Starting /dee2/code/volunteer_pipeline.sh SRR6941571 current disk space = 1551311335424 free memory = 1595799424 SRR6941571 SRAfilesize 7b0eb7d622be8519b29d2c9172960f29 SRR6941571.sra SRR6941571.sra file validated SRR6941571 is single end SRR6941571 is conventional basespace SRR6941571 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6941571_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 33.299 34.0 33.0 34.0 32.0 34.0 2 33.3865 34.0 33.0 34.0 33.0 34.0 3 33.23775 34.0 33.0 34.0 33.0 34.0 4 33.3695 34.0 33.0 34.0 33.0 34.0 5 33.30025 34.0 33.0 34.0 33.0 34.0 6 37.03675 38.0 37.0 38.0 36.0 38.0 7 37.385 38.0 38.0 38.0 37.0 38.0 8 37.554 38.0 38.0 38.0 38.0 38.0 9 37.639 38.0 38.0 38.0 38.0 38.0 10-11 37.547250000000005 38.0 38.0 38.0 38.0 38.0 12-13 37.48175 38.0 38.0 38.0 37.5 38.0 14-15 37.548249999999996 38.0 38.0 38.0 38.0 38.0 16-17 35.874875 38.0 36.5 38.0 27.0 38.0 18-19 36.829625 38.0 37.5 38.0 33.5 38.0 20-21 36.417249999999996 38.0 38.0 38.0 32.5 38.0 22-23 37.35487500000001 38.0 38.0 38.0 36.5 38.0 24-25 37.507875 38.0 38.0 38.0 38.0 38.0 26-27 37.400125 38.0 38.0 38.0 37.0 38.0 28-29 37.48825 38.0 38.0 38.0 38.0 38.0 30-31 37.41525 38.0 38.0 38.0 37.5 38.0 32-33 37.278999999999996 38.0 38.0 38.0 37.0 38.0 34-35 37.248999999999995 38.0 38.0 38.0 37.0 38.0 36-37 37.25475 38.0 38.0 38.0 37.0 38.0 38-39 37.231875 38.0 38.0 38.0 37.0 38.0 40-41 37.19125 38.0 38.0 38.0 37.0 38.0 42-43 37.139125 38.0 38.0 38.0 37.0 38.0 44-45 37.0975 38.0 38.0 38.0 36.5 38.0 46-47 37.031875 38.0 38.0 38.0 36.0 38.0 48-49 37.20275 38.0 38.0 38.0 37.0 38.0 50-51 37.044250000000005 38.0 38.0 38.0 36.0 38.0 52-53 37.150499999999994 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 37.1475 38.0 38.0 38.0 37.0 38.0 58-59 37.2535 38.0 38.0 38.0 37.0 38.0 60-61 37.291624999999996 38.0 38.0 38.0 37.0 38.0 62-63 37.138374999999996 38.0 38.0 38.0 36.5 38.0 64-65 36.925625 38.0 38.0 38.0 35.5 38.0 66-67 36.764 38.0 38.0 38.0 35.0 38.0 68-69 37.082 38.0 38.0 38.0 36.0 38.0 70-71 36.572625 38.0 37.5 38.0 34.0 38.0 72-73 36.267375 38.0 37.0 38.0 33.0 38.0 74-75 35.73725 38.0 37.0 38.0 29.0 38.0 76-77 35.874625 38.0 37.0 38.0 30.0 38.0 78-79 36.38375 38.0 37.5 38.0 33.5 38.0 80-81 36.66175 38.0 38.0 38.0 35.5 38.0 82-83 36.600750000000005 38.0 38.0 38.0 35.0 38.0 84-85 36.667500000000004 38.0 38.0 38.0 35.5 38.0 86-87 36.53475 38.0 38.0 38.0 34.5 38.0 88-89 36.596375 38.0 38.0 38.0 35.0 38.0 90-91 36.585875 38.0 38.0 38.0 35.0 38.0 92-93 36.608625 38.0 38.0 38.0 35.0 38.0 94-95 36.470749999999995 38.0 38.0 38.0 35.0 38.0 96-97 35.329 38.0 37.5 38.0 31.5 38.0 98-99 33.533500000000004 38.0 35.5 38.0 14.5 38.0 100-101 31.119875 38.0 31.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 2.0 19 0.0 20 0.0 21 0.0 22 0.0 23 2.0 24 4.0 25 9.0 26 10.0 27 22.0 28 28.0 29 26.0 30 36.0 31 35.0 32 67.0 33 80.0 34 123.0 35 309.0 36 682.0 37 2565.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.025 24.375 12.25 21.349999999999998 2 34.82611958969227 28.77157868401301 19.014260695521642 17.38804103077308 3 31.55 18.75 26.700000000000003 23.0 4 28.08202050512628 31.032758189547387 16.52913228307077 24.356089022255563 5 41.775 16.7 24.55 16.975 6 22.0 31.374999999999996 25.95 20.674999999999997 7 45.525 21.25 21.7 11.525 8 24.125 13.075000000000001 48.175000000000004 14.625 9 16.725 46.150000000000006 22.625 14.499999999999998 10-11 38.9 25.2875 19.55 16.2625 12-13 16.150000000000002 13.775 28.1375 41.9375 14-15 20.0625 41.125 26.35 12.4625 16-17 28.1 15.675 42.85 13.375 18-19 45.1 20.4875 22.6 11.8125 20-21 13.675 27.6 38.8125 19.9125 22-23 32.337500000000006 30.775000000000002 22.2125 14.674999999999999 24-25 29.5375 32.7125 20.7375 17.0125 26-27 35.7875 24.6625 22.0125 17.5375 28-29 16.75 35.175 20.125 27.950000000000003 30-31 22.125 12.625 40.425 24.825 32-33 27.775 12.625 30.7625 28.8375 34-35 35.3375 21.0375 28.9 14.725 36-37 40.9375 22.3875 27.025 9.65 38-39 23.0 23.2375 35.85 17.9125 40-41 19.9125 13.8625 29.912499999999998 36.3125 42-43 32.824999999999996 21.2625 23.5125 22.400000000000002 44-45 54.8125 10.9625 16.45 17.775 46-47 34.75 24.0 17.45 23.799999999999997 48-49 25.45 21.637500000000003 19.4875 33.425 50-51 27.1 26.137500000000003 7.9 38.8625 52-53 31.874999999999996 44.224999999999994 5.7375 18.1625 54-55 23.45 31.137500000000003 17.962500000000002 27.450000000000003 56-57 12.837499999999999 34.925 12.825000000000001 39.4125 58-59 14.662500000000001 30.8 23.3875 31.15 60-61 21.25 29.3375 15.975 33.4375 62-63 22.162499999999998 26.974999999999998 16.412499999999998 34.449999999999996 64-65 11.1625 33.5625 27.712500000000002 27.5625 66-67 16.625 29.062500000000004 23.625 30.6875 68-69 28.6875 26.625 18.975 25.7125 70-71 23.5 31.912499999999998 26.3 18.2875 72-73 22.25 20.1 27.625 30.025000000000002 74-75 15.437500000000002 13.362499999999999 27.900000000000002 43.3 76-77 20.0875 12.812499999999998 41.462500000000006 25.637500000000003 78-79 21.8625 10.975 39.45 27.712500000000002 80-81 20.0125 13.1375 34.675 32.175 82-83 29.349999999999998 6.862500000000001 35.425000000000004 28.3625 84-85 20.7 4.7 36.3 38.3 86-87 20.3125 9.049999999999999 42.9375 27.700000000000003 88-89 13.525 25.174999999999997 39.287499999999994 22.0125 90-91 11.6875 27.6125 36.512499999999996 24.1875 92-93 19.9375 32.475 29.7125 17.875 94-95 13.7125 48.199999999999996 26.85 11.2375 96-97 12.2875 66.0875 16.625 5.0 98-99 6.4 83.675 6.9750000000000005 2.9499999999999997 100-101 2.825 90.325 3.8375 3.0124999999999997 >>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 1.5 35 2.0 36 2.5 37 2.5 38 1.0 39 2.0 40 8.5 41 18.5 42 70.5 43 161.5 44 420.0 45 539.0 46 356.5 47 314.0 48 284.0 49 223.5 50 317.5 51 413.5 52 355.5 53 211.0 54 97.0 55 67.5 56 53.0 57 21.0 58 28.0 59 21.5 60 3.5 61 1.5 62 0.0 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 0.075 3 0.0 4 0.025 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 46.7 #Duplication Level Percentage of deduplicated Percentage of total 1 85.49250535331906 39.925 2 5.728051391862955 5.35 3 2.194860813704497 3.075 4 1.7130620985010707 3.2 5 1.0171306209850108 2.375 6 0.5353319057815845 1.5 7 0.3747323340471092 1.225 8 0.26766595289079226 1.0 9 0.10706638115631692 0.44999999999999996 >10 2.0342612419700217 20.775 >50 0.4282655246252677 14.649999999999999 >100 0.10706638115631692 6.4750000000000005 >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 158 3.95 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 101 2.5250000000000004 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 93 2.325 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 87 2.175 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 83 2.075 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTGGAATTCTCGGGTGCCAA 76 1.9 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 74 1.8499999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 62 1.55 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGC 60 1.5 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 51 1.275 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAGG 50 1.25 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 49 1.225 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 48 1.2 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 40 1.0 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTGGAATTCTCGGGTGCCA 40 1.0 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 33 0.8250000000000001 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTGGAATTCTCGGGTGCCA 32 0.8 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 31 0.775 RNA PCR Primer, Index 1 (100% over 28bp) TCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 26bp) CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 29 0.7250000000000001 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 27 0.675 RNA PCR Primer, Index 1 (100% over 29bp) GAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGC 26 0.65 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTGGAATTCTCGGGTG 26 0.65 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 23 0.575 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTTGGAATTCTCGGGTGC 23 0.575 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGTTGGAATTCTCGGGT 22 0.5499999999999999 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 20 0.5 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 20 0.5 Illumina Small RNA Adapter 2 (100% over 21bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACCTGGAATTCTCGGGTGCC 20 0.5 No Hit GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 18 0.44999999999999996 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATGGAATTCTCGGGTGCCAAGGA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 22bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGGAATTCTCGGGTGC 16 0.4 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGTGGAATTCTCGGGTGCC 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATGGAATTCTCGGGTGCCAA 14 0.35000000000000003 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTTGGAATTCTCGGGTGCCA 13 0.325 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 13 0.325 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTGGAATTCTCGGGTGCC 13 0.325 No Hit AGAAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTG 12 0.3 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTGGAATTCTCGGGTGCCAA 12 0.3 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTATGGAATTCTCGGGTGCCAA 12 0.3 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCC 12 0.3 No Hit ACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 12 0.3 RNA PCR Primer, Index 1 (100% over 28bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 12 0.3 Illumina Small RNA Adapter 2 (100% over 21bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGGAATTCTCGGGTGCCAA 12 0.3 No Hit TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGC 11 0.27499999999999997 RNA PCR Primer, Index 26 (100% over 50bp) AATATTGGGTAGGTTGTGGTATTTCATTGCTTGGAATTCTCGGGTGCCAA 10 0.25 No Hit AATATTGGGTAGGTTGTGGTATTTCATTGCTGGAATTCTCGGGTGCCAAG 10 0.25 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCCTGGAATTCTCGGGT 10 0.25 No Hit TTGACAGAAGAGAGTGAGCACTGGAATTCTCGGGTGCCAAGGAACTCCAG 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAATGGAATTCTCGGGTG 9 0.22499999999999998 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGTGGAATTCT 8 0.2 No Hit GAACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) AACTTTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTGGAATTCTCGGGTGCC 8 0.2 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 8 0.2 RNA PCR Primer, Index 1 (100% over 25bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 7 0.17500000000000002 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 7 0.17500000000000002 Illumina Small RNA Adapter 2 (100% over 21bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGAATCTGGAATTC 7 0.17500000000000002 No Hit CATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) AAGATACGGGTTCGATTCCCGCCGCTCGCCCCATGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TGTCGTGCCAATTCAACATAAACCCCTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTGGAATTCTCGGGT 6 0.15 No Hit AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCAATGGAATTCTCGGGTGCC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTAAATGGAATTCTCGGGTGCC 6 0.15 No Hit AAGCTGAAGCGGAAATGCAATTCTCGGGTGAGATGGAATTCTCGGGTGCC 6 0.15 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTGGAATTCTCGGGTGCCA 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAGGCTGGAATTC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCATGGAATTCTCGGGTGCC 6 0.15 No Hit GGCGGATGTAGCCAAGAGGATCAAGGCAGTGGATTTGGAATTCTCGGGTG 5 0.125 No Hit GGGATTGTAGTTCAATTGGACAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGCTGTGGAATTCTCGGGTGCC 5 0.125 No Hit TTGTATCGCGCGCATGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAATGGAATTCTCGGGTG 5 0.125 No Hit GGGATTGTAGTTCAATAGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 5 0.125 No Hit GGGTGTTTGGTCTAGTGGTATGATTCTCGCTTTGGAATTCTCGGGTGCCA 5 0.125 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCCATGGAATTCTCGGG 5 0.125 No Hit GTCAGGATAGCTCAGTTGGAAGAGCAGAGGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) TGTCGTGCCAATTCAACATAAACCCTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAAAATGGAATTCTCGG 5 0.125 No Hit TCCCGTGCTGTAAAATAACTGATTTGCCTATCTGATCTGGAATTCTCGGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GGGGATATGGCGAAATCGGTAGACGCTACGGACTTTGGAATTCTCGGGTG 5 0.125 No Hit GCGTCTGTAGTCCAACGGTTAGGATAATTGCCTTCTGGAATTCTCGGGTG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAATGGAATTCTCGGGT 5 0.125 No Hit GCGAGCGTAGTTCAATTGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 5 0.125 No Hit ATATTGGGTAGGTTGTAGTATTTCATTGCTTGGAATTCTCGGGTGCCAAG 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 0.35 0.0 0.0 0.0 2 0.0 0.35 0.0 0.0 0.0 3 0.0 0.375 0.0 0.0 0.0 4 0.0 0.375 0.0 0.0 0.0 5 0.0 0.375 0.0 0.0 0.0 6 0.0 0.375 0.0 0.0 0.0 7 0.0 0.4 0.0 0.0 0.0 8 0.0 0.4 0.0 0.0 0.0 9 0.0 0.425 0.0 0.0 0.0 10-11 0.0 0.425 0.0 0.0 0.0 12-13 0.0 0.425 0.0 0.0 0.0 14-15 0.0 0.45 0.0 0.0 0.0 16-17 0.0 0.5375 0.0 0.0 0.0 18-19 0.0 0.7875 0.0 0.0 0.0 20-21 0.0 1.2125 0.0 0.0 0.0 22-23 0.0 5.2125 0.0 0.0 0.0 24-25 0.0 15.5625 0.0 0.0 0.0 26-27 0.0 25.450000000000003 0.0 0.0 0.0 28-29 0.0 28.2875 0.0 0.0 0.0 30-31 0.0 39.2 0.0 0.0 0.0 32-33 0.0 54.9375 0.0 0.0 0.0 34-35 0.0 75.17500000000001 0.0 0.0 0.0 36-37 0.0 87.25 0.0 0.0 0.0 38-39 0.0 91.15 0.0 0.0 0.0 40-41 0.0 93.1875 0.0 0.0 0.0 42-43 0.0 95.7125 0.0 0.0 0.0 44-45 0.0 96.6125 0.0 0.0 0.0 46-47 0.0 97.05 0.0 0.0 0.0 48-49 0.0 97.3 0.0 0.0 0.0 50-51 0.0 97.35 0.0 0.0 0.0 52-53 0.0 97.4 0.0 0.0 0.0 54-55 0.0 97.4 0.0 0.0 0.0 56-57 0.0 97.4 0.0 0.0 0.0 58-59 0.0 97.4 0.0 0.0 0.0 60-61 0.0 97.4 0.0 0.0 0.0 62-63 0.0 97.4 0.0 0.0 0.0 64-65 0.0 97.4 0.0 0.0 0.0 66-67 0.0 97.4 0.0 0.0 0.0 68-69 0.0 97.4 0.0 0.0 0.0 70-71 0.0 97.4 0.0 0.0 0.0 72-73 0.0 97.4 0.0 0.0 0.0 74-75 0.0 97.4 0.0 0.0 0.0 76-77 0.0 97.4 0.0 0.0 0.0 78-79 0.0 97.4 0.0 0.0 0.0 80-81 0.0 97.4 0.0 0.0 0.0 82-83 0.0 97.4 0.0 0.0 0.0 84-85 0.0 97.4 0.0 0.0 0.0 86-87 0.0 97.4 0.0 0.0 0.0 88-89 0.0 97.4 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 20 1.5392321E-5 95.00001 9 TAGCTCA 20 1.5392321E-5 95.00001 8 GGCTGTA 20 1.5392321E-5 95.00001 4 TAGTTTA 20 1.5392321E-5 95.00001 9 GCTGTAG 20 1.5392321E-5 95.00001 5 GTGGCTG 20 1.5392321E-5 95.00001 2 GGTGGCT 20 1.5392321E-5 95.00001 1 GTAGTTT 20 1.5392321E-5 95.00001 8 TGGCTGT 20 1.5392321E-5 95.00001 3 GTAGACC 65 0.0 95.0 7 TTGTAGT 45 0.0 95.0 5 AGTAGAC 65 0.0 95.0 6 AGGATAG 15 6.142176E-4 95.0 4 TCAGGAT 15 6.142176E-4 95.0 2 GGACCAG 15 6.142176E-4 95.0 3 GGATTGT 45 0.0 95.0 2 CGGACCA 15 6.142176E-4 95.0 2 TCGGACC 15 6.142176E-4 95.0 1 GATTGTA 45 0.0 95.0 3 TAGTTCA 55 0.0 95.0 8 >>END_MODULE Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra Rejected 318152 READS because READLEN < 1 Read 318152 spots for SRR6941571.sra Written 318152 spots for SRR6941571.sra Rejected 318145 READS because READLEN < 1 Read 318145 spots for SRR6941571.sra Written 318145 spots for SRR6941571.sra SRR ids: ['SRR6941571.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_z424vgxr SRR6941571.sra spots: 6362907 blocks: [[1, 318145], [318146, 636290], [636291, 954435], [954436, 1272580], [1272581, 1590725], [1590726, 1908870], [1908871, 2227015], [2227016, 2545160], [2545161, 2863305], [2863306, 3181450], [3181451, 3499595], [3499596, 3817740], [3817741, 4135885], [4135886, 4454030], [4454031, 4772175], [4772176, 5090320], [5090321, 5408465], [5408466, 5726610], [5726611, 6044755], [6044756, 6362907]] SRR6941571 file size 1520206 SRR6941571 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 SRR6941571 SRR6941571_1.fastq Input file: SRR6941571_1.fastq trimmed: SRR6941571-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 11:42:10 2024 >> started Fri Dec 6 11:42:13 2024 >> done (2.806s) 6362907 reads processed; of these: 76 ( 0.00%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 6362821 (100.00%) reads available; of these: 678471 (10.66%) trimmed reads available after processing 5684350 (89.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 4 0.00% 20 7 0.00% 21 3 0.00% 22 16 0.00% 23 10 0.00% 24 16 0.00% 25 14 0.00% 26 14 0.00% 27 15 0.00% 28 26 0.00% 29 47 0.00% 30 61 0.00% 31 39 0.00% 32 53 0.00% 33 32 0.00% 34 59 0.00% 35 55 0.00% 36 51 0.00% 37 64 0.00% 38 69 0.00% 39 66 0.00% 40 89 0.00% 41 85 0.00% 42 99 0.00% 43 119 0.00% 44 117 0.00% 45 147 0.00% 46 162 0.00% 47 138 0.00% 48 124 0.00% 49 112 0.00% 50 120 0.00% 51 93 0.00% 52 84 0.00% 53 69 0.00% 54 75 0.00% 55 74 0.00% 56 62 0.00% 57 31 0.00% 58 43 0.00% 59 63 0.00% 60 87 0.00% 61 62 0.00% 62 73 0.00% 63 68 0.00% 64 40 0.00% 65 52 0.00% 66 82 0.00% 67 94 0.00% 68 129 0.00% 69 147 0.00% 70 215 0.00% 71 221 0.00% 72 386 0.01% 73 950 0.01% 74 5434 0.09% 75 3719 0.06% 76 1316 0.02% 77 497 0.01% 78 652 0.01% 79 675 0.01% 80 732 0.01% 81 740 0.01% 82 846 0.01% 83 969 0.02% 84 1540 0.02% 85 1746 0.03% 86 1757 0.03% 87 1917 0.03% 88 1966 0.03% 89 2517 0.04% 90 3980 0.06% 91 5506 0.09% 92 6818 0.11% 93 12693 0.20% 94 22798 0.36% 95 68204 1.07% 96 70694 1.11% 97 74370 1.17% 98 148609 2.34% 99 167377 2.63% 100 65157 1.02% 101 5684350 89.34% 6362821 reads passed initial QC criterion=sequence-density sequence-density=97.69 sequence-density-rank=1 fanout-score=28.31 fanout-score-rank=1 prefix-density=97.85 prefix-fanout=28.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=97.69 sequence-density-rank=1 fanout-score=28.31 fanout-score-rank=1 prefix-density=97.85 prefix-fanout=28.3 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -o SRR6941571 - Input file: STDIN trimmed: SRR6941571-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGA -- 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 11:42:36 2024 >> started Fri Dec 6 11:42:43 2024 >> done (6.983s) 6232968 reads processed; of these: 21403 ( 0.34%) short reads filtered out after trimming by size control 22209 ( 0.36%) empty reads filtered out after trimming by size control 6189356 (99.30%) reads available; of these: 6152481 (99.40%) trimmed reads available after processing 36875 ( 0.60%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7178 0.12% 19 19028 0.31% 20 26371 0.43% 21 182285 2.95% 22 130475 2.11% 23 106795 1.73% 24 915963 14.80% 25 121778 1.97% 26 103943 1.68% 27 86745 1.40% 28 102581 1.66% 29 329879 5.33% 30 594080 9.60% 31 406433 6.57% 32 566196 9.15% 33 771703 12.47% 34 566901 9.16% 35 396075 6.40% 36 200421 3.24% 37 109757 1.77% 38 59485 0.96% 39 46971 0.76% 40 80379 1.30% 41 78744 1.27% 42 61064 0.99% 43 18698 0.30% 44 24362 0.39% 45 19066 0.31% 46 6152 0.10% 47 6576 0.11% 48 2116 0.03% 49 1010 0.02% 50 605 0.01% 51 633 0.01% 52 352 0.01% 53 235 0.00% 54 149 0.00% 55 127 0.00% 56 74 0.00% 57 81 0.00% 58 40 0.00% 59 43 0.00% 60 27 0.00% 61 19 0.00% 62 34 0.00% 63 23 0.00% 64 20 0.00% 65 20 0.00% 66 28 0.00% 67 18 0.00% 68 35 0.00% 69 44 0.00% 70 74 0.00% 71 43 0.00% 72 50 0.00% 73 54 0.00% 74 55 0.00% 75 84 0.00% 76 113 0.00% 77 352 0.01% 78 126 0.00% 79 141 0.00% 80 462 0.01% 81 178 0.00% 82 308 0.00% 83 229 0.00% 84 83 0.00% 85 101 0.00% 86 136 0.00% 87 162 0.00% 88 97 0.00% 89 103 0.00% 90 133 0.00% 91 187 0.00% 92 216 0.00% 93 261 0.00% 94 282 0.00% 95 391 0.01% 96 401 0.01% 97 436 0.01% 98 777 0.01% 99 515 0.01% 100 578 0.01% 101 30411 0.49% criterion=sequence-density sequence-density=12.49 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=0.14 sequence-density-rank=28 fanout-score=91.00 fanout-score-rank=1 prefix-density=12.34 prefix-fanout=1.0 sequence=TATTGTGAGAAAAAA Started job on | Dec 06 11:42:56 Started mapping on | Dec 06 11:42:57 Finished on | Dec 06 11:43:16 Mapping speed, Million of reads per hour | 1197.32 Number of input reads | 6319209 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 961864 Uniquely mapped reads % | 15.22% Average mapped length | 27.01 Number of splices: Total | 22711 Number of splices: Annotated (sjdb) | 2724 Number of splices: GT/AG | 21773 Number of splices: GC/AG | 739 Number of splices: AT/AC | 2 Number of splices: Non-canonical | 197 Mismatch rate per base, % | 0.94% Deletion rate per base | 0.01% Deletion average length | 1.33 Insertion rate per base | 0.00% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4124697 % of reads mapped to multiple loci | 65.27% Number of reads mapped to too many loci | 942142 % of reads mapped to too many loci | 14.91% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.02% % of reads unmapped: other | 0.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1232648 1232648 1232648 N_multimapping 4124697 4124697 4124697 N_noFeature 595501 749089 802918 N_ambiguous 13283 7416 621 UnstrandedReadsAssigned:353080 PositiveStrandReadsAssigned:205359 NegativeStrandReadsAssigned:158325 Dataset is classified unstranded MeadianReadLen=31 20thPercentileLength=24 echo kmer=19 SRR6941571 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: SRR6941571-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,319,209 reads, 2,971,997 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 970 rounds 52973 SRR6941571.ke.tsv 35125 SRR6941571.se.tsv 88098 total ==> SRR6941571.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 0 0 PNS24243 293 194 1 0.806453 KQK14069 1603 1504 29.6408 3.08335 KQK14071 474 375 0 0 ==> SRR6941571.se.tsv <== BRADI_1g14170v3 84 BRADI_1g53295v3 2 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 1 BRADI_1g74790v3 12 BRADI_1g09890v3 25 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR6941571 completed mapping pipeline successfully