Starting /dee2/code/volunteer_pipeline.sh SRR6941582 current disk space = 1551390015488 free memory = 1602334020 SRR6941582 SRAfilesize aff26bea32ac78c7fe3fda303ac9c403 SRR6941582.sra SRR6941582.sra file validated SRR6941582 is single end SRR6941582 is conventional basespace SRR6941582 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941582_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 33.22975 34.0 33.0 34.0 32.0 34.0 2 33.356 34.0 33.0 34.0 33.0 34.0 3 33.10675 34.0 33.0 34.0 31.0 34.0 4 33.25525 34.0 33.0 34.0 32.0 34.0 5 33.1875 34.0 33.0 34.0 33.0 34.0 6 37.01725 38.0 37.0 38.0 36.0 38.0 7 37.3365 38.0 38.0 38.0 37.0 38.0 8 37.4325 38.0 38.0 38.0 37.0 38.0 9 37.491 38.0 38.0 38.0 38.0 38.0 10-11 37.53975 38.0 38.0 38.0 38.0 38.0 12-13 37.47325 38.0 38.0 38.0 38.0 38.0 14-15 37.431875000000005 38.0 38.0 38.0 37.0 38.0 16-17 36.075 38.0 37.0 38.0 27.0 38.0 18-19 36.881125 38.0 37.5 38.0 33.5 38.0 20-21 36.15 38.0 37.5 38.0 29.5 38.0 22-23 37.308875 38.0 38.0 38.0 36.5 38.0 24-25 37.484125000000006 38.0 38.0 38.0 37.5 38.0 26-27 37.40925 38.0 38.0 38.0 37.0 38.0 28-29 37.425250000000005 38.0 38.0 38.0 38.0 38.0 30-31 37.385875 38.0 38.0 38.0 37.5 38.0 32-33 37.24075 38.0 38.0 38.0 37.0 38.0 34-35 37.1575 38.0 38.0 38.0 37.0 38.0 36-37 37.071375 38.0 38.0 38.0 36.5 38.0 38-39 37.04275 38.0 38.0 38.0 36.0 38.0 40-41 37.057 38.0 38.0 38.0 36.0 38.0 42-43 37.069374999999994 38.0 38.0 38.0 36.5 38.0 44-45 37.095375000000004 38.0 38.0 38.0 37.0 38.0 46-47 37.038875000000004 38.0 38.0 38.0 36.5 38.0 48-49 37.1745 38.0 38.0 38.0 37.0 38.0 50-51 37.055499999999995 38.0 38.0 38.0 36.0 38.0 52-53 37.153499999999994 38.0 38.0 38.0 36.5 38.0 54-55 37.22 38.0 38.0 38.0 37.0 38.0 56-57 37.04825 38.0 38.0 38.0 36.5 38.0 58-59 37.155375 38.0 38.0 38.0 37.0 38.0 60-61 37.1655 38.0 38.0 38.0 37.0 38.0 62-63 36.82925 38.0 38.0 38.0 35.5 38.0 64-65 36.532 38.0 37.5 38.0 34.0 38.0 66-67 36.355374999999995 38.0 37.5 38.0 33.0 38.0 68-69 36.807375 38.0 38.0 38.0 35.0 38.0 70-71 36.347375 38.0 37.5 38.0 33.5 38.0 72-73 36.367374999999996 38.0 37.0 38.0 33.5 38.0 74-75 35.868875 38.0 37.0 38.0 30.0 38.0 76-77 36.156375 38.0 37.5 38.0 33.5 38.0 78-79 36.224625 38.0 38.0 38.0 33.5 38.0 80-81 36.473625 38.0 38.0 38.0 34.5 38.0 82-83 36.560249999999996 38.0 38.0 38.0 35.5 38.0 84-85 36.484625 38.0 38.0 38.0 35.0 38.0 86-87 36.27075 38.0 38.0 38.0 34.0 38.0 88-89 36.212375 38.0 38.0 38.0 34.0 38.0 90-91 36.116875 38.0 38.0 38.0 34.0 38.0 92-93 35.866875 38.0 38.0 38.0 34.0 38.0 94-95 35.276250000000005 38.0 38.0 38.0 32.0 38.0 96-97 33.145624999999995 38.0 36.0 38.0 8.5 38.0 98-99 30.582124999999998 38.0 30.0 38.0 2.0 38.0 100-101 27.68175 38.0 24.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 0.0 10 0.0 11 0.0 12 1.0 13 0.0 14 1.0 15 0.0 16 1.0 17 0.0 18 0.0 19 0.0 20 0.0 21 3.0 22 2.0 23 4.0 24 9.0 25 10.0 26 17.0 27 38.0 28 33.0 29 29.0 30 33.0 31 51.0 32 77.0 33 98.0 34 177.0 35 425.0 36 757.0 37 2233.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.275 25.575 16.35 23.799999999999997 2 30.882720680170046 31.15778944736184 19.079769942485623 18.879719929982496 3 31.574999999999996 18.375 28.299999999999997 21.75 4 24.525 32.550000000000004 14.725 28.199999999999996 5 42.95 18.15 22.175 16.725 6 21.45 33.25 25.1 20.200000000000003 7 45.475 20.925 20.325 13.275 8 21.125 15.75 46.9 16.225 9 18.125 46.525 20.525 14.825 10-11 37.8625 25.837500000000002 19.2 17.1 12-13 17.962500000000002 14.374999999999998 25.674999999999997 41.9875 14-15 20.125 37.05 29.099999999999998 13.725000000000001 16-17 27.737499999999997 17.65 40.3375 14.274999999999999 18-19 39.8375 22.125 24.3125 13.725000000000001 20-21 15.375 26.7625 38.5375 19.325 22-23 33.025 28.050000000000004 25.0125 13.9125 24-25 30.8125 29.4875 23.674999999999997 16.025 26-27 38.7625 26.137500000000003 20.150000000000002 14.95 28-29 16.6125 37.3625 23.1125 22.912499999999998 30-31 20.575 11.2875 46.1125 22.025 32-33 29.562500000000004 11.862499999999999 30.15 28.425 34-35 38.45 19.537499999999998 25.3125 16.7 36-37 42.662499999999994 19.8375 25.687500000000004 11.8125 38-39 23.425 19.400000000000002 35.9375 21.2375 40-41 22.975 14.0375 23.5375 39.45 42-43 33.85 27.150000000000002 18.0 21.0 44-45 55.175 13.825000000000001 13.0375 17.962500000000002 46-47 28.037499999999998 29.7125 16.5125 25.7375 48-49 21.3625 24.7375 17.349999999999998 36.55 50-51 25.874999999999996 27.05 7.8 39.275 52-53 30.4625 43.375 7.112499999999999 19.05 54-55 21.2625 26.6 20.4625 31.674999999999997 56-57 15.299999999999999 31.112499999999997 13.8 39.787499999999994 58-59 34.300000000000004 20.0875 17.4625 28.15 60-61 15.937499999999998 29.175 23.525 31.362499999999997 62-63 26.924999999999997 19.5875 19.225 34.2625 64-65 22.45 25.4625 26.187500000000004 25.900000000000002 66-67 27.025 17.5875 26.8 28.5875 68-69 33.650000000000006 19.125 21.3 25.924999999999997 70-71 21.5375 27.987499999999997 30.5 19.975 72-73 22.1875 16.0625 31.9625 29.7875 74-75 15.987499999999999 9.2625 29.5 45.25 76-77 21.4875 11.025 43.3875 24.099999999999998 78-79 20.3625 9.2125 41.1875 29.2375 80-81 19.950000000000003 11.200000000000001 35.075 33.775 82-83 28.462500000000002 6.75 37.625 27.1625 84-85 19.3125 9.049999999999999 37.3625 34.275 86-87 18.65 15.975 41.4875 23.8875 88-89 12.4 36.8625 32.85 17.8875 90-91 10.237499999999999 41.15 30.5375 18.075 92-93 16.950000000000003 47.425 22.45 13.175 94-95 10.299999999999999 62.9875 20.150000000000002 6.5625 96-97 9.4125 78.875 9.2 2.5125 98-99 3.5875 91.2625 3.3000000000000003 1.8499999999999999 100-101 1.6 93.65 2.3875 2.3625 >>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 0.0 34 2.0 35 3.5 36 5.0 37 6.0 38 7.5 39 7.5 40 8.0 41 22.0 42 52.0 43 119.0 44 235.0 45 532.0 46 637.5 47 409.0 48 322.5 49 285.5 50 208.0 51 260.0 52 330.5 53 259.5 54 129.0 55 47.5 56 35.0 57 29.0 58 11.5 59 14.5 60 15.0 61 4.0 62 0.5 63 0.5 64 1.0 65 0.5 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 0.025 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 49.95 #Duplication Level Percentage of deduplicated Percentage of total 1 88.13813813813813 44.025 2 4.904904904904905 4.9 3 1.2012012012012012 1.7999999999999998 4 1.1011011011011012 2.1999999999999997 5 0.9009009009009009 2.25 6 0.20020020020020018 0.6 7 0.40040040040040037 1.4000000000000001 8 0.35035035035035034 1.4000000000000001 9 0.35035035035035034 1.575 >10 2.1021021021021022 23.925 >50 0.2502502502502503 8.674999999999999 >100 0.10010010010010009 7.249999999999999 >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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 147 3.675 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 143 3.5749999999999997 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 96 2.4 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 73 1.825 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 72 1.7999999999999998 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 53 1.325 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 53 1.325 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 50 1.25 RNA PCR Primer, Index 1 (100% over 28bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 49 1.225 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 45 1.125 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 44 1.0999999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 43 1.075 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 42 1.05 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 40 1.0 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGC 39 0.975 RNA PCR Primer, Index 24 (100% over 50bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 35 0.8750000000000001 RNA PCR Primer, Index 1 (100% over 26bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 34 0.8500000000000001 Illumina Small RNA Adapter 2 (100% over 21bp) ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 32 0.8 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 27 0.675 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 27 0.675 Illumina Small RNA Adapter 2 (100% over 21bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 27 0.675 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 27 0.675 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 22 0.5499999999999999 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 21 0.525 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 21 0.525 RNA PCR Primer, Index 1 (100% over 22bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 21 0.525 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 21 0.525 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 21 0.525 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 18 0.44999999999999996 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 17 0.42500000000000004 Illumina Small RNA Adapter 2 (100% over 21bp) GGGGACGTAGCTCATATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACG 17 0.42500000000000004 RNA PCR Primer, Index 6 (100% over 34bp) TCGGACCAGGCTTCGATCCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 29bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 13 0.325 No Hit TGAAGCTGCCAGCATGATCTGATGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 13 0.325 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 13 0.325 No Hit TCGCTTGGTGCAGATCGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAG 13 0.325 RNA PCR Primer, Index 1 (100% over 29bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 12 0.3 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 12 0.3 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 27bp) AGAAGAGAGAGAGTACAGCCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 29bp) TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 24bp) TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 10 0.25 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 10 0.25 RNA PCR Primer, Index 1 (100% over 25bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 9 0.22499999999999998 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 9 0.22499999999999998 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 9 0.22499999999999998 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) TGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 8 0.2 RNA PCR Primer, Index 1 (100% over 30bp) GGGCCTGTAGCTCAGAGGATGGAATTCTCGGGTGCCAAGGAACTCCAGTC 8 0.2 RNA PCR Primer, Index 1 (100% over 31bp) TAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) ACGAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAAC 8 0.2 RNA PCR Primer, Index 1 (100% over 24bp) CATCGAGTAGACCTTGTTAATGTGAGAATTTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit CACCATGCGCGGGTTCAATTCCCGTCGTTCGCCCCATGGAATTCTCGGGT 7 0.17500000000000002 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit GTCAGGATAGCTCAGTTGGAAGAGCAGAGGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTA 7 0.17500000000000002 No Hit GAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 33bp) TTTCGTGCTTATCCTAGTTGTTGGTTTAGTTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 6 0.15 No Hit AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 6 0.15 No Hit CACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) GCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) CACAAAACCTTCAGCTACCCATGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) ACCTGCTCTGATACCATGTTGTGATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GTCAGGATAGCTCAGTAGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit GTCCTGCGGCAAAATAGCTCGATGCCAGAATTGGAATTCTCGGGTGCCAA 5 0.125 No Hit TGTCGTGCCAATTCAACATAAACCCCTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATAGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTAATGTGAGAATTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 5 0.125 No Hit TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CCCGCCTTGCACCAAGTGAATTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTTGGAATTCTCGGGTGC 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAAAATGGAATTCTCGGGTGCCAAG 5 0.125 No Hit CTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) >>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 1.025 0.0 0.0 0.0 2 0.0 1.025 0.0 0.0 0.0 3 0.0 1.025 0.0 0.0 0.0 4 0.0 1.025 0.0 0.0 0.0 5 0.0 1.025 0.0 0.0 0.0 6 0.0 1.025 0.0 0.0 0.0 7 0.0 1.025 0.0 0.0 0.0 8 0.0 1.05 0.0 0.0 0.0 9 0.0 1.05 0.0 0.0 0.0 10-11 0.0 1.0625 0.0 0.0 0.0 12-13 0.0 1.125 0.0 0.0 0.0 14-15 0.0 1.2125 0.0 0.0 0.0 16-17 0.0 1.6 0.0 0.0 0.0 18-19 0.0 2.8125 0.0 0.0 0.0 20-21 0.0 4.5 0.0 0.0 0.0 22-23 0.0 12.375 0.0 0.0 0.0 24-25 0.0 25.6 0.0 0.0 0.0 26-27 0.0 38.412499999999994 0.0 0.0 0.0 28-29 0.0 42.425 0.0 0.0 0.0 30-31 0.0 54.75 0.0 0.0 0.0 32-33 0.0 69.5625 0.0 0.0 0.0 34-35 0.0 86.65 0.0 0.0 0.0 36-37 0.0 93.9375 0.0 0.0 0.0 38-39 0.0 95.875 0.0 0.0 0.0 40-41 0.0 96.38749999999999 0.0 0.0 0.0 42-43 0.0 96.975 0.0 0.0 0.0 44-45 0.0 97.15 0.0 0.0 0.0 46-47 0.0 97.25 0.0 0.0 0.0 48-49 0.0 97.25 0.0 0.0 0.0 50-51 0.0 97.25 0.0 0.0 0.0 52-53 0.0 97.25 0.0 0.0 0.0 54-55 0.0 97.25 0.0 0.0 0.0 56-57 0.0 97.25 0.0 0.0 0.0 58-59 0.0 97.25 0.0 0.0 0.0 60-61 0.0 97.25 0.0 0.0 0.0 62-63 0.0 97.25 0.0 0.0 0.0 64-65 0.0 97.25 0.0 0.0 0.0 66-67 0.0 97.25 0.0 0.0 0.0 68-69 0.0 97.25 0.0 0.0 0.0 70-71 0.0 97.25 0.0 0.0 0.0 72-73 0.0 97.25 0.0 0.0 0.0 74-75 0.0 97.25 0.0 0.0 0.0 76-77 0.0 97.25 0.0 0.0 0.0 78-79 0.0 97.275 0.0 0.0 0.0 80-81 0.0 97.275 0.0 0.0 0.0 82-83 0.0 97.3 0.0 0.0 0.0 84-85 0.0 97.325 0.0 0.0 0.0 86-87 0.0 97.325 0.0 0.0 0.0 88-89 0.0 97.35 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGACC 100 0.0 95.0 7 AGCTCAG 25 3.8289727E-7 95.0 9 TTGTAGT 50 0.0 95.0 5 AGTAGAC 100 0.0 95.0 6 AGGATAG 25 3.8289727E-7 95.0 4 TCAGGAT 25 3.8289727E-7 95.0 2 TAGCTCA 30 9.458745E-9 95.0 8 GGATTGT 50 0.0 95.0 2 GATTGTA 50 0.0 95.0 3 TAGTTCA 55 0.0 95.0 8 GGATAGC 25 3.8289727E-7 95.0 5 ATAGCTC 25 3.8289727E-7 95.0 7 GAGTAGA 105 0.0 95.0 5 ATTGTAG 50 0.0 95.0 4 GGGATTG 50 0.0 95.0 1 CGAGTAG 100 0.0 95.0 4 AGACCTT 100 0.0 95.0 9 CAGGATA 25 3.8289727E-7 95.0 3 ATCGAGT 100 0.0 95.0 2 GTCAGGA 25 3.8289727E-7 95.0 1 >>END_MODULE Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305558 READS because READLEN < 1 Read 305558 spots for SRR6941582.sra Written 305558 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra Rejected 305542 READS because READLEN < 1 Read 305542 spots for SRR6941582.sra Written 305542 spots for SRR6941582.sra SRR ids: ['SRR6941582.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_h_mrf52p SRR6941582.sra spots: 6110856 blocks: [[1, 305542], [305543, 611084], [611085, 916626], [916627, 1222168], [1222169, 1527710], [1527711, 1833252], [1833253, 2138794], [2138795, 2444336], [2444337, 2749878], [2749879, 3055420], [3055421, 3360962], [3360963, 3666504], [3666505, 3972046], [3972047, 4277588], [4277589, 4583130], [4583131, 4888672], [4888673, 5194214], [5194215, 5499756], [5499757, 5805298], [5805299, 6110856]] SRR6941582 file size 1459900 SRR6941582 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 SRR6941582 SRR6941582_1.fastq Input file: SRR6941582_1.fastq trimmed: SRR6941582-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 12:06:48 2024 >> started Fri Dec 6 12:06:52 2024 >> done (3.459s) 6110856 reads processed; of these: 110 ( 0.00%) short reads filtered out after trimming by size control 18 ( 0.00%) empty reads filtered out after trimming by size control 6110728 (100.00%) reads available; of these: 1051275 (17.20%) trimmed reads available after processing 5059453 (82.80%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 8 0.00% 20 14 0.00% 21 9 0.00% 22 18 0.00% 23 24 0.00% 24 18 0.00% 25 22 0.00% 26 25 0.00% 27 27 0.00% 28 36 0.00% 29 63 0.00% 30 58 0.00% 31 34 0.00% 32 51 0.00% 33 48 0.00% 34 55 0.00% 35 56 0.00% 36 60 0.00% 37 45 0.00% 38 35 0.00% 39 50 0.00% 40 86 0.00% 41 41 0.00% 42 86 0.00% 43 108 0.00% 44 72 0.00% 45 122 0.00% 46 133 0.00% 47 97 0.00% 48 83 0.00% 49 76 0.00% 50 58 0.00% 51 64 0.00% 52 79 0.00% 53 62 0.00% 54 65 0.00% 55 57 0.00% 56 69 0.00% 57 65 0.00% 58 62 0.00% 59 81 0.00% 60 115 0.00% 61 83 0.00% 62 92 0.00% 63 102 0.00% 64 102 0.00% 65 117 0.00% 66 141 0.00% 67 162 0.00% 68 280 0.00% 69 336 0.01% 70 505 0.01% 71 559 0.01% 72 879 0.01% 73 2356 0.04% 74 15723 0.26% 75 10766 0.18% 76 3558 0.06% 77 996 0.02% 78 1251 0.02% 79 1192 0.02% 80 1377 0.02% 81 1376 0.02% 82 1638 0.03% 83 2059 0.03% 84 3272 0.05% 85 3354 0.05% 86 3477 0.06% 87 4034 0.07% 88 4706 0.08% 89 6853 0.11% 90 18228 0.30% 91 21102 0.35% 92 20985 0.34% 93 34883 0.57% 94 54665 0.89% 95 128549 2.10% 96 122724 2.01% 97 115635 1.89% 98 183095 3.00% 99 198341 3.25% 100 79279 1.30% 101 5059453 82.80% 6110728 reads passed initial QC criterion=sequence-density sequence-density=97.39 sequence-density-rank=1 fanout-score=28.62 fanout-score-rank=2 prefix-density=96.89 prefix-fanout=28.6 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=10 fanout-score=89.74 fanout-score-rank=1 prefix-density=0.47 prefix-fanout=1.0 sequence=CCATCGAGTAGACCTTGTTATTGTGAGAATT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR6941582 - Input file: STDIN trimmed: SRR6941582-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 12:07:13 2024 >> started Fri Dec 6 12:07:19 2024 >> done (6.760s) 5986019 reads processed; of these: 97690 ( 1.63%) short reads filtered out after trimming by size control 61838 ( 1.03%) empty reads filtered out after trimming by size control 5826491 (97.33%) reads available; of these: 5772838 (99.08%) trimmed reads available after processing 53653 ( 0.92%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 23380 0.40% 19 63781 1.09% 20 66915 1.15% 21 329915 5.66% 22 206884 3.55% 23 158722 2.72% 24 1063087 18.25% 25 163695 2.81% 26 139496 2.39% 27 121817 2.09% 28 129512 2.22% 29 358630 6.16% 30 608110 10.44% 31 402282 6.90% 32 457728 7.86% 33 587638 10.09% 34 379452 6.51% 35 217916 3.74% 36 110850 1.90% 37 52000 0.89% 38 24909 0.43% 39 17624 0.30% 40 24753 0.42% 41 21395 0.37% 42 16409 0.28% 43 4899 0.08% 44 5758 0.10% 45 3549 0.06% 46 1140 0.02% 47 1089 0.02% 48 416 0.01% 49 239 0.00% 50 140 0.00% 51 155 0.00% 52 96 0.00% 53 81 0.00% 54 73 0.00% 55 49 0.00% 56 61 0.00% 57 59 0.00% 58 66 0.00% 59 61 0.00% 60 52 0.00% 61 55 0.00% 62 53 0.00% 63 50 0.00% 64 33 0.00% 65 41 0.00% 66 48 0.00% 67 45 0.00% 68 97 0.00% 69 123 0.00% 70 151 0.00% 71 80 0.00% 72 66 0.00% 73 82 0.00% 74 79 0.00% 75 146 0.00% 76 276 0.00% 77 1520 0.03% 78 135 0.00% 79 216 0.00% 80 1717 0.03% 81 511 0.01% 82 965 0.02% 83 641 0.01% 84 205 0.00% 85 198 0.00% 86 380 0.01% 87 556 0.01% 88 221 0.00% 89 169 0.00% 90 165 0.00% 91 409 0.01% 92 359 0.01% 93 256 0.00% 94 347 0.01% 95 495 0.01% 96 514 0.01% 97 508 0.01% 98 899 0.02% 99 559 0.01% 100 714 0.01% 101 47524 0.82% criterion=sequence-density sequence-density=9.27 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCGGAAGCTGCGGGTTCGAGCCCCGTCAGTCCCGCCA criterion=fanout-score sequence-density=0.15 sequence-density-rank=31 fanout-score=105.24 fanout-score-rank=1 prefix-density=15.36 prefix-fanout=1.0 sequence=TATTGTGAGAAAAA Started job on | Dec 06 12:07:50 Started mapping on | Dec 06 12:07:50 Finished on | Dec 06 12:08:09 Mapping speed, Million of reads per hour | 1127.60 Number of input reads | 5951200 Average input read length | 30 UNIQUE READS: Uniquely mapped reads number | 974844 Uniquely mapped reads % | 16.38% Average mapped length | 25.14 Number of splices: Total | 24906 Number of splices: Annotated (sjdb) | 2351 Number of splices: GT/AG | 24079 Number of splices: GC/AG | 698 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 127 Mismatch rate per base, % | 1.06% Deletion rate per base | 0.01% Deletion average length | 1.24 Insertion rate per base | 0.00% Insertion average length | 1.20 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3781456 % of reads mapped to multiple loci | 63.54% Number of reads mapped to too many loci | 927220 % of reads mapped to too many loci | 15.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.79% % of reads unmapped: other | 0.71% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1194900 1194900 1194900 N_multimapping 3781456 3781456 3781456 N_noFeature 677119 771105 876016 N_ambiguous 10471 5021 709 UnstrandedReadsAssigned:287254 PositiveStrandReadsAssigned:198718 NegativeStrandReadsAssigned:98119 Dataset is classified unstranded MeadianReadLen=30 20thPercentileLength=24 echo kmer=19 SRR6941582 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: SRR6941582-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,951,200 reads, 2,704,657 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 982 rounds 52973 SRR6941582.ke.tsv 35125 SRR6941582.se.tsv 88098 total ==> SRR6941582.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 1 0.106395 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 31.8577 4.12195 KQK14071 474 375 0 0 ==> SRR6941582.se.tsv <== BRADI_1g14170v3 58 BRADI_1g53295v3 5 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 4 BRADI_1g74790v3 18 BRADI_1g09890v3 24 BRADI_1g77505v3 1 BRADI_1g48960v3 0 SRR6941582 completed mapping pipeline successfully