 1476 0.01% 66 3299 0.03% 67 16086 0.12% 68 20873 0.16% 69 16013 0.12% 70 15911 0.12% 71 23798 0.18% 72 9949 0.08% 73 2203 0.02% 74 1549 0.01% 75 978 0.01% 76 919 0.01% 77 1575 0.01% 78 1038 0.01% 79 1132 0.01% 80 1639 0.01% 81 1245 0.01% 82 1225 0.01% 83 1532 0.01% 84 875 0.01% 85 755 0.01% 86 707 0.01% 87 664 0.01% 88 530 0.00% 89 517 0.00% 90 593 0.00% 91 625 0.00% 92 673 0.01% 93 718 0.01% 94 877 0.01% 95 1122 0.01% 96 1514 0.01% 97 2185 0.02% 98 3139 0.02% 99 3414 0.03% 100 4497 0.03% 101 116966 0.91% criterion=sequence-density sequence-density=6.31 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=16 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=35.04 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=1.1 sequence=AAGGAGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCA Started job on | Mar 17 01:50:18 Started mapping on | Mar 17 01:50:18 Finished on | Mar 17 01:51:12 Mapping speed, Million of reads per hour | 878.47 Number of input reads | 13176992 Average input read length | 34 UNIQUE READS: Uniquely mapped reads number | 1803638 Uniquely mapped reads % | 13.69% Average mapped length | 28.60 Number of splices: Total | 36092 Number of splices: Annotated (sjdb) | 24444 Number of splices: GT/AG | 34153 Number of splices: GC/AG | 1294 Number of splices: AT/AC | 20 Number of splices: Non-canonical | 625 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4509387 % of reads mapped to multiple loci | 34.22% Number of reads mapped to too many loci | 5975439 % of reads mapped to too many loci | 45.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.16% % of reads unmapped: other | 0.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6863967 6863967 6863967 N_multimapping 4509387 4509387 4509387 N_noFeature 953984 1097462 1649887 N_ambiguous 31354 20806 412 UnstrandedReadsAssigned:818300 PositiveStrandReadsAssigned:685370 NegativeStrandReadsAssigned:153339 Dataset is classified unstranded MeadianReadLen=32 20thPercentileLength=25 echo kmer=21 SRR8846524 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=21 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 21 [index] number of targets: 52,972 [index] number of k-mers: 65,978,135 [index] number of equivalence classes: 190,841 [quant] running in single-end mode [quant] will process file 1: SRR8846524-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,176,992 reads, 3,518,310 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 932 rounds 52973 SRR8846524.ke.tsv 35125 SRR8846524.se.tsv 88098 total ==> SRR8846524.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 2.41133 0.29319 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.58867 0.419594 PNS24243 293 194 2 2.29263 KQK14069 1603 1504 32.5103 4.80707 KQK14071 474 375 8.28189 4.91139 ==> SRR8846524.se.tsv <== BRADI_1g14170v3 136 BRADI_1g53295v3 1 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 29 BRADI_1g74790v3 18 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846524 completed mapping pipeline successfully