Starting /dee2/code/volunteer_pipeline.sh SRR6941566 current disk space = 1551667687424 free memory = 1607268840 SRR6941566 SRAfilesize 8126959923d3237827ba2e62903b67d2 SRR6941566.sra SRR6941566.sra file validated SRR6941566 is single end SRR6941566 is conventional basespace SRR6941566 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941566_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.28475 34.0 33.0 34.0 32.0 34.0 2 33.31275 34.0 33.0 34.0 33.0 34.0 3 33.166 34.0 33.0 34.0 31.0 34.0 4 33.301 34.0 33.0 34.0 32.0 34.0 5 33.297 34.0 33.0 34.0 33.0 34.0 6 37.0385 38.0 37.0 38.0 36.0 38.0 7 37.39125 38.0 38.0 38.0 37.0 38.0 8 37.4825 38.0 38.0 38.0 37.0 38.0 9 37.5505 38.0 38.0 38.0 38.0 38.0 10-11 37.520375 38.0 38.0 38.0 38.0 38.0 12-13 37.4675 38.0 38.0 38.0 38.0 38.0 14-15 37.525999999999996 38.0 38.0 38.0 38.0 38.0 16-17 36.098625 38.0 37.0 38.0 27.0 38.0 18-19 36.896625 38.0 37.5 38.0 33.5 38.0 20-21 36.234125 38.0 38.0 38.0 30.0 38.0 22-23 37.312 38.0 38.0 38.0 36.5 38.0 24-25 37.456875 38.0 38.0 38.0 37.0 38.0 26-27 37.40675 38.0 38.0 38.0 37.0 38.0 28-29 37.441 38.0 38.0 38.0 37.0 38.0 30-31 37.366625 38.0 38.0 38.0 37.5 38.0 32-33 37.2175 38.0 38.0 38.0 37.0 38.0 34-35 37.147000000000006 38.0 38.0 38.0 37.0 38.0 36-37 37.103125000000006 38.0 38.0 38.0 36.5 38.0 38-39 37.16225 38.0 38.0 38.0 37.0 38.0 40-41 37.194374999999994 38.0 38.0 38.0 37.0 38.0 42-43 37.119625 38.0 38.0 38.0 36.5 38.0 44-45 37.165375 38.0 38.0 38.0 37.0 38.0 46-47 37.096125 38.0 38.0 38.0 36.5 38.0 48-49 37.15125 38.0 38.0 38.0 37.0 38.0 50-51 37.083875 38.0 38.0 38.0 36.0 38.0 52-53 37.06425 38.0 38.0 38.0 36.5 38.0 54-55 37.202375 38.0 38.0 38.0 37.0 38.0 56-57 37.09725 38.0 38.0 38.0 37.0 38.0 58-59 37.225125 38.0 38.0 38.0 37.0 38.0 60-61 37.131 38.0 38.0 38.0 37.0 38.0 62-63 36.769625000000005 38.0 38.0 38.0 35.5 38.0 64-65 36.56725 38.0 37.5 38.0 34.5 38.0 66-67 36.445750000000004 38.0 37.5 38.0 34.0 38.0 68-69 36.89625 38.0 38.0 38.0 36.0 38.0 70-71 36.50925 38.0 37.5 38.0 34.0 38.0 72-73 36.32225 38.0 37.0 38.0 33.5 38.0 74-75 36.16675 38.0 37.0 38.0 33.0 38.0 76-77 36.219625 38.0 38.0 38.0 33.5 38.0 78-79 36.385 38.0 38.0 38.0 34.0 38.0 80-81 36.614374999999995 38.0 38.0 38.0 35.5 38.0 82-83 36.700374999999994 38.0 38.0 38.0 36.0 38.0 84-85 36.647875 38.0 38.0 38.0 36.0 38.0 86-87 36.501375 38.0 38.0 38.0 35.0 38.0 88-89 36.443875 38.0 38.0 38.0 34.0 38.0 90-91 36.390125 38.0 38.0 38.0 34.5 38.0 92-93 36.175875000000005 38.0 38.0 38.0 34.0 38.0 94-95 35.642625 38.0 38.0 38.0 33.0 38.0 96-97 32.983625 38.0 35.5 38.0 8.5 38.0 98-99 29.61025 38.0 29.0 38.0 2.0 38.0 100-101 26.024375 38.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 0.0 15 0.0 16 1.0 17 1.0 18 1.0 19 0.0 20 2.0 21 1.0 22 4.0 23 4.0 24 9.0 25 11.0 26 17.0 27 21.0 28 26.0 29 28.0 30 26.0 31 29.0 32 67.0 33 110.0 34 202.0 35 496.0 36 831.0 37 2110.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.75 25.674999999999997 16.675 30.9 2 25.925925925925924 38.33833833833834 18.21821821821822 17.51751751751752 3 27.875 18.85 34.425 18.85 4 22.725 28.549999999999997 14.099999999999998 34.625 5 44.6 18.625 21.375 15.4 6 17.724999999999998 41.675000000000004 24.0 16.6 7 47.3 18.775 20.125 13.8 8 18.925 16.125 46.800000000000004 18.15 9 16.25 48.85 18.099999999999998 16.8 10-11 37.6625 28.825 17.625 15.8875 12-13 16.900000000000002 15.75 21.6125 45.7375 14-15 19.162499999999998 31.7125 34.2 14.924999999999999 16-17 28.7 18.1125 39.3375 13.850000000000001 18-19 33.2125 25.162499999999998 28.449999999999996 13.175 20-21 13.9625 24.0 41.4125 20.625 22-23 33.35 24.5125 28.025 14.1125 24-25 33.2 30.675 23.2125 12.9125 26-27 41.2625 28.875 17.6875 12.174999999999999 28-29 12.725 41.099999999999994 26.5875 19.5875 30-31 17.2 9.700000000000001 49.925000000000004 23.175 32-33 32.8125 10.575 29.6875 26.924999999999997 34-35 36.987500000000004 23.0 23.5 16.5125 36-37 43.725 16.25 27.6625 12.3625 38-39 23.45 18.0375 34.4375 24.075 40-41 24.4 16.05 20.3625 39.1875 42-43 36.975 29.849999999999998 15.662499999999998 17.5125 44-45 52.337500000000006 15.525 14.224999999999998 17.9125 46-47 24.887500000000003 30.575000000000003 14.512500000000001 30.025000000000002 48-49 18.6 27.762500000000003 18.1875 35.449999999999996 50-51 28.4 24.224999999999998 8.712499999999999 38.6625 52-53 26.637499999999996 45.675 6.950000000000001 20.7375 54-55 15.0625 24.8625 21.325 38.75 56-57 10.5625 35.0125 9.9 44.525 58-59 15.1 33.75 16.275000000000002 34.875 60-61 18.1125 31.0125 18.1625 32.7125 62-63 9.8375 23.1875 26.400000000000002 40.575 64-65 8.4 31.574999999999996 25.587500000000002 34.4375 66-67 16.675 24.2375 25.374999999999996 33.7125 68-69 20.075000000000003 25.15 22.7375 32.0375 70-71 14.2875 31.0 34.0375 20.674999999999997 72-73 19.3625 13.5625 35.362500000000004 31.7125 74-75 16.45 8.6 28.5875 46.362500000000004 76-77 20.0625 11.799999999999999 45.7375 22.400000000000002 78-79 19.125 7.9750000000000005 42.75 30.15 80-81 19.825 8.35 33.800000000000004 38.025 82-83 29.175 5.7375 40.5875 24.5 84-85 17.9375 9.0375 39.4 33.625 86-87 19.275000000000002 18.5375 40.300000000000004 21.8875 88-89 13.2875 41.137499999999996 28.825 16.75 90-91 8.8375 45.4125 28.262500000000003 17.4875 92-93 15.937499999999998 51.237500000000004 22.4875 10.337499999999999 94-95 9.0875 69.28750000000001 15.575 6.05 96-97 7.625 81.125 8.6375 2.6125 98-99 3.175 91.4375 3.35 2.0375 100-101 1.5375 93.475 2.3875 2.6 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.5 34 1.5 35 3.5 36 3.5 37 5.5 38 7.5 39 11.5 40 23.5 41 54.0 42 132.5 43 271.0 44 642.0 45 790.0 46 480.0 47 337.0 48 261.0 49 138.0 50 162.0 51 230.5 52 202.5 53 100.5 54 43.0 55 43.0 56 31.0 57 6.5 58 8.0 59 7.5 60 1.5 61 0.5 62 0.5 63 0.5 64 0.0 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 pass #Base N-Count 1 0.0 2 0.1 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 46.550000000000004 #Duplication Level Percentage of deduplicated Percentage of total 1 86.51987110633728 40.275 2 5.746509129967777 5.35 3 1.7185821697099892 2.4 4 0.966702470461869 1.7999999999999998 5 1.0204081632653061 2.375 6 0.322234156820623 0.8999999999999999 7 0.4833512352309345 1.575 8 0.37593984962406013 1.4000000000000001 9 0.10741138560687433 0.44999999999999996 >10 2.309344790547798 23.0 >50 0.21482277121374865 7.625 >100 0.21482277121374865 12.85 >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 CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 204 5.1 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 106 2.65 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 103 2.5749999999999997 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 101 2.5250000000000004 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 88 2.1999999999999997 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 77 1.925 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 77 1.925 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 63 1.575 No Hit TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 50 1.25 RNA PCR Primer, Index 1 (100% over 26bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 49 1.225 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 46 1.15 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 43 1.075 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 41 1.0250000000000001 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 39 0.975 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 35 0.8750000000000001 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 31 0.775 RNA PCR Primer, Index 1 (100% over 28bp) TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 30 0.75 RNA PCR Primer, Index 1 (100% over 29bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 30 0.75 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 28 0.7000000000000001 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 27 0.675 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 26 0.65 RNA PCR Primer, Index 1 (100% over 22bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 24 0.6 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 23 0.575 RNA PCR Primer, Index 1 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 22 0.5499999999999999 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 19 0.475 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGC 18 0.44999999999999996 RNA PCR Primer, Index 7 (100% over 50bp) ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 26bp) GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 15 0.375 RNA PCR Primer, Index 1 (100% over 26bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 15 0.375 RNA PCR Primer, Index 1 (100% over 29bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 15 0.375 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 15 0.375 RNA PCR Primer, Index 1 (100% over 29bp) AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 14 0.35000000000000003 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 14 0.35000000000000003 Illumina Small RNA Adapter 2 (100% over 21bp) GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 14 0.35000000000000003 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 29bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 12 0.3 RNA PCR Primer, Index 1 (100% over 23bp) ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 12 0.3 RNA PCR Primer, Index 1 (100% over 24bp) GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 12 0.3 RNA PCR Primer, Index 1 (100% over 33bp) TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 11 0.27499999999999997 Illumina Small RNA Adapter 2 (100% over 21bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 10 0.25 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTAATGTGAGAATTTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 10 0.25 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 25bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 8 0.2 RNA PCR Primer, Index 1 (100% over 31bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 8 0.2 No Hit TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 8 0.2 No Hit GGTAGTTCGACCGCGGAATTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 8 0.2 RNA PCR Primer, Index 1 (100% over 31bp) AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 8 0.2 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCTGGAATTCTCGGG 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTAATGTGAGAATTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAATGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTATTGTGAGAATTAATGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit TTTGGATTGAAGGGAGCTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGATATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) CCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTA 6 0.15 No Hit ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 6 0.15 RNA PCR Primer, Index 1 (100% over 25bp) CTAACGAACGAACGATATGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAATGGAATTCTCGGGT 5 0.125 No Hit TAATTCATGATCTGGCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TAGAACTCCACATCCTTGGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAAATGGAATTCTCGGG 5 0.125 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTATGGAATTCTCGGGTGCC 5 0.125 No Hit CCCTATAGAACTCCACATCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 5 0.125 No Hit AACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) CATCGAGTAGACCTTGTTATTGTGAGAAAATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 5 0.125 No Hit TGAAGCTGCCAGCATGATCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTAGTGTGAGAATTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 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 0.55 0.0 0.0 0.0 2 0.0 0.55 0.0 0.0 0.0 3 0.0 0.55 0.0 0.0 0.0 4 0.0 0.55 0.0 0.0 0.0 5 0.0 0.575 0.0 0.0 0.0 6 0.0 0.575 0.0 0.0 0.0 7 0.0 0.6 0.0 0.0 0.0 8 0.0 0.6 0.0 0.0 0.0 9 0.0 0.625 0.0 0.0 0.0 10-11 0.0 0.6375 0.0 0.0 0.0 12-13 0.0 0.675 0.0 0.0 0.0 14-15 0.0 0.7375 0.0 0.0 0.0 16-17 0.0 1.0625 0.0 0.0 0.0 18-19 0.0 1.8499999999999999 0.0 0.0 0.0 20-21 0.0 3.5999999999999996 0.0 0.0 0.0 22-23 0.0 13.7625 0.0 0.0 0.0 24-25 0.0 29.2 0.0 0.0 0.0 26-27 0.0 42.6125 0.0 0.0 0.0 28-29 0.0 46.1375 0.0 0.0 0.0 30-31 0.0 59.237500000000004 0.0 0.0 0.0 32-33 0.0 74.2125 0.0 0.0 0.0 34-35 0.0 86.9875 0.0 0.0 0.0 36-37 0.0 94.125 0.0 0.0 0.0 38-39 0.0 96.07499999999999 0.0 0.0 0.0 40-41 0.0 96.5375 0.0 0.0 0.0 42-43 0.0 97.0375 0.0 0.0 0.0 44-45 0.0 97.275 0.0 0.0 0.0 46-47 0.0 97.3875 0.0 0.0 0.0 48-49 0.0 97.4125 0.0 0.0 0.0 50-51 0.0 97.45 0.0 0.0 0.0 52-53 0.0 97.45 0.0 0.0 0.0 54-55 0.0 97.45 0.0 0.0 0.0 56-57 0.0 97.45 0.0 0.0 0.0 58-59 0.0 97.45 0.0 0.0 0.0 60-61 0.0 97.45 0.0 0.0 0.0 62-63 0.0 97.45 0.0 0.0 0.0 64-65 0.0 97.45 0.0 0.0 0.0 66-67 0.0 97.45 0.0 0.0 0.0 68-69 0.0 97.45 0.0 0.0 0.0 70-71 0.0 97.4625 0.0 0.0 0.0 72-73 0.0 97.475 0.0 0.0 0.0 74-75 0.0 97.475 0.0 0.0 0.0 76-77 0.0 97.475 0.0 0.0 0.0 78-79 0.0 97.475 0.0 0.0 0.0 80-81 0.0 97.475 0.0 0.0 0.0 82-83 0.0 97.475 0.0 0.0 0.0 84-85 0.0 97.475 0.0 0.0 0.0 86-87 0.0 97.5 0.0 0.0 0.0 88-89 0.0 97.5 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATTGT 20 1.5392321E-5 95.00001 2 GATTGTA 20 1.5392321E-5 95.00001 3 ATTGTAG 20 1.5392321E-5 95.00001 4 GGGATTG 20 1.5392321E-5 95.00001 1 ATCCTAA 30 9.458745E-9 95.0 6 GAGGCAT 30 9.458745E-9 95.0 1 GTAGACC 65 0.0 95.0 7 GGCATCC 30 9.458745E-9 95.0 3 AGTAGAC 65 0.0 95.0 6 GGGTAGG 15 6.142176E-4 95.0 6 CATCCTA 30 9.458745E-9 95.0 5 ATTGGGT 15 6.142176E-4 95.0 3 TATTGGG 15 6.142176E-4 95.0 2 TAGTTCA 30 9.458745E-9 95.0 8 TTGGGTA 15 6.142176E-4 95.0 4 GAGTAGA 65 0.0 95.0 5 GGTAGGT 15 6.142176E-4 95.0 7 CGAGTAG 65 0.0 95.0 4 AGGCATC 30 9.458745E-9 95.0 2 GTAGGTT 15 6.142176E-4 95.0 8 >>END_MODULE Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301030 READS because READLEN < 1 Read 301030 spots for SRR6941566.sra Written 301030 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra Rejected 301015 READS because READLEN < 1 Read 301015 spots for SRR6941566.sra Written 301015 spots for SRR6941566.sra SRR ids: ['SRR6941566.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kcyu8_vf SRR6941566.sra spots: 6020315 blocks: [[1, 301015], [301016, 602030], [602031, 903045], [903046, 1204060], [1204061, 1505075], [1505076, 1806090], [1806091, 2107105], [2107106, 2408120], [2408121, 2709135], [2709136, 3010150], [3010151, 3311165], [3311166, 3612180], [3612181, 3913195], [3913196, 4214210], [4214211, 4515225], [4515226, 4816240], [4816241, 5117255], [5117256, 5418270], [5418271, 5719285], [5719286, 6020315]] SRR6941566 file size 1438238 SRR6941566 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 SRR6941566 SRR6941566_1.fastq Input file: SRR6941566_1.fastq trimmed: SRR6941566-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Fri Dec 6 11:33:26 2024 >> started Fri Dec 6 11:33:30 2024 >> done (4.239s) 6020315 reads processed; of these: 90 ( 0.00%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 6020209 (100.00%) reads available; of these: 1234000 (20.50%) trimmed reads available after processing 4786209 (79.50%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 8 0.00% 20 8 0.00% 21 11 0.00% 22 14 0.00% 23 17 0.00% 24 10 0.00% 25 19 0.00% 26 18 0.00% 27 24 0.00% 28 31 0.00% 29 58 0.00% 30 52 0.00% 31 39 0.00% 32 57 0.00% 33 41 0.00% 34 53 0.00% 35 48 0.00% 36 51 0.00% 37 38 0.00% 38 42 0.00% 39 36 0.00% 40 50 0.00% 41 39 0.00% 42 59 0.00% 43 50 0.00% 44 48 0.00% 45 75 0.00% 46 76 0.00% 47 54 0.00% 48 44 0.00% 49 24 0.00% 50 33 0.00% 51 39 0.00% 52 35 0.00% 53 30 0.00% 54 20 0.00% 55 29 0.00% 56 35 0.00% 57 31 0.00% 58 25 0.00% 59 34 0.00% 60 51 0.00% 61 45 0.00% 62 38 0.00% 63 38 0.00% 64 40 0.00% 65 51 0.00% 66 66 0.00% 67 81 0.00% 68 139 0.00% 69 153 0.00% 70 242 0.00% 71 274 0.00% 72 399 0.01% 73 1025 0.02% 74 6048 0.10% 75 4269 0.07% 76 1423 0.02% 77 477 0.01% 78 654 0.01% 79 709 0.01% 80 708 0.01% 81 778 0.01% 82 941 0.02% 83 1165 0.02% 84 1946 0.03% 85 2212 0.04% 86 2330 0.04% 87 2960 0.05% 88 3798 0.06% 89 5694 0.09% 90 8628 0.14% 91 14211 0.24% 92 18254 0.30% 93 34080 0.57% 94 57473 0.95% 95 151427 2.52% 96 155919 2.59% 97 148273 2.46% 98 234651 3.90% 99 265235 4.41% 100 105579 1.75% 101 4786209 79.50% 6020209 reads passed initial QC criterion=sequence-density sequence-density=97.57 sequence-density-rank=1 fanout-score=23.64 fanout-score-rank=2 prefix-density=97.59 prefix-fanout=23.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=1.29 sequence-density-rank=9 fanout-score=77.07 fanout-score-rank=1 prefix-density=98.32 prefix-fanout=1.0 sequence=CACCAGATCATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR6941566 - Input file: STDIN trimmed: SRR6941566-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTGA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Fri Dec 6 11:33:49 2024 >> started Fri Dec 6 11:33:57 2024 >> done (7.219s) 5897348 reads processed; of these: 65234 ( 1.11%) short reads filtered out after trimming by size control 24493 ( 0.42%) empty reads filtered out after trimming by size control 5807621 (98.48%) reads available; of these: 5751885 (99.04%) trimmed reads available after processing 55736 ( 0.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 23213 0.40% 19 62819 1.08% 20 70527 1.21% 21 396919 6.83% 22 285973 4.92% 23 172169 2.96% 24 1203299 20.72% 25 158693 2.73% 26 129008 2.22% 27 97255 1.67% 28 104158 1.79% 29 384176 6.62% 30 675493 11.63% 31 376401 6.48% 32 408358 7.03% 33 442503 7.62% 34 316918 5.46% 35 218187 3.76% 36 83774 1.44% 37 41875 0.72% 38 19948 0.34% 39 12464 0.21% 40 18679 0.32% 41 19532 0.34% 42 14721 0.25% 43 3199 0.06% 44 4234 0.07% 45 2274 0.04% 46 628 0.01% 47 962 0.02% 48 341 0.01% 49 188 0.00% 50 72 0.00% 51 70 0.00% 52 43 0.00% 53 38 0.00% 54 21 0.00% 55 30 0.00% 56 24 0.00% 57 31 0.00% 58 34 0.00% 59 23 0.00% 60 21 0.00% 61 27 0.00% 62 21 0.00% 63 21 0.00% 64 19 0.00% 65 18 0.00% 66 26 0.00% 67 33 0.00% 68 56 0.00% 69 51 0.00% 70 102 0.00% 71 86 0.00% 72 63 0.00% 73 69 0.00% 74 56 0.00% 75 90 0.00% 76 134 0.00% 77 591 0.01% 78 97 0.00% 79 173 0.00% 80 427 0.01% 81 186 0.00% 82 298 0.01% 83 288 0.00% 84 147 0.00% 85 126 0.00% 86 216 0.00% 87 264 0.00% 88 177 0.00% 89 179 0.00% 90 209 0.00% 91 389 0.01% 92 472 0.01% 93 590 0.01% 94 664 0.01% 95 1057 0.02% 96 835 0.01% 97 727 0.01% 98 1119 0.02% 99 889 0.02% 100 904 0.02% 101 46430 0.80% criterion=sequence-density sequence-density=21.20 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=12 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.13 sequence-density-rank=29 fanout-score=163.42 fanout-score-rank=1 prefix-density=21.16 prefix-fanout=1.0 sequence=TATTGTGAGAAAAA Started job on | Dec 06 11:34:14 Started mapping on | Dec 06 11:34:14 Finished on | Dec 06 11:34:33 Mapping speed, Million of reads per hour | 1123.67 Number of input reads | 5930482 Average input read length | 30 UNIQUE READS: Uniquely mapped reads number | 1292451 Uniquely mapped reads % | 21.79% Average mapped length | 24.67 Number of splices: Total | 3467 Number of splices: Annotated (sjdb) | 957 Number of splices: GT/AG | 3319 Number of splices: GC/AG | 93 Number of splices: AT/AC | 1 Number of splices: Non-canonical | 54 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.00% Deletion average length | 1.60 Insertion rate per base | 0.00% Insertion average length | 1.06 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3921341 % of reads mapped to multiple loci | 66.12% Number of reads mapped to too many loci | 472069 % of reads mapped to too many loci | 7.96% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.35% % of reads unmapped: other | 0.77% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 716690 716690 716690 N_multimapping 3921341 3921341 3921341 N_noFeature 970873 1087302 1172320 N_ambiguous 8212 4294 257 UnstrandedReadsAssigned:313366 PositiveStrandReadsAssigned:200855 NegativeStrandReadsAssigned:119874 Dataset is classified unstranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR6941566 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: SRR6941566-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,930,482 reads, 2,982,304 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 967 rounds 52973 SRR6941566.ke.tsv 35125 SRR6941566.se.tsv 88098 total ==> SRR6941566.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 1 0.155361 PNS24243 293 194 0 0 KQK14069 1603 1504 0 0 KQK14071 474 375 0 0 ==> SRR6941566.se.tsv <== BRADI_1g14170v3 19 BRADI_1g53295v3 1 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 1 BRADI_1g74790v3 20 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941566 completed mapping pipeline successfully