Starting /dee2/code/volunteer_pipeline.sh SRR8846482 current disk space = 1505588580352 free memory = 1349341464 SRR8846482 SRAfilesize 4fdb50ccebe03af411dfd7bb264a599e SRR8846482.sra SRR8846482.sra file validated SRR8846482 is single end SRR8846482 is conventional basespace SRR8846482 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846482_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 31.35625 34.0 33.0 34.0 31.0 34.0 2 32.91175 34.0 33.0 34.0 31.0 34.0 3 33.0385 34.0 33.0 34.0 32.0 34.0 4 33.20175 34.0 33.0 34.0 32.0 34.0 5 33.26175 34.0 33.0 34.0 33.0 34.0 6 36.899 38.0 37.0 38.0 36.0 38.0 7 37.25825 38.0 38.0 38.0 36.0 38.0 8 37.473 38.0 38.0 38.0 37.0 38.0 9 37.529 38.0 38.0 38.0 37.0 38.0 10-11 37.459875 38.0 38.0 38.0 37.5 38.0 12-13 37.515 38.0 38.0 38.0 38.0 38.0 14-15 37.4725 38.0 38.0 38.0 37.0 38.0 16-17 37.438375 38.0 38.0 38.0 37.0 38.0 18-19 37.534125 38.0 38.0 38.0 37.5 38.0 20-21 37.456 38.0 38.0 38.0 37.0 38.0 22-23 37.412125 38.0 38.0 38.0 37.0 38.0 24-25 37.505875 38.0 38.0 38.0 38.0 38.0 26-27 37.426625 38.0 38.0 38.0 37.0 38.0 28-29 37.43125 38.0 38.0 38.0 37.0 38.0 30-31 37.446125 38.0 38.0 38.0 37.0 38.0 32-33 37.464124999999996 38.0 38.0 38.0 37.0 38.0 34-35 37.28875 38.0 38.0 38.0 37.0 38.0 36-37 37.162 38.0 38.0 38.0 37.0 38.0 38-39 37.04025 38.0 38.0 38.0 36.0 38.0 40-41 37.157875 38.0 38.0 38.0 36.5 38.0 42-43 37.0945 38.0 38.0 38.0 36.0 38.0 44-45 37.089 38.0 38.0 38.0 36.5 38.0 46-47 37.051874999999995 38.0 38.0 38.0 36.0 38.0 48-49 37.07575 38.0 38.0 38.0 36.0 38.0 50-51 37.06225 38.0 38.0 38.0 36.5 38.0 52-53 37.085125000000005 38.0 38.0 38.0 36.0 38.0 54-55 36.966499999999996 38.0 38.0 38.0 36.0 38.0 56-57 36.896874999999994 38.0 38.0 38.0 35.5 38.0 58-59 36.93875 38.0 38.0 38.0 36.0 38.0 60-61 36.5905 38.0 38.0 38.0 34.0 38.0 62-63 36.46825 38.0 38.0 38.0 34.0 38.0 64-65 36.260999999999996 38.0 37.5 38.0 32.5 38.0 66-67 36.068625 38.0 37.0 38.0 31.5 38.0 68-69 35.731624999999994 38.0 37.0 38.0 31.0 38.0 70-71 35.329375 38.0 37.0 38.0 29.0 38.0 72-73 34.988625 38.0 37.0 38.0 28.0 38.0 74-75 34.66275 38.0 36.5 38.0 26.5 38.0 76-77 34.244 38.0 36.0 38.0 25.0 38.0 78-79 34.038375 38.0 35.5 38.0 24.5 38.0 80-81 33.952 38.0 35.0 38.0 20.5 38.0 82-83 33.832375 38.0 34.5 38.0 24.0 38.0 84-85 33.720124999999996 38.0 34.0 38.0 16.0 38.0 86-87 33.745125 38.0 34.5 38.0 15.5 38.0 88-89 34.3225 38.0 36.0 38.0 25.0 38.0 90-91 33.899375 38.0 35.5 38.0 15.5 38.0 92-93 33.867 38.0 35.5 38.0 19.5 38.0 94-95 32.952375 38.0 34.0 38.0 15.0 38.0 96-97 32.081375 38.0 33.5 38.0 8.5 38.0 98-99 30.907875 38.0 32.0 38.0 2.0 38.0 100-101 28.583 38.0 24.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 8 0.0 9 0.0 10 0.0 11 1.0 12 0.0 13 0.0 14 0.0 15 0.0 16 2.0 17 0.0 18 1.0 19 0.0 20 3.0 21 4.0 22 10.0 23 11.0 24 31.0 25 47.0 26 39.0 27 20.0 28 34.0 29 40.0 30 44.0 31 84.0 32 99.0 33 146.0 34 225.0 35 420.0 36 890.0 37 1848.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.22222222222222 27.433862433862434 17.962962962962965 27.380952380952383 2 24.5 32.875 18.6 24.025 3 23.9 20.349999999999998 24.0 31.75 4 27.224999999999998 27.150000000000002 19.975 25.650000000000002 5 34.2 26.275 18.75 20.775 6 26.400000000000002 32.75 21.675 19.175 7 35.099999999999994 25.6 21.2 18.099999999999998 8 24.0 21.825 33.275 20.9 9 23.05 35.625 22.35 18.975 10-11 31.724999999999998 27.675 21.087500000000002 19.5125 12-13 22.6 25.587500000000002 19.375 32.4375 14-15 23.5125 35.2375 24.775 16.475 16-17 26.5875 28.4125 27.8125 17.1875 18-19 29.799999999999997 28.825 23.549999999999997 17.825 20-21 20.3375 29.95 28.9125 20.8 22-23 26.987499999999997 29.349999999999998 26.924999999999997 16.7375 24-25 26.8125 28.4125 24.462500000000002 20.3125 26-27 33.9125 27.35 21.525 17.2125 28-29 23.1375 30.7375 26.525 19.6 30-31 25.025 20.6375 36.175000000000004 18.1625 32-33 24.675 21.0125 32.875 21.4375 34-35 25.687500000000004 21.4375 30.337500000000002 22.537499999999998 36-37 32.65 16.25 32.487500000000004 18.6125 38-39 29.8875 20.525 29.9625 19.625 40-41 28.962500000000002 17.712500000000002 28.499999999999996 24.825 42-43 30.175 22.075 26.187500000000004 21.5625 44-45 37.6125 17.875 21.0375 23.474999999999998 46-47 33.375 25.525 16.950000000000003 24.15 48-49 28.9375 22.8 22.4625 25.8 50-51 27.700000000000003 20.8125 17.3625 34.125 52-53 26.137500000000003 31.0 14.475 28.3875 54-55 25.4 24.425 20.3875 29.7875 56-57 21.75 30.6875 16.3875 31.175000000000004 58-59 19.375 27.450000000000003 24.9 28.275 60-61 18.725 30.55 19.5625 31.162499999999998 62-63 20.599999999999998 29.037499999999998 19.825 30.5375 64-65 16.9125 28.8875 28.199999999999996 26.0 66-67 17.7375 26.187500000000004 25.937500000000004 30.1375 68-69 18.5375 22.8 27.625 31.0375 70-71 19.1875 25.874999999999996 30.662499999999998 24.275 72-73 24.1375 18.95 29.925 26.987499999999997 74-75 19.9625 18.3 28.762500000000003 32.975 76-77 19.525000000000002 15.950000000000001 37.15 27.375 78-79 21.6625 12.049999999999999 35.3375 30.95 80-81 20.75 12.1 35.4375 31.7125 82-83 21.8875 12.1625 39.4625 26.487500000000004 84-85 19.45 10.5375 38.15 31.8625 86-87 21.8 12.9 37.724999999999994 27.575 88-89 18.212500000000002 23.4375 35.15 23.200000000000003 90-91 14.2125 29.525000000000002 36.125 20.1375 92-93 16.3875 37.225 27.987499999999997 18.4 94-95 12.925 48.025 23.724999999999998 15.325 96-97 10.3875 56.65 22.975 9.9875 98-99 9.0125 67.575 15.45 7.9625 100-101 6.5625 75.05 12.0 6.3875 >>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 0.5 28 0.5 29 0.0 30 0.0 31 0.0 32 2.5 33 7.0 34 12.5 35 19.5 36 25.5 37 27.0 38 27.0 39 49.5 40 63.5 41 85.0 42 132.0 43 176.5 44 314.5 45 374.5 46 331.0 47 338.5 48 341.0 49 348.0 50 361.5 51 295.5 52 171.0 53 124.5 54 115.0 55 108.5 56 78.5 57 29.0 58 13.5 59 6.0 60 5.0 61 6.5 62 2.5 63 4.0 64 3.0 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 warn #Base N-Count 1 5.5 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 55.35 #Duplication Level Percentage of deduplicated Percentage of total 1 83.10749774164408 46.0 2 7.723577235772358 8.55 3 2.9810298102981028 4.95 4 1.8066847335140017 4.0 5 0.40650406504065045 1.125 6 0.49683830171635046 1.6500000000000001 7 0.49683830171635046 1.925 8 0.49683830171635046 2.1999999999999997 9 0.31616982836495033 1.575 >10 2.077687443541102 24.9 >50 0.09033423667570009 3.125 >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 AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 70 1.7500000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 55 1.375 Illumina Small RNA Adapter 2 (100% over 21bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 45 1.125 No Hit AATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGT 45 1.125 RNA PCR Primer, Index 3 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 41 1.0250000000000001 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTT 39 0.975 RNA PCR Primer, Index 3 (100% over 50bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 38 0.95 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 38 0.95 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 36 0.8999999999999999 RNA PCR Primer, Index 1 (100% over 22bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 36 0.8999999999999999 No Hit CTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTC 33 0.8250000000000001 RNA PCR Primer, Index 3 (100% over 50bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 30 0.75 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 29 0.7250000000000001 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 24bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 25bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 27 0.675 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 27 0.675 Illumina Small RNA Adapter 2 (100% over 21bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 26 0.65 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 25 0.625 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 24 0.6 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 20 0.5 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCT 19 0.475 RNA PCR Primer, Index 3 (100% over 50bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 19 0.475 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 19 0.475 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 17 0.42500000000000004 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 17 0.42500000000000004 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 17 0.42500000000000004 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 16 0.4 Illumina Small RNA Adapter 2 (100% over 21bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 16 0.4 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 14 0.35000000000000003 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 13 0.325 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 13 0.325 RNA PCR Primer, Index 1 (100% over 25bp) AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 13 0.325 No Hit ATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTC 13 0.325 RNA PCR Primer, Index 3 (100% over 50bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 12 0.3 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 12 0.3 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 12 0.3 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 12 0.3 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAATGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 11 0.27499999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 11 0.27499999999999997 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGAATT 11 0.27499999999999997 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTC 10 0.25 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGGAATTCTCG 10 0.25 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTG 9 0.22499999999999998 No Hit CAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATT 9 0.22499999999999998 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 9 0.22499999999999998 Illumina Small RNA Adapter 2 (100% over 21bp) ATAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 23bp) CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 8 0.2 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 8 0.2 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTC 8 0.2 No Hit GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 8 0.2 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 8 0.2 No Hit TGCCACGATCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAAT 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 8 0.2 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACCGAGATGGAAT 8 0.2 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 8 0.2 No Hit GCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGT 7 0.17500000000000002 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 7 0.17500000000000002 No Hit CCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) ACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTCT 7 0.17500000000000002 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 7 0.17500000000000002 No Hit CTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TCGTGACCCTGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTA 6 0.15 RNA PCR Primer, Index 3 (100% over 36bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 6 0.15 No Hit TGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCT 6 0.15 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 6 0.15 No Hit TAACCGTAGTAATTCTAGAGCTAATATGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAATGGAATTCTCGGGTGCC 6 0.15 No Hit TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 6 0.15 No Hit ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTTGGAATTC 5 0.125 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGCC 5 0.125 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GCAAGTATGAACTAATTTGAACTGTGAAACTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit NTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 5 0.125 No Hit GGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCT 5 0.125 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGATGGAATTC 5 0.125 No Hit GCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) >>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 0.075 0.0 0.0 0.0 2 0.0 0.075 0.0 0.0 0.0 3 0.0 0.075 0.0 0.0 0.0 4 0.0 0.075 0.0 0.0 0.0 5 0.0 0.075 0.0 0.0 0.0 6 0.0 0.075 0.0 0.0 0.0 7 0.0 0.1 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.1 0.0 0.0 0.0 10-11 0.0 0.175 0.0 0.0 0.0 12-13 0.0 0.25 0.0 0.0 0.0 14-15 0.0 0.41250000000000003 0.0 0.0 0.0 16-17 0.0 1.0 0.0 0.0 0.0 18-19 0.0 1.5375 0.0 0.0 0.0 20-21 0.0 2.9875 0.0 0.0 0.0 22-23 0.0 6.475 0.0 0.0 0.0 24-25 0.0 13.6625 0.0 0.0 0.0 26-27 0.0 22.75 0.0 0.0 0.0 28-29 0.0 29.575000000000003 0.0 0.0 0.0 30-31 0.0 40.0375 0.0 0.0 0.0 32-33 0.0 48.724999999999994 0.0 0.0 0.0 34-35 0.0 58.0625 0.0 0.0 0.0 36-37 0.0 69.1875 0.0 0.0 0.0 38-39 0.0 75.19999999999999 0.0 0.0 0.0 40-41 0.0 79.80000000000001 0.0 0.0 0.0 42-43 0.0 84.2875 0.0 0.0 0.0 44-45 0.0 87.8125 0.0 0.0 0.0 46-47 0.0 89.6375 0.0 0.0 0.0 48-49 0.0 90.3875 0.0 0.0 0.0 50-51 0.0 90.85 0.0 0.0 0.0 52-53 0.0 91.025 0.0 0.0 0.0 54-55 0.0 91.1 0.0 0.0 0.0 56-57 0.0 91.17500000000001 0.0 0.0 0.0 58-59 0.0 91.225 0.0 0.0 0.0 60-61 0.0 91.225 0.0 0.0 0.0 62-63 0.0 91.225 0.0 0.0 0.0 64-65 0.0 91.225 0.0 0.0 0.0 66-67 0.0 91.225 0.0 0.0 0.0 68-69 0.0 91.225 0.0 0.0 0.0 70-71 0.0 91.225 0.0 0.0 0.0 72-73 0.0 91.225 0.0 0.0 0.0 74-75 0.0 91.225 0.0 0.0 0.0 76-77 0.0 91.225 0.0 0.0 0.0 78-79 0.0 91.25 0.0 0.0 0.0 80-81 0.0 91.25 0.0 0.0 0.0 82-83 0.0 91.25 0.0 0.0 0.0 84-85 0.0 91.3 0.0 0.0 0.0 86-87 0.0 91.3 0.0 0.0 0.0 88-89 0.0 91.35 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATATATT 15 4.9992715E-4 99.947365 1 GTAGACC 25 3.8410144E-7 94.950005 7 AGTAGAC 25 3.8410144E-7 94.950005 6 GAGTAGA 25 3.8410144E-7 94.950005 5 CGAGTAG 25 3.8410144E-7 94.950005 4 AGACCTT 25 3.8410144E-7 94.950005 9 TCGAGTA 25 3.8410144E-7 94.950005 3 TAGACCT 25 3.8410144E-7 94.950005 8 TCAAGTT 15 6.1550457E-4 94.95 8 TATATTT 15 6.1550457E-4 94.95 2 TTCAAGT 15 6.1550457E-4 94.95 7 TTTCAAG 15 6.1550457E-4 94.95 6 ATATTTC 15 6.1550457E-4 94.95 3 ATTTCAA 15 6.1550457E-4 94.95 5 CATCGAG 30 8.2970837E-7 83.289474 1 TATTTCA 20 0.0019298021 71.212494 4 CAAGTTA 20 0.0019298021 71.212494 9 ATCGAGT 35 2.8442191E-6 67.82143 2 CCAGACA 25 0.0037994494 59.968422 1 TGTGAGA 25 2.5895028E-5 47.475002 20-21 >>END_MODULE Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra Rejected 642305 READS because READLEN < 1 Read 642305 spots for SRR8846482.sra Written 642305 spots for SRR8846482.sra SRR ids: ['SRR8846482.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_h198mizo SRR8846482.sra spots: 12846100 blocks: [[1, 642305], [642306, 1284610], [1284611, 1926915], [1926916, 2569220], [2569221, 3211525], [3211526, 3853830], [3853831, 4496135], [4496136, 5138440], [5138441, 5780745], [5780746, 6423050], [6423051, 7065355], [7065356, 7707660], [7707661, 8349965], [8349966, 8992270], [8992271, 9634575], [9634576, 10276880], [10276881, 10919185], [10919186, 11561490], [11561491, 12203795], [12203796, 12846100]] SRR8846482 file size 3076919 SRR8846482 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 SRR8846482 SRR8846482_1.fastq Input file: SRR8846482_1.fastq trimmed: SRR8846482-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 17:03:44 2024 >> started Sun Dec 8 17:04:18 2024 >> done (34.003s) 12846100 reads processed; of these: 237 ( 0.00%) short reads filtered out after trimming by size control 38 ( 0.00%) empty reads filtered out after trimming by size control 12845825 (100.00%) reads available; of these: 2157021 (16.79%) trimmed reads available after processing 10688804 (83.21%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 30 0.00% 19 24 0.00% 20 30 0.00% 21 29 0.00% 22 37 0.00% 23 39 0.00% 24 38 0.00% 25 72 0.00% 26 66 0.00% 27 76 0.00% 28 75 0.00% 29 82 0.00% 30 86 0.00% 31 105 0.00% 32 90 0.00% 33 152 0.00% 34 136 0.00% 35 120 0.00% 36 158 0.00% 37 142 0.00% 38 184 0.00% 39 196 0.00% 40 270 0.00% 41 302 0.00% 42 357 0.00% 43 386 0.00% 44 468 0.00% 45 429 0.00% 46 449 0.00% 47 445 0.00% 48 367 0.00% 49 442 0.00% 50 506 0.00% 51 471 0.00% 52 417 0.00% 53 359 0.00% 54 285 0.00% 55 213 0.00% 56 322 0.00% 57 286 0.00% 58 353 0.00% 59 602 0.00% 60 969 0.01% 61 1137 0.01% 62 1803 0.01% 63 2306 0.02% 64 4632 0.04% 65 5788 0.05% 66 13099 0.10% 67 67095 0.52% 68 78402 0.61% 69 57068 0.44% 70 47370 0.37% 71 66387 0.52% 72 26778 0.21% 73 7176 0.06% 74 9195 0.07% 75 5609 0.04% 76 3972 0.03% 77 3989 0.03% 78 4670 0.04% 79 4883 0.04% 80 5002 0.04% 81 5362 0.04% 82 7170 0.06% 83 7402 0.06% 84 7431 0.06% 85 8570 0.07% 86 9330 0.07% 87 12506 0.10% 88 18651 0.15% 89 26973 0.21% 90 35961 0.28% 91 38305 0.30% 92 41670 0.32% 93 62463 0.49% 94 79185 0.62% 95 159839 1.24% 96 192467 1.50% 97 208564 1.62% 98 305010 2.37% 99 315824 2.46% 100 187312 1.46% 101 10688804 83.21% 12845825 reads passed initial QC criterion=sequence-density sequence-density=90.14 sequence-density-rank=1 fanout-score=32.73 fanout-score-rank=1 prefix-density=90.50 prefix-fanout=32.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=90.14 sequence-density-rank=1 fanout-score=32.73 fanout-score-rank=1 prefix-density=90.50 prefix-fanout=32.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846482 - Input file: STDIN trimmed: SRR8846482-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 17:06:37 2024 >> started Sun Dec 8 17:07:39 2024 >> done (61.847s) 12563499 reads processed; of these: 187512 ( 1.49%) short reads filtered out after trimming by size control 14582 ( 0.12%) empty reads filtered out after trimming by size control 12361405 (98.39%) reads available; of these: 11682653 (94.51%) trimmed reads available after processing 678752 ( 5.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 48686 0.39% 19 83456 0.68% 20 98748 0.80% 21 333034 2.69% 22 213576 1.73% 23 301605 2.44% 24 959703 7.76% 25 440232 3.56% 26 424424 3.43% 27 421158 3.41% 28 467393 3.78% 29 762983 6.17% 30 699234 5.66% 31 477811 3.87% 32 501188 4.05% 33 603577 4.88% 34 734615 5.94% 35 738797 5.98% 36 615407 4.98% 37 444204 3.59% 38 404036 3.27% 39 323382 2.62% 40 279661 2.26% 41 315871 2.56% 42 303184 2.45% 43 169100 1.37% 44 184913 1.50% 45 100405 0.81% 46 61895 0.50% 47 42785 0.35% 48 42776 0.35% 49 21699 0.18% 50 14625 0.12% 51 13726 0.11% 52 7257 0.06% 53 5765 0.05% 54 5884 0.05% 55 1948 0.02% 56 1692 0.01% 57 1130 0.01% 58 912 0.01% 59 962 0.01% 60 1117 0.01% 61 1305 0.01% 62 1782 0.01% 63 2245 0.02% 64 4464 0.04% 65 5586 0.05% 66 12721 0.10% 67 65473 0.53% 68 76393 0.62% 69 55502 0.45% 70 45962 0.37% 71 64386 0.52% 72 23974 0.19% 73 5213 0.04% 74 4162 0.03% 75 2723 0.02% 76 2518 0.02% 77 4065 0.03% 78 2786 0.02% 79 2849 0.02% 80 4021 0.03% 81 3096 0.03% 82 2974 0.02% 83 4143 0.03% 84 1960 0.02% 85 1978 0.02% 86 1756 0.01% 87 1650 0.01% 88 1222 0.01% 89 1278 0.01% 90 1197 0.01% 91 1276 0.01% 92 1247 0.01% 93 1390 0.01% 94 1610 0.01% 95 2201 0.02% 96 3118 0.03% 97 4758 0.04% 98 6460 0.05% 99 8508 0.07% 100 11053 0.09% 101 235844 1.91% criterion=sequence-density sequence-density=6.93 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGAGT criterion=fanout-score sequence-density=0.26 sequence-density-rank=16 fanout-score=24.14 fanout-score-rank=1 prefix-density=6.28 prefix-fanout=1.0 sequence=TTGTGAGAATTAAAAA Started job on | Dec 08 17:09:59 Started mapping on | Dec 08 17:10:00 Finished on | Dec 08 17:17:57 Mapping speed, Million of reads per hour | 95.42 Number of input reads | 12643731 Average input read length | 36 UNIQUE READS: Uniquely mapped reads number | 1699606 Uniquely mapped reads % | 13.44% Average mapped length | 29.20 Number of splices: Total | 28141 Number of splices: Annotated (sjdb) | 19468 Number of splices: GT/AG | 26083 Number of splices: GC/AG | 1343 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 702 Mismatch rate per base, % | 0.16% Deletion rate per base | 0.00% Deletion average length | 1.25 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4455569 % of reads mapped to multiple loci | 35.24% Number of reads mapped to too many loci | 5329989 % of reads mapped to too many loci | 42.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.64% % of reads unmapped: other | 0.52% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6488556 6488556 6488556 N_multimapping 4455569 4455569 4455569 N_noFeature 861026 976659 1574575 N_ambiguous 33910 24336 300 UnstrandedReadsAssigned:804670 PositiveStrandReadsAssigned:698611 NegativeStrandReadsAssigned:124731 Dataset is classified positive stranded MeadianReadLen=32 20thPercentileLength=25 echo kmer=21 SRR8846482 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: SRR8846482-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,643,731 reads, 2,029,623 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 923 rounds 52973 SRR8846482.ke.tsv 35125 SRR8846482.se.tsv 88098 total ==> SRR8846482.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 2 1.56684 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 45.5293 19.8501 KQK14071 474 375 4.05807 7.09591 ==> SRR8846482.se.tsv <== BRADI_1g14170v3 103 BRADI_1g53295v3 0 BRADI_1g59795v3 17 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 24 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR8846482 completed mapping pipeline successfully