Starting /dee2/code/volunteer_pipeline.sh SRR7472590 current disk space = 3088599228416 free memory = 1438390444 SRR7472590 SRAfilesize ba95e8059af86f83ec7a7332a67f22d1 SRR7472590.sra SRR7472590.sra file validated SRR7472590 is single end SRR7472590 is conventional basespace SRR7472590 read1 length is 51 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7472590_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 51 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.10225 34.0 33.0 34.0 32.0 34.0 2 33.18625 34.0 33.0 34.0 33.0 34.0 3 33.15575 34.0 34.0 34.0 33.0 34.0 4 33.1835 34.0 34.0 34.0 33.0 34.0 5 33.18725 34.0 34.0 34.0 33.0 34.0 6 36.9375 38.0 38.0 38.0 36.0 38.0 7 37.137 38.0 38.0 38.0 37.0 38.0 8 37.22325 38.0 38.0 38.0 37.0 38.0 9 37.2665 38.0 38.0 38.0 38.0 38.0 10 36.89625 38.0 38.0 38.0 36.0 38.0 11 37.16575 38.0 38.0 38.0 37.0 38.0 12 37.21475 38.0 38.0 38.0 37.0 38.0 13 37.2135 38.0 38.0 38.0 37.0 38.0 14 37.2735 38.0 38.0 38.0 38.0 38.0 15 37.2185 38.0 38.0 38.0 38.0 38.0 16 37.22625 38.0 38.0 38.0 37.0 38.0 17 37.12725 38.0 38.0 38.0 37.0 38.0 18 37.15725 38.0 38.0 38.0 37.0 38.0 19 37.13875 38.0 38.0 38.0 37.0 38.0 20 37.15 38.0 38.0 38.0 37.0 38.0 21 37.09125 38.0 38.0 38.0 37.0 38.0 22 37.12875 38.0 38.0 38.0 37.0 38.0 23 37.112 38.0 38.0 38.0 37.0 38.0 24 36.9575 38.0 38.0 38.0 37.0 38.0 25 37.10725 38.0 38.0 38.0 37.0 38.0 26 37.0905 38.0 38.0 38.0 37.0 38.0 27 37.254 38.0 38.0 38.0 37.0 38.0 28 37.24875 38.0 38.0 38.0 38.0 38.0 29 37.31775 38.0 38.0 38.0 38.0 38.0 30 37.3365 38.0 38.0 38.0 38.0 38.0 31 37.12975 38.0 38.0 38.0 37.0 38.0 32 37.0945 38.0 38.0 38.0 37.0 38.0 33 37.21325 38.0 38.0 38.0 37.0 38.0 34 37.273 38.0 38.0 38.0 38.0 38.0 35 37.3775 38.0 38.0 38.0 38.0 38.0 36 37.1525 38.0 38.0 38.0 38.0 38.0 37 37.278 38.0 38.0 38.0 38.0 38.0 38 37.32625 38.0 38.0 38.0 38.0 38.0 39 37.3085 38.0 38.0 38.0 38.0 38.0 40 37.2835 38.0 38.0 38.0 38.0 38.0 41 37.197 38.0 38.0 38.0 38.0 38.0 42 37.169 38.0 38.0 38.0 38.0 38.0 43 37.1665 38.0 38.0 38.0 38.0 38.0 44 37.2465 38.0 38.0 38.0 38.0 38.0 45 37.25775 38.0 38.0 38.0 38.0 38.0 46 37.25975 38.0 38.0 38.0 38.0 38.0 47 37.21775 38.0 38.0 38.0 38.0 38.0 48 37.3075 38.0 38.0 38.0 38.0 38.0 49 37.321 38.0 38.0 38.0 38.0 38.0 50 37.3005 38.0 38.0 38.0 38.0 38.0 51 37.2635 38.0 38.0 38.0 38.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 20.0 3 0.0 4 4.0 5 1.0 6 1.0 7 2.0 8 0.0 9 0.0 10 1.0 11 0.0 12 2.0 13 2.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 1.0 22 2.0 23 4.0 24 1.0 25 4.0 26 3.0 27 4.0 28 12.0 29 14.0 30 16.0 31 26.0 32 38.0 33 50.0 34 75.0 35 125.0 36 231.0 37 3360.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 16.900000000000002 29.625 33.900000000000006 19.575 2 22.225 22.625 20.200000000000003 34.949999999999996 3 31.225 23.25 23.400000000000002 22.125 4 35.675000000000004 23.150000000000002 16.925 24.25 5 27.55 36.025 14.725 21.7 6 26.325 21.85 16.8 35.025 7 25.1 24.224999999999998 21.15 29.525000000000002 8 23.375 34.35 19.725 22.55 9 33.875 24.925 18.125 23.075000000000003 10 37.025000000000006 23.0 18.925 21.05 11 31.424999999999997 18.575 23.1 26.900000000000002 12 29.275000000000002 18.224999999999998 30.675 21.825 13 23.025000000000002 20.0 31.025000000000002 25.95 14 21.95 24.6 25.7 27.750000000000004 15 27.775 32.7 21.2 18.325 16 22.6 25.15 29.4 22.85 17 19.8 26.825 35.275 18.099999999999998 18 23.974999999999998 20.575 24.45 31.0 19 22.3 21.525 29.625 26.55 20 26.525 22.3 22.6 28.575 21 24.9 23.875 21.25 29.975 22 20.974999999999998 22.175 40.300000000000004 16.55 23 39.300000000000004 19.425 24.725 16.55 24 42.925000000000004 17.775 26.474999999999998 12.825000000000001 25 24.75 34.150000000000006 30.2 10.9 26 31.465732866433214 37.06853426713357 20.36018009004502 11.105552776388194 27 28.549999999999997 21.625 37.925 11.899999999999999 28 17.599999999999998 26.35 42.3 13.750000000000002 29 18.15 21.975 28.4 31.474999999999998 30 19.075 10.75 52.2 17.974999999999998 31 21.575 8.649999999999999 33.925 35.85 32 39.81990995497749 9.129564782391196 20.335167583791897 30.71535767883942 33 45.2 10.15 27.275 17.375 34 48.15 10.725 16.675 24.45 35 41.6 9.775 33.1 15.525 36 54.574999999999996 11.075 18.125 16.225 37 36.975 13.425 14.649999999999999 34.949999999999996 38 23.674999999999997 14.549999999999999 22.6 39.175 39 31.5 33.95 10.5 24.05 40 22.075 39.25 9.325 29.349999999999998 41 39.5 24.65 9.15 26.700000000000003 42 41.91691691691692 32.08208208208208 8.008008008008009 17.992992992992992 43 25.775 49.175000000000004 8.725 16.325 44 31.225 43.125 7.324999999999999 18.325 45 26.974999999999998 26.375 8.774999999999999 37.875 46 14.307153576788394 32.96648324162081 27.71385692846423 25.012506253126567 47 12.9 32.05 12.725 42.325 48 12.375 21.25 12.15 54.225 49 13.25 37.225 19.525000000000002 30.0 50 29.775000000000002 24.75 10.6 34.875 51 15.225 23.7 27.900000000000002 33.175 >>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 0.5 27 1.0 28 1.0 29 1.0 30 1.0 31 1.0 32 1.5 33 2.0 34 1.5 35 1.0 36 4.0 37 7.0 38 15.0 39 23.0 40 34.0 41 45.0 42 82.5 43 120.0 44 139.0 45 158.0 46 238.5 47 319.0 48 321.0 49 323.0 50 451.0 51 579.0 52 599.0 53 619.0 54 590.5 55 562.0 56 651.5 57 741.0 58 481.0 59 221.0 60 175.5 61 130.0 62 101.5 63 73.0 64 58.0 65 43.0 66 31.5 67 20.0 68 12.5 69 5.0 70 4.5 71 4.0 72 3.0 73 2.0 74 1.0 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 0.0 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 0.05 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.05 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.1 43 0.0 44 0.0 45 0.0 46 0.05 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 51 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 59.599999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 89.93288590604027 53.6 2 5.117449664429531 6.1 3 1.5939597315436242 2.85 4 0.5453020134228188 1.3 5 0.5033557046979865 1.5 6 0.25167785234899326 0.8999999999999999 7 0.37751677852348997 1.575 8 0.20973154362416108 1.0 9 0.04194630872483222 0.22499999999999998 >10 1.2583892617449663 12.625 >50 0.08389261744966443 3.975 >100 0.08389261744966443 14.35 >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 TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 412 10.299999999999999 RNA PCR Primer, Index 1 (100% over 30bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 162 4.05 RNA PCR Primer, Index 1 (100% over 30bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 81 2.025 RNA PCR Primer, Index 1 (100% over 29bp) CTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 78 1.95 RNA PCR Primer, Index 1 (100% over 28bp) AACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 30bp) TCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 27 0.675 RNA PCR Primer, Index 1 (100% over 26bp) CCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 26 0.65 RNA PCR Primer, Index 1 (100% over 27bp) ATCCGGTTAGGATCGATCTAAACCAGCCCTGGAATTCTCGGGTGCCAAGGA 26 0.65 RNA PCR Primer, Index 1 (100% over 22bp) CATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAAC 24 0.6 RNA PCR Primer, Index 1 (100% over 24bp) ATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACT 24 0.6 RNA PCR Primer, Index 1 (100% over 25bp) TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 29bp) TTTGGATTGAAGGGAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 21 0.525 RNA PCR Primer, Index 1 (100% over 31bp) CAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 20 0.5 RNA PCR Primer, Index 1 (100% over 27bp) ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 19 0.475 RNA PCR Primer, Index 1 (100% over 31bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGCTGGAATTCTCGGGTGCCAA 19 0.475 No Hit CAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 32bp) ACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAC 18 0.44999999999999996 RNA PCR Primer, Index 5 (100% over 35bp) TAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGT 17 0.42500000000000004 No Hit GCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAA 17 0.42500000000000004 RNA PCR Primer, Index 1 (100% over 23bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCC 17 0.42500000000000004 RNA PCR Primer, Index 5 (100% over 51bp) CCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACA 17 0.42500000000000004 RNA PCR Primer, Index 5 (100% over 36bp) TCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 13 0.325 RNA PCR Primer, Index 1 (100% over 26bp) AGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCA 13 0.325 RNA PCR Primer, Index 1 (100% over 28bp) GCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAG 12 0.3 RNA PCR Primer, Index 1 (100% over 29bp) AACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAG 12 0.3 No Hit AGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 12 0.3 RNA PCR Primer, Index 1 (100% over 33bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCCA 11 0.27499999999999997 No Hit GAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAG 11 0.27499999999999997 No Hit GACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA 10 0.25 RNA PCR Primer, Index 1 (100% over 34bp) CAAGATGAGTGCTCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 10 0.25 RNA PCR Primer, Index 1 (100% over 33bp) CCAAGATGAGTGCTCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 10 0.25 RNA PCR Primer, Index 1 (100% over 32bp) GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 10 0.25 RNA PCR Primer, Index 1 (100% over 28bp) AGTTACTAATTCATGATCTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC 10 0.25 RNA PCR Primer, Index 1 (100% over 27bp) AGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGG 10 0.25 Illumina Small RNA Adapter 2 (100% over 21bp) GTGGGAATGAACATTATGAGATGGAATTCTCGGGTGCCAAGGAACTCCAGT 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 30bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) TTTGGATTGAAGGGAGCTCTATGGAATTCTCGGGTGCCAAGGAACTCCAGT 8 0.2 RNA PCR Primer, Index 1 (100% over 30bp) AACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) AGTTACTAATTCATGATCTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA 8 0.2 RNA PCR Primer, Index 1 (100% over 28bp) TCACGGGGTGTTGTAGACACCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 8 0.2 RNA PCR Primer, Index 1 (100% over 30bp) GATGGAGGACGAGGAAGTTTCTTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit TTCCACAGCTTTCTTGAACTTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 30bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGCTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit ATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GCACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) TGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit CCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 30bp) GGTAGTTCGATCGTGGAATTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GGGGATGTAGCTCAAATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) TGTGTTCTCAGGTCGCCCCTGTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) CTAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACG 6 0.15 No Hit CGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) AGTTACTAATTCATGATCTGGCATATGGAATTCTCGGGTGCCAAGGAACTC 6 0.15 RNA PCR Primer, Index 1 (100% over 26bp) TTTCCCGGCTGGTGCACCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 5 0.125 RNA PCR Primer, Index 1 (100% over 32bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) ATAGCTCGACGCCAGGATTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 5 0.125 RNA PCR Primer, Index 1 (100% over 33bp) TAAAATTTTAAGATAGAGACTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) ACAGCAGGACGGTGGTCATGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) CCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) AGTTACTAATTCATGATCTGGCCTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) ACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 5 0.125 RNA PCR Primer, Index 1 (100% over 30bp) AACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) TCCCGGTAGGACCTCCATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACA 5 0.125 RNA PCR Primer, Index 1 (100% over 34bp) TAAACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 5 0.125 RNA PCR Primer, Index 1 (100% over 32bp) CCCAAGATGAGTGCTCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) >>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 0.425 0.0 0.0 0.0 2 0.0 0.425 0.0 0.0 0.0 3 0.0 0.425 0.0 0.0 0.0 4 0.0 0.425 0.0 0.0 0.0 5 0.0 0.425 0.0 0.0 0.0 6 0.0 0.45 0.0 0.0 0.0 7 0.0 0.475 0.0 0.0 0.0 8 0.0 0.575 0.0 0.0 0.0 9 0.0 0.625 0.0 0.0 0.0 10 0.0 0.8 0.0 0.0 0.0 11 0.0 0.975 0.0 0.0 0.0 12 0.0 1.325 0.0 0.0 0.0 13 0.0 1.975 0.0 0.0 0.0 14 0.0 2.575 0.0 0.0 0.0 15 0.0 3.55 0.0 0.0 0.0 16 0.0 5.15 0.0 0.0 0.0 17 0.0 7.15 0.0 0.0 0.0 18 0.0 9.175 0.0 0.0 0.0 19 0.0 12.175 0.0 0.0 0.0 20 0.0 15.725 0.0 0.0 0.0 21 0.0 20.125 0.0 0.0 0.0 22 0.0 42.85 0.0 0.0 0.0 23 0.0 51.8 0.0 0.0 0.0 24 0.0 58.675 0.0 0.0 0.0 25 0.0 73.175 0.0 0.0 0.0 26 0.0 77.275 0.0 0.0 0.0 27 0.0 80.375 0.0 0.0 0.0 28 0.0 83.05 0.0 0.0 0.0 29 0.0 85.875 0.0 0.0 0.0 30 0.0 88.625 0.0 0.0 0.0 31 0.0 90.35 0.0 0.0 0.0 32 0.0 91.875 0.0 0.0 0.0 33 0.0 93.525 0.0 0.0 0.0 34 0.0 94.575 0.0 0.0 0.0 35 0.0 95.375 0.0 0.0 0.0 36 0.0 95.75 0.0 0.0 0.0 37 0.0 96.025 0.0 0.0 0.0 38 0.0 96.125 0.0 0.0 0.0 39 0.0 96.15 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAGCCCT 20 6.222983E-4 45.0 24 AAACCAG 20 6.222983E-4 45.0 20 TAGGATC 20 6.222983E-4 45.0 8 TAAACCA 20 6.222983E-4 45.0 19 TCGATCT 20 6.222983E-4 45.0 13 CCAGCCC 20 6.222983E-4 45.0 23 AGGATCG 20 6.222983E-4 45.0 9 ATCTAAA 20 6.222983E-4 45.0 16 GGATCGA 20 6.222983E-4 45.0 10 GATCGAT 20 6.222983E-4 45.0 11 GGTTAGG 20 6.222983E-4 45.0 5 TCCGGTT 20 6.222983E-4 45.0 2 AACCAGC 20 6.222983E-4 45.0 21 TCTAAAC 20 6.222983E-4 45.0 17 GATCTAA 20 6.222983E-4 45.0 15 GTTAGGA 20 6.222983E-4 45.0 6 CTAAACC 20 6.222983E-4 45.0 18 TTAGGAT 20 6.222983E-4 45.0 7 ATCCGGT 20 6.222983E-4 45.0 1 CGGTTAG 20 6.222983E-4 45.0 4 >>END_MODULE Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728321 READS because READLEN < 1 Read 728321 spots for SRR7472590.sra Written 728321 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra Rejected 728305 READS because READLEN < 1 Read 728305 spots for SRR7472590.sra Written 728305 spots for SRR7472590.sra SRR ids: ['SRR7472590.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_amen4ghm SRR7472590.sra spots: 14566116 blocks: [[1, 728305], [728306, 1456610], [1456611, 2184915], [2184916, 2913220], [2913221, 3641525], [3641526, 4369830], [4369831, 5098135], [5098136, 5826440], [5826441, 6554745], [6554746, 7283050], [7283051, 8011355], [8011356, 8739660], [8739661, 9467965], [9467966, 10196270], [10196271, 10924575], [10924576, 11652880], [11652881, 12381185], [12381186, 13109490], [13109491, 13837795], [13837796, 14566116]] SRR7472590 file size 2055109 SRR7472590 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 SRR7472590 SRR7472590_1.fastq Input file: SRR7472590_1.fastq trimmed: SRR7472590-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 Thu Feb 13 18:03:58 2025 >> started Thu Feb 13 18:04:04 2025 >> done (6.278s) 14566116 reads processed; of these: 11062 ( 0.08%) short reads filtered out after trimming by size control 22004 ( 0.15%) empty reads filtered out after trimming by size control 14533050 (99.77%) reads available; of these: 27319 ( 0.19%) trimmed reads available after processing 14505731 (99.81%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 385 0.00% 19 490 0.00% 20 363 0.00% 21 421 0.00% 22 501 0.00% 23 374 0.00% 24 304 0.00% 25 427 0.00% 26 372 0.00% 27 328 0.00% 28 446 0.00% 29 531 0.00% 30 478 0.00% 31 527 0.00% 32 406 0.00% 33 518 0.00% 34 502 0.00% 35 609 0.00% 36 475 0.00% 37 455 0.00% 38 492 0.00% 39 584 0.00% 40 558 0.00% 41 520 0.00% 42 546 0.00% 43 533 0.00% 44 637 0.00% 45 735 0.01% 46 826 0.01% 47 1441 0.01% 48 1436 0.01% 49 2104 0.01% 50 7995 0.06% 51 14505731 99.81% 14533050 reads passed initial QC criterion=sequence-density sequence-density=96.94 sequence-density-rank=1 fanout-score=21.16 fanout-score-rank=4 prefix-density=97.04 prefix-fanout=21.1 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCG criterion=fanout-score sequence-density=1.22 sequence-density-rank=5 fanout-score=28.88 fanout-score-rank=1 prefix-density=1.19 prefix-fanout=28.9 sequence=GACTGGAATTCT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCG -o SRR7472590 - Input file: STDIN trimmed: SRR7472590-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACAGTGATCTCGTATGCCG -- 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 Thu Feb 13 18:04:24 2025 >> started Thu Feb 13 18:04:34 2025 >> done (10.203s) 14233400 reads processed; of these: 1214823 ( 8.54%) short reads filtered out after trimming by size control 56914 ( 0.40%) empty reads filtered out after trimming by size control 12961663 (91.07%) reads available; of these: 12705124 (98.02%) trimmed reads available after processing 256539 ( 1.98%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 409307 3.16% 19 442000 3.41% 20 655976 5.06% 21 3430061 26.46% 22 1239101 9.56% 23 1053595 8.13% 24 2059694 15.89% 25 650794 5.02% 26 432279 3.34% 27 398996 3.08% 28 345897 2.67% 29 444013 3.43% 30 244358 1.89% 31 237020 1.83% 32 260290 2.01% 33 167040 1.29% 34 84813 0.65% 35 62460 0.48% 36 33695 0.26% 37 18915 0.15% 38 12133 0.09% 39 7808 0.06% 40 5337 0.04% 41 2924 0.02% 42 3906 0.03% 43 2065 0.02% 44 1256 0.01% 45 1069 0.01% 46 949 0.01% 47 1074 0.01% 48 2378 0.02% 49 641 0.00% 50 1084 0.01% 51 248735 1.92% criterion=sequence-density sequence-density=4.86 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=TCTCGGACCAGGCTTCATTCCCCTGGAATTCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=34.93 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=1.0 sequence=AGCCAAGTGCGGAGCGGATAACTGCTGAAAGCATCTAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCCTATT Started job on | Feb 13 18:04:51 Started mapping on | Feb 13 18:04:51 Finished on | Feb 13 18:05:20 Mapping speed, Million of reads per hour | 1646.23 Number of input reads | 13261313 Average input read length | 24 UNIQUE READS: Uniquely mapped reads number | 4027815 Uniquely mapped reads % | 30.37% Average mapped length | 24.34 Number of splices: Total | 32769 Number of splices: Annotated (sjdb) | 14401 Number of splices: GT/AG | 32261 Number of splices: GC/AG | 352 Number of splices: AT/AC | 35 Number of splices: Non-canonical | 121 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.00% Deletion average length | 1.19 Insertion rate per base | 0.00% Insertion average length | 1.05 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2692611 % of reads mapped to multiple loci | 20.30% Number of reads mapped to too many loci | 5940235 % of reads mapped to too many loci | 44.79% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.23% % of reads unmapped: other | 1.30% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6540887 6540887 6540887 N_multimapping 2692611 2692611 2692611 N_noFeature 1928378 2043119 3312418 N_ambiguous 602716 1324 749 UnstrandedReadsAssigned:1496721 PositiveStrandReadsAssigned:1983372 NegativeStrandReadsAssigned:714648 Dataset is classified unstranded MeadianReadLen=23 20thPercentileLength=21 echo kmer=19 SRR7472590 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: 52,400 [index] number of k-mers: 59,590,899 [index] number of equivalence classes: 293,668 [quant] running in single-end mode [quant] will process file 1: SRR7472590-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,261,313 reads, 7,534,503 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,165 rounds 52401 SRR7472590.ke.tsv 34699 SRR7472590.se.tsv 87100 total ==> SRR7472590.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 11.1666 0.593119 Potri.005G024800.1.v4.1 1035 936 2 0.217796 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 9.22407 0.330589 Potri.016G087400.1.v4.1 270 171 1 0.596072 Potri.015G069301.1.v4.1 564 465 5 1.096 Potri.010G195200.1.v4.1 1773 1674 2 0.121778 Potri.012G127500.1.v4.1 977 878 22 2.55401 ==> SRR7472590.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 2 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 1 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 0 SRR7472590 completed mapping pipeline successfully