Starting /dee2/code/volunteer_pipeline.sh SRR8846507 current disk space = 1507324059648 free memory = 1423752636 SRR8846507 SRAfilesize c29eae5abba990722fee54dab6fcb255 SRR8846507.sra SRR8846507.sra file validated SRR8846507 is single end SRR8846507 is conventional basespace SRR8846507 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846507_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 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.7275 34.0 33.0 34.0 2.0 34.0 2 32.37125 34.0 33.0 34.0 28.0 34.0 3 32.69525 34.0 33.0 34.0 28.0 34.0 4 33.0485 34.0 33.0 34.0 32.0 34.0 5 33.14475 34.0 33.0 34.0 32.0 34.0 6 36.7315 38.0 37.0 38.0 35.0 38.0 7 37.09975 38.0 38.0 38.0 36.0 38.0 8 37.37425 38.0 38.0 38.0 37.0 38.0 9 37.435 38.0 38.0 38.0 37.0 38.0 10-11 37.48425 38.0 38.0 38.0 37.0 38.0 12-13 37.52675 38.0 38.0 38.0 38.0 38.0 14-15 37.444 38.0 38.0 38.0 37.5 38.0 16-17 37.400125 38.0 38.0 38.0 37.0 38.0 18-19 37.451499999999996 38.0 38.0 38.0 37.0 38.0 20-21 37.43275 38.0 38.0 38.0 37.0 38.0 22-23 37.4945 38.0 38.0 38.0 37.5 38.0 24-25 37.495999999999995 38.0 38.0 38.0 38.0 38.0 26-27 37.49025 38.0 38.0 38.0 38.0 38.0 28-29 37.39975 38.0 38.0 38.0 37.5 38.0 30-31 37.36725 38.0 38.0 38.0 37.0 38.0 32-33 37.31825 38.0 38.0 38.0 37.0 38.0 34-35 37.090125 38.0 38.0 38.0 36.5 38.0 36-37 36.979625 38.0 38.0 38.0 36.0 38.0 38-39 36.877375 38.0 38.0 38.0 35.5 38.0 40-41 36.953374999999994 38.0 38.0 38.0 36.0 38.0 42-43 37.021625 38.0 38.0 38.0 36.5 38.0 44-45 37.1055 38.0 38.0 38.0 36.5 38.0 46-47 37.149874999999994 38.0 38.0 38.0 36.5 38.0 48-49 37.16675 38.0 38.0 38.0 36.5 38.0 50-51 37.182375 38.0 38.0 38.0 37.0 38.0 52-53 37.195625 38.0 38.0 38.0 37.0 38.0 54-55 37.110875 38.0 38.0 38.0 36.5 38.0 56-57 36.954125000000005 38.0 38.0 38.0 36.0 38.0 58-59 36.9045 38.0 38.0 38.0 35.5 38.0 60-61 36.75275 38.0 38.0 38.0 35.5 38.0 62-63 36.022625 38.0 37.5 38.0 30.5 38.0 64-65 35.7975 38.0 37.0 38.0 29.5 38.0 66-67 35.54025 38.0 36.5 38.0 28.5 38.0 68-69 35.216499999999996 38.0 36.0 38.0 28.0 38.0 70-71 35.126000000000005 38.0 37.0 38.0 27.5 38.0 72-73 35.116875 38.0 37.0 38.0 27.5 38.0 74-75 34.816375 38.0 36.0 38.0 27.0 38.0 76-77 34.831625 38.0 36.5 38.0 27.0 38.0 78-79 34.83525 38.0 36.5 38.0 27.5 38.0 80-81 34.869749999999996 38.0 37.0 38.0 27.0 38.0 82-83 34.675875000000005 38.0 36.5 38.0 26.0 38.0 84-85 34.737625 38.0 36.5 38.0 27.0 38.0 86-87 34.71325 38.0 37.0 38.0 27.0 38.0 88-89 34.609125 38.0 37.0 38.0 26.5 38.0 90-91 34.3835 38.0 37.0 38.0 25.5 38.0 92-93 34.031125 38.0 36.5 38.0 19.5 38.0 94-95 32.85525 38.0 35.0 38.0 8.5 38.0 96-97 30.698500000000003 38.0 32.5 38.0 2.0 38.0 98-99 28.633 38.0 20.5 38.0 2.0 38.0 100-101 26.24575 36.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 0.0 6 0.0 7 0.0 8 1.0 9 1.0 10 0.0 11 0.0 12 0.0 13 1.0 14 0.0 15 0.0 16 2.0 17 2.0 18 0.0 19 1.0 20 2.0 21 2.0 22 7.0 23 10.0 24 21.0 25 36.0 26 40.0 27 25.0 28 33.0 29 30.0 30 72.0 31 87.0 32 111.0 33 168.0 34 283.0 35 456.0 36 829.0 37 1779.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.9859943977591 23.669467787114844 20.896358543417367 20.448179271708682 2 26.325 28.175 18.35 27.150000000000002 3 26.974999999999998 20.45 18.775 33.800000000000004 4 26.900000000000002 33.45 17.2 22.45 5 27.200000000000003 23.775 22.8 26.224999999999998 6 26.55 26.474999999999998 25.025 21.95 7 36.425000000000004 25.924999999999997 18.675 18.975 8 19.85 21.5 35.4 23.25 9 24.625 33.425 23.400000000000002 18.55 10-11 29.612500000000004 22.5625 26.775 21.05 12-13 22.975 21.4 23.175 32.45 14-15 25.05 35.4125 20.2875 19.25 16-17 23.8625 28.6875 29.812499999999996 17.6375 18-19 33.4625 23.3 21.025 22.2125 20-21 23.275000000000002 28.799999999999997 26.0 21.925 22-23 27.450000000000003 30.112499999999997 27.950000000000003 14.4875 24-25 27.450000000000003 27.250000000000004 25.974999999999998 19.325 26-27 28.425 26.9625 25.087500000000002 19.525000000000002 28-29 24.175 25.5 26.0125 24.3125 30-31 28.050000000000004 20.1875 30.5125 21.25 32-33 26.150000000000002 19.0 31.95 22.900000000000002 34-35 31.112499999999997 16.275000000000002 30.662499999999998 21.95 36-37 33.0625 17.05 28.9375 20.95 38-39 34.050000000000004 19.0875 26.2625 20.599999999999998 40-41 31.362499999999997 18.787499999999998 24.75 25.1 42-43 31.95 22.05 21.075 24.925 44-45 35.325 21.837500000000002 15.962499999999999 26.875 46-47 31.825 27.0 15.725 25.45 48-49 28.625 25.887500000000003 16.037499999999998 29.45 50-51 22.725 27.500000000000004 15.537500000000001 34.2375 52-53 23.075000000000003 29.525000000000002 13.362499999999999 34.0375 54-55 19.8875 29.7125 14.5375 35.862500000000004 56-57 19.275000000000002 28.849999999999998 13.925 37.95 58-59 15.387500000000001 28.9375 13.175 42.5 60-61 15.975 27.025 12.7 44.3 62-63 19.7625 25.387500000000003 15.25 39.6 64-65 18.9375 25.4625 17.5875 38.012499999999996 66-67 18.9 22.1 20.2625 38.737500000000004 68-69 19.2 21.475 21.5375 37.7875 70-71 22.0625 19.037499999999998 24.325 34.575 72-73 26.174999999999997 16.662499999999998 26.575 30.587500000000002 74-75 21.7 15.299999999999999 30.0875 32.9125 76-77 21.45 12.4375 35.112500000000004 31.0 78-79 21.224999999999998 10.325 35.525 32.925 80-81 20.825 11.200000000000001 37.325 30.65 82-83 20.3875 12.0125 41.0125 26.5875 84-85 20.5625 14.2375 36.275 28.925 86-87 19.4625 20.4375 34.362500000000004 25.7375 88-89 15.287500000000001 31.362499999999997 35.025 18.325 90-91 14.149999999999999 41.6375 28.425 15.787499999999998 92-93 12.2125 52.300000000000004 21.3625 14.124999999999998 94-95 10.65 61.2375 18.912499999999998 9.2 96-97 8.075000000000001 71.2 13.9625 6.7625 98-99 6.3375 79.53750000000001 9.55 4.575 100-101 4.0375000000000005 84.8 6.0375 5.125 >>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 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 1.0 35 3.5 36 7.5 37 8.0 38 9.5 39 17.5 40 24.5 41 58.5 42 82.5 43 123.0 44 177.0 45 204.0 46 284.5 47 326.5 48 371.5 49 413.0 50 383.0 51 330.0 52 293.5 53 257.0 54 170.5 55 107.5 56 94.5 57 118.5 58 81.0 59 15.5 60 6.0 61 10.5 62 9.5 63 4.5 64 3.5 65 2.0 66 0.5 67 0.5 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 10.75 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 59.8 #Duplication Level Percentage of deduplicated Percentage of total 1 84.65719063545151 50.625 2 6.981605351170568 8.35 3 3.2190635451505014 5.775 4 1.4214046822742474 3.4000000000000004 5 0.794314381270903 2.375 6 0.459866220735786 1.6500000000000001 7 0.459866220735786 1.925 8 0.33444816053511706 1.6 9 0.2508361204013378 1.35 >10 1.2123745819397993 14.249999999999998 >50 0.20903010033444816 8.7 >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 GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 86 2.15 RNA PCR Primer, Index 1 (100% over 23bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 78 1.95 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 77 1.925 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 56 1.4000000000000001 RNA PCR Primer, Index 1 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 51 1.275 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 50 1.25 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 42 1.05 RNA PCR Primer, Index 1 (100% over 24bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 40 1.0 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 25bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 33 0.8250000000000001 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 28 0.7000000000000001 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGTCTTC 25 0.625 RNA PCR Primer, Index 30 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 23 0.575 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 22 0.5499999999999999 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGTCTT 20 0.5 RNA PCR Primer, Index 30 (100% over 50bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 17 0.42500000000000004 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 25bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGT 15 0.375 RNA PCR Primer, Index 30 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 15 0.375 RNA PCR Primer, Index 1 (100% over 23bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 13 0.325 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 12 0.3 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 11 0.27499999999999997 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 10 0.25 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 10 0.25 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 10 0.25 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 10 0.25 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTATGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 26bp) GACACGACTCTCGGCAACGGATATGGAATTCTCGGGTGCCAAGGAACTCC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 27bp) TTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGTCT 9 0.22499999999999998 RNA PCR Primer, Index 30 (100% over 50bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGTC 9 0.22499999999999998 RNA PCR Primer, Index 30 (100% over 50bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 8 0.2 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 7 0.17500000000000002 No Hit GCACCAGTAGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 7 0.17500000000000002 No Hit ACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) TGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit NACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGGTGGAATTC 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 6 0.15 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 6 0.15 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 6 0.15 RNA PCR Primer, Index 1 (100% over 29bp) NCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 6 0.15 No Hit ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) TCCAGAAAGGATGTAAGGAAGCTGAAGCGGAAATGGAATTCTCGGGTGCC 6 0.15 No Hit NACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) CCCCGAGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATC 6 0.15 RNA PCR Primer, Index 30 (100% over 42bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit NGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCTC 5 0.125 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 5 0.125 No Hit GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) ATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) AAGTATGAACTAATTTGAACTGTGAAACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGTGGAATT 5 0.125 No Hit ACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) TAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) NATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGT 5 0.125 RNA PCR Primer, Index 30 (98% over 50bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 5 0.125 No Hit GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 5 0.125 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 5 0.125 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 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 0.05 0.0 0.0 0.0 2 0.0 0.05 0.0 0.0 0.0 3 0.0 0.05 0.0 0.0 0.0 4 0.0 0.05 0.0 0.0 0.0 5 0.0 0.05 0.0 0.0 0.0 6 0.0 0.05 0.0 0.0 0.0 7 0.0 0.075 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.4 0.0 0.0 0.0 10-11 0.0 0.5625 0.0 0.0 0.0 12-13 0.0 0.8625 0.0 0.0 0.0 14-15 0.0 1.4375 0.0 0.0 0.0 16-17 0.0 2.6875 0.0 0.0 0.0 18-19 0.0 4.1 0.0 0.0 0.0 20-21 0.0 7.2125 0.0 0.0 0.0 22-23 0.0 14.662500000000001 0.0 0.0 0.0 24-25 0.0 23.25 0.0 0.0 0.0 26-27 0.0 33.8375 0.0 0.0 0.0 28-29 0.0 45.55 0.0 0.0 0.0 30-31 0.0 55.224999999999994 0.0 0.0 0.0 32-33 0.0 64.26249999999999 0.0 0.0 0.0 34-35 0.0 74.6875 0.0 0.0 0.0 36-37 0.0 82.925 0.0 0.0 0.0 38-39 0.0 87.5625 0.0 0.0 0.0 40-41 0.0 89.975 0.0 0.0 0.0 42-43 0.0 91.975 0.0 0.0 0.0 44-45 0.0 93.4 0.0 0.0 0.0 46-47 0.0 93.875 0.0 0.0 0.0 48-49 0.0 93.975 0.0 0.0 0.0 50-51 0.0 94.025 0.0 0.0 0.0 52-53 0.0 94.0625 0.0 0.0 0.0 54-55 0.0 94.0875 0.0 0.0 0.0 56-57 0.0 94.125 0.0 0.0 0.0 58-59 0.0 94.125 0.0 0.0 0.0 60-61 0.0 94.125 0.0 0.0 0.0 62-63 0.0 94.125 0.0 0.0 0.0 64-65 0.0 94.125 0.0 0.0 0.0 66-67 0.0 94.125 0.0 0.0 0.0 68-69 0.0 94.125 0.0 0.0 0.0 70-71 0.0 94.1375 0.0 0.0 0.0 72-73 0.0 94.1625 0.0 0.0 0.0 74-75 0.0 94.175 0.0 0.0 0.0 76-77 0.0 94.175 0.0 0.0 0.0 78-79 0.0 94.175 0.0 0.0 0.0 80-81 0.0 94.175 0.0 0.0 0.0 82-83 0.0 94.1875 0.0 0.0 0.0 84-85 0.0 94.225 0.0 0.0 0.0 86-87 0.0 94.225 0.0 0.0 0.0 88-89 0.0 94.25 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCACTG 15 3.8020255E-4 106.9155 1 TCCGTCG 15 3.8020255E-4 106.9155 1 CATCGAG 15 3.8020255E-4 106.9155 1 GTAGACC 15 6.17118E-4 94.887505 7 AGTAGAC 15 6.17118E-4 94.887505 6 GTCGTAG 15 6.17118E-4 94.887505 4 CGTAGTC 15 6.17118E-4 94.887505 6 TAGTTCA 15 6.17118E-4 94.887505 8 GAGTAGA 15 6.17118E-4 94.887505 5 CGAGTAG 15 6.17118E-4 94.887505 4 CGTCGTA 15 6.17118E-4 94.887505 3 AGACCTT 15 6.17118E-4 94.887505 9 ATCGAGT 15 6.17118E-4 94.887505 2 TCGAGTA 15 6.17118E-4 94.887505 3 AGTTCAA 15 6.17118E-4 94.887505 9 GTAGTTC 15 6.17118E-4 94.887505 7 TAGACCT 15 6.17118E-4 94.887505 8 TAGTCTA 20 1.5483185E-5 94.8875 8 AGTCTAG 20 1.5483185E-5 94.8875 9 GTAGTCT 20 1.5483185E-5 94.8875 7 >>END_MODULE Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249286 READS because READLEN < 1 Read 1249286 spots for SRR8846507.sra Written 1249286 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra Rejected 1249276 READS because READLEN < 1 Read 1249276 spots for SRR8846507.sra Written 1249276 spots for SRR8846507.sra SRR ids: ['SRR8846507.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yil_avkj SRR8846507.sra spots: 24985530 blocks: [[1, 1249276], [1249277, 2498552], [2498553, 3747828], [3747829, 4997104], [4997105, 6246380], [6246381, 7495656], [7495657, 8744932], [8744933, 9994208], [9994209, 11243484], [11243485, 12492760], [12492761, 13742036], [13742037, 14991312], [14991313, 16240588], [16240589, 17489864], [17489865, 18739140], [18739141, 19988416], [19988417, 21237692], [21237693, 22486968], [22486969, 23736244], [23736245, 24985530]] SRR8846507 file size 6005082 SRR8846507 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 SRR8846507 SRR8846507_1.fastq Input file: SRR8846507_1.fastq trimmed: SRR8846507-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 Dec 9 03:31:31 2024 >> started Mon Dec 9 03:32:37 2024 >> done (66.123s) 24985530 reads processed; of these: 641 ( 0.00%) short reads filtered out after trimming by size control 88 ( 0.00%) empty reads filtered out after trimming by size control 24984801 (100.00%) reads available; of these: 5995535 (24.00%) trimmed reads available after processing 18989266 (76.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 80 0.00% 19 57 0.00% 20 83 0.00% 21 104 0.00% 22 105 0.00% 23 138 0.00% 24 156 0.00% 25 234 0.00% 26 287 0.00% 27 361 0.00% 28 509 0.00% 29 685 0.00% 30 612 0.00% 31 641 0.00% 32 629 0.00% 33 608 0.00% 34 615 0.00% 35 551 0.00% 36 512 0.00% 37 441 0.00% 38 410 0.00% 39 416 0.00% 40 323 0.00% 41 336 0.00% 42 356 0.00% 43 375 0.00% 44 444 0.00% 45 485 0.00% 46 403 0.00% 47 416 0.00% 48 432 0.00% 49 444 0.00% 50 507 0.00% 51 503 0.00% 52 550 0.00% 53 674 0.00% 54 775 0.00% 55 795 0.00% 56 1062 0.00% 57 1220 0.00% 58 1423 0.01% 59 1767 0.01% 60 2151 0.01% 61 3602 0.01% 62 5420 0.02% 63 5342 0.02% 64 9231 0.04% 65 10953 0.04% 66 23902 0.10% 67 92587 0.37% 68 107615 0.43% 69 72471 0.29% 70 62381 0.25% 71 78936 0.32% 72 32578 0.13% 73 11855 0.05% 74 16877 0.07% 75 10288 0.04% 76 8658 0.03% 77 7872 0.03% 78 10281 0.04% 79 10636 0.04% 80 14039 0.06% 81 17836 0.07% 82 34521 0.14% 83 31202 0.12% 84 25894 0.10% 85 29228 0.12% 86 37211 0.15% 87 42968 0.17% 88 69347 0.28% 89 96529 0.39% 90 141303 0.57% 91 146123 0.58% 92 186775 0.75% 93 294178 1.18% 94 333554 1.34% 95 593358 2.37% 96 630246 2.52% 97 656353 2.63% 98 737843 2.95% 99 757469 3.03% 100 514398 2.06% 101 18989266 76.00% 24984801 reads passed initial QC criterion=sequence-density sequence-density=94.20 sequence-density-rank=1 fanout-score=36.11 fanout-score-rank=2 prefix-density=94.55 prefix-fanout=36.0 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.70 sequence-density-rank=6 fanout-score=58.47 fanout-score-rank=1 prefix-density=98.62 prefix-fanout=1.0 sequence=CACCACCGGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846507 - Input file: STDIN trimmed: SRR8846507-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCACCGGATCTCGTATGCCGTCTTCTGCTTGA -- 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 Dec 9 03:36:47 2024 >> started Mon Dec 9 03:38:46 2024 >> done (119.595s) 24458805 reads processed; of these: 808069 ( 3.30%) short reads filtered out after trimming by size control 28258 ( 0.12%) empty reads filtered out after trimming by size control 23622478 (96.58%) reads available; of these: 22763010 (96.36%) trimmed reads available after processing 859468 ( 3.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 234212 0.99% 19 414098 1.75% 20 420798 1.78% 21 1186287 5.02% 22 721673 3.06% 23 925959 3.92% 24 1889902 8.00% 25 1150581 4.87% 26 1254918 5.31% 27 1536347 6.50% 28 1315431 5.57% 29 1168060 4.94% 30 1336351 5.66% 31 895326 3.79% 32 1379632 5.84% 33 1304209 5.52% 34 1164097 4.93% 35 996467 4.22% 36 1110037 4.70% 37 464707 1.97% 38 360714 1.53% 39 302104 1.28% 40 275848 1.17% 41 259989 1.10% 42 294359 1.25% 43 132861 0.56% 44 113427 0.48% 45 52457 0.22% 46 26320 0.11% 47 13685 0.06% 48 10981 0.05% 49 6907 0.03% 50 4834 0.02% 51 4188 0.02% 52 2732 0.01% 53 2091 0.01% 54 2354 0.01% 55 949 0.00% 56 1457 0.01% 57 874 0.00% 58 985 0.00% 59 1167 0.00% 60 1429 0.01% 61 2873 0.01% 62 4492 0.02% 63 4310 0.02% 64 8078 0.03% 65 9741 0.04% 66 22305 0.09% 67 89554 0.38% 68 103998 0.44% 69 69599 0.29% 70 59324 0.25% 71 75263 0.32% 72 27564 0.12% 73 6862 0.03% 74 4741 0.02% 75 3581 0.02% 76 4241 0.02% 77 5597 0.02% 78 4322 0.02% 79 4126 0.02% 80 7610 0.03% 81 6087 0.03% 82 5081 0.02% 83 8510 0.04% 84 3354 0.01% 85 3081 0.01% 86 2942 0.01% 87 2593 0.01% 88 1943 0.01% 89 2241 0.01% 90 1809 0.01% 91 1876 0.01% 92 2112 0.01% 93 2464 0.01% 94 2369 0.01% 95 3199 0.01% 96 4439 0.02% 97 6438 0.03% 98 8828 0.04% 99 10360 0.04% 100 13270 0.06% 101 269497 1.14% criterion=sequence-density sequence-density=3.95 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAG criterion=fanout-score sequence-density=0.36 sequence-density-rank=13 fanout-score=9.67 fanout-score-rank=1 prefix-density=1.11 prefix-fanout=3.1 sequence=ATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGA Started job on | Dec 09 03:41:24 Started mapping on | Dec 09 03:41:24 Finished on | Dec 09 03:53:00 Mapping speed, Million of reads per hour | 124.91 Number of input reads | 24148474 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 3000017 Uniquely mapped reads % | 12.42% Average mapped length | 27.78 Number of splices: Total | 47759 Number of splices: Annotated (sjdb) | 30914 Number of splices: GT/AG | 43204 Number of splices: GC/AG | 3735 Number of splices: AT/AC | 33 Number of splices: Non-canonical | 787 Mismatch rate per base, % | 0.17% Deletion rate per base | 0.00% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.05 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 8636412 % of reads mapped to multiple loci | 35.76% Number of reads mapped to too many loci | 10829426 % of reads mapped to too many loci | 44.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.55% % of reads unmapped: other | 0.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 12512045 12512045 12512045 N_multimapping 8636412 8636412 8636412 N_noFeature 1567163 1759530 2784397 N_ambiguous 67875 44256 553 UnstrandedReadsAssigned:1364979 PositiveStrandReadsAssigned:1196231 NegativeStrandReadsAssigned:215067 Dataset is classified positive stranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846507 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: SRR8846507-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,148,474 reads, 3,647,554 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 989 rounds 52973 SRR8846507.ke.tsv 35125 SRR8846507.se.tsv 88098 total ==> SRR8846507.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.50226 0.180985 PNS24249 1928 1829 4.19203 0.78047 PNS24246 1044 945 0.50226 0.180985 PNS24248 1044 945 0.50226 0.180985 PNS24244 1471 1372 3.30119 0.819335 PNS24243 293 194 0 0 KQK14069 1603 1504 327.244 74.0917 KQK14071 474 375 3.86178 3.50672 ==> SRR8846507.se.tsv <== BRADI_1g14170v3 375 BRADI_1g53295v3 4 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 31 BRADI_1g74790v3 21 BRADI_1g09890v3 0 BRADI_1g77505v3 5 BRADI_1g48960v3 0 SRR8846507 completed mapping pipeline successfully