Starting /dee2/code/volunteer_pipeline.sh SRR13165353 current disk space = 1542128054272 free memory = 1602248116 SRR13165353 SRAfilesize f222793bef96477ace83a3398b0d29f4 SRR13165353.sra SRR13165353.sra file validated SRR13165353 is paired end SRR13165353 is conventional basespace SRR13165353 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165353_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.557 37.0 37.0 37.0 37.0 37.0 2 36.166 37.0 37.0 37.0 37.0 37.0 3 36.5485 37.0 37.0 37.0 37.0 37.0 4 36.552 37.0 37.0 37.0 37.0 37.0 5 36.598 37.0 37.0 37.0 37.0 37.0 6 36.553 37.0 37.0 37.0 37.0 37.0 7 36.4145 37.0 37.0 37.0 37.0 37.0 8 36.623 37.0 37.0 37.0 37.0 37.0 9 36.479 37.0 37.0 37.0 37.0 37.0 10-14 36.5431 37.0 37.0 37.0 37.0 37.0 15-19 36.5114 37.0 37.0 37.0 37.0 37.0 20-24 36.5246 37.0 37.0 37.0 37.0 37.0 25-29 36.4519 37.0 37.0 37.0 37.0 37.0 30-34 36.4568 37.0 37.0 37.0 37.0 37.0 35-39 36.397800000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.4077 37.0 37.0 37.0 37.0 37.0 45-49 36.3483 37.0 37.0 37.0 37.0 37.0 50-54 36.3587 37.0 37.0 37.0 37.0 37.0 55-59 36.3174 37.0 37.0 37.0 37.0 37.0 60-64 36.3472 37.0 37.0 37.0 37.0 37.0 65-69 36.2508 37.0 37.0 37.0 37.0 37.0 70-74 36.3228 37.0 37.0 37.0 37.0 37.0 75-79 36.3292 37.0 37.0 37.0 37.0 37.0 80-84 36.2106 37.0 37.0 37.0 37.0 37.0 85-89 36.2498 37.0 37.0 37.0 37.0 37.0 90-94 36.19 37.0 37.0 37.0 37.0 37.0 95-99 36.1968 37.0 37.0 37.0 37.0 37.0 100-104 36.13720000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.1798 37.0 37.0 37.0 37.0 37.0 110-114 36.033100000000005 37.0 37.0 37.0 37.0 37.0 115-119 36.06269999999999 37.0 37.0 37.0 37.0 37.0 120-124 35.9759 37.0 37.0 37.0 37.0 37.0 125-129 35.9788 37.0 37.0 37.0 37.0 37.0 130-134 35.846999999999994 37.0 37.0 37.0 37.0 37.0 135-139 35.7807 37.0 37.0 37.0 37.0 37.0 140-144 35.6217 37.0 37.0 37.0 37.0 37.0 145-149 35.35080000000001 37.0 37.0 37.0 37.0 37.0 150-151 35.0 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 1.0 24 3.0 25 4.0 26 5.0 27 9.0 28 16.0 29 15.0 30 27.0 31 38.0 32 47.0 33 97.0 34 151.0 35 358.0 36 2799.0 37 429.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.85 9.5 5.0 35.65 2 22.275238573581117 10.82370668006027 33.77699648417881 33.124058262179815 3 20.525 14.025000000000002 26.325 39.125 4 26.775 20.125 20.625 32.475 5 27.900000000000002 25.424999999999997 24.349999999999998 22.325 6 24.0 30.7 22.2 23.1 7 18.95 25.324999999999996 36.525 19.2 8 20.025000000000002 22.925 30.375000000000004 26.674999999999997 9 20.3 21.4 33.375 24.925 10-14 23.13 25.919999999999998 26.745 24.205 15-19 23.985 24.560000000000002 25.95 25.505 20-24 23.885 25.27 25.990000000000002 24.855 25-29 23.61 25.369999999999997 25.240000000000002 25.779999999999998 30-34 23.23 24.715 25.495 26.56 35-39 23.84 24.94 25.495 25.724999999999998 40-44 23.195 24.865000000000002 26.31 25.629999999999995 45-49 22.830000000000002 25.525 25.674999999999997 25.97 50-54 23.325000000000003 25.415 24.585 26.674999999999997 55-59 23.169999999999998 24.605 25.2 27.025 60-64 23.119999999999997 25.074999999999996 26.56 25.245 65-69 23.755000000000003 24.959999999999997 26.009999999999998 25.275 70-74 24.279999999999998 24.875 24.705 26.14 75-79 24.275 24.52 25.430000000000003 25.775 80-84 23.395 25.585 25.069999999999997 25.95 85-89 24.015 24.9 24.94 26.145000000000003 90-94 23.455000000000002 25.105 25.900000000000002 25.540000000000003 95-99 24.05 24.595 25.615 25.740000000000002 100-104 23.745 25.28 25.180000000000003 25.795 105-109 23.965 24.915000000000003 24.86 26.26 110-114 23.400000000000002 25.105 24.48 27.015 115-119 24.044999999999998 24.68 25.515 25.759999999999998 120-124 24.154999999999998 25.4 24.490000000000002 25.955000000000002 125-129 24.2 25.195 24.310000000000002 26.295 130-134 24.16 24.875 24.834999999999997 26.13 135-139 23.785 25.995 24.355 25.865 140-144 24.985 25.145 23.86 26.009999999999998 145-149 24.07 25.014999999999997 24.93 25.985000000000003 150-151 25.2 25.912499999999998 23.4625 25.424999999999997 >>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 1.0 17 1.0 18 0.5 19 0.5 20 0.0 21 0.0 22 2.0 23 2.0 24 0.0 25 0.0 26 1.0 27 2.5 28 4.5 29 4.5 30 7.0 31 8.5 32 13.5 33 23.5 34 29.0 35 39.5 36 49.5 37 52.5 38 74.0 39 99.0 40 106.0 41 115.0 42 146.5 43 177.5 44 189.5 45 184.0 46 171.5 47 187.5 48 181.5 49 180.0 50 190.5 51 150.5 52 123.5 53 129.0 54 130.5 55 137.0 56 128.0 57 113.5 58 96.0 59 87.5 60 85.5 61 66.0 62 68.5 63 61.0 64 47.5 65 41.0 66 35.5 67 47.0 68 42.5 69 33.5 70 31.0 71 26.5 72 25.5 73 19.0 74 12.5 75 6.5 76 2.5 77 3.5 78 2.5 79 0.0 80 0.0 81 0.0 82 1.0 83 1.0 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 0.44999999999999996 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.425 #Duplication Level Percentage of deduplicated Percentage of total 1 73.45529858474283 53.2 2 18.39834311356576 26.650000000000002 3 5.730065585088022 12.45 4 1.725923369002416 5.0 5 0.5177770107007249 1.875 6 0.10355540214014498 0.44999999999999996 7 0.03451846738004832 0.17500000000000002 8 0.03451846738004832 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CCCCTTCCCACGACACTGGCTGCTCAGCTCATCGTTGCGAAGATACACAT 8 0.2 No Hit GTTCATGGTAGCGGTAGATCGAGTAGCTATATGTAGATGGTCGTTGCATG 7 0.17500000000000002 No Hit GCTAGTAGTGTAGTACGGGTAGAGGCATCAGAGGCTGCTGCTTCAGTGGC 6 0.15 No Hit GTCATCAAATACGCAGGTACCGGCTGCATCAGTAGCTGCGCCTACAGAAA 6 0.15 No Hit GCCGTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTG 6 0.15 No Hit CTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGG 5 0.125 No Hit GCTGTACCTTTCAGTGTTTGCAGTCCACAGCACCACCACCTTGTCCACTT 5 0.125 No Hit GGGTGAGACCGCCAACCAGGTTTCCAATGTTGTCAAGGCCGAGGCTACCC 5 0.125 No Hit CTTTGGCGATGAGTTCTCTTCTCAAAATCTTGCCTGAAGCTGACTTTGGC 5 0.125 No Hit AGTAGGGCCTCTGGACCTTTGGATGGACAAGGAAATCCGCCCTTTACCAT 5 0.125 No Hit GCTATCGCGGCACGGTCATCAGTAGGGTAAAACTAACCTGTCTCACGACG 5 0.125 No Hit CCCAGCAATTCGTTTCAAGGACCTTCAAGAGTCATTTGCTTAAAACCACG 5 0.125 No Hit CCCACAGATAACAAAGTTCTCAAAGGCATAGCAACTACAATACTCAGCTT 5 0.125 No Hit GCAATCTGCTTATCTTGTTCCATTTACCAATCTCCGTAGTAACAAGTGCA 5 0.125 No Hit GGGGGACTTCAAGAAACAGAAGCATTTACAATTCCAGCAGCAGCTTAACA 5 0.125 No Hit GTGGAATTCCCCGGGTGGCATGGGCAGTTGTAGCCCCCCGGCGTGTTCAC 5 0.125 No Hit GTTCGATTTCTCCCATAAATTTCTGTTCAAGAAAAGACTAACACAAGAGC 5 0.125 No Hit CCCCGTAATATCTTGGCCGACGAAACAGACGCCGACAATATTTTTAGTGT 5 0.125 No Hit GCACAAACTTGAGTGGATCCTTTCCAGGGCTGAAACTCGCGGCTGAGATT 5 0.125 No Hit GGCCGCTACAGAAGACAATTAGCTCAGTCTGTCCACTTGGGTTGTTTCCC 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 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.2375 0.0 0.0 0.0 0.0 62-63 0.3 0.0 0.0 0.0 0.0 64-65 0.3 0.0 0.0 0.0 0.0 66-67 0.325 0.0 0.0 0.0 0.0 68-69 0.325 0.0 0.0 0.0 0.0 70-71 0.325 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.3875 0.0 0.0 0.0 0.0 76-77 0.4 0.0 0.0 0.0 0.0 78-79 0.44999999999999996 0.0 0.0 0.0 0.0 80-81 0.6000000000000001 0.0 0.0 0.0 0.0 82-83 0.8375 0.0 0.0 0.0 0.0 84-85 1.025 0.0 0.0 0.0 0.0 86-87 1.2374999999999998 0.0 0.0 0.0 0.0 88-89 1.4375 0.0 0.0 0.0 0.0 90-91 1.5625 0.0 0.0 0.0 0.0 92-93 1.6875 0.0 0.0 0.0 0.0 94-95 1.9375 0.0 0.0 0.0 0.0 96-97 2.4125 0.0 0.0 0.0 0.0 98-99 2.8499999999999996 0.0 0.0 0.0 0.0 100-101 3.225 0.0 0.0 0.0 0.025 102-103 3.75 0.0 0.0 0.0 0.025 104-105 4.525 0.0 0.0 0.0 0.025 106-107 5.0125 0.0 0.0 0.0 0.025 108-109 5.4 0.0 0.0 0.0 0.025 110-111 6.0 0.0 0.0 0.0 0.025 112-113 6.550000000000001 0.0 0.0 0.0 0.025 114-115 7.137499999999999 0.0 0.0 0.0 0.025 116-117 7.875 0.0 0.0 0.0 0.025 118-119 8.55 0.0 0.0 0.0 0.025 120-121 8.9875 0.0 0.0 0.0 0.025 122-123 9.475 0.0 0.0 0.0 0.025 124-125 10.024999999999999 0.0 0.0 0.0 0.025 126-127 10.875 0.0 0.0 0.0 0.025 128-129 11.5 0.0 0.0 0.0 0.025 130-131 12.15 0.0 0.0 0.0 0.025 132-133 12.625 0.0 0.0 0.0 0.025 134-135 13.5625 0.0 0.0 0.0 0.025 136-137 14.4625 0.0 0.0 0.0 0.025 138-139 15.3 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTGTAAT 10 0.006830828 145.0 6 >>END_MODULE SRR13165353 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR13165353_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.101 37.0 37.0 37.0 37.0 37.0 2 36.1865 37.0 37.0 37.0 37.0 37.0 3 36.213 37.0 37.0 37.0 37.0 37.0 4 36.2245 37.0 37.0 37.0 37.0 37.0 5 36.2495 37.0 37.0 37.0 37.0 37.0 6 36.2905 37.0 37.0 37.0 37.0 37.0 7 36.1875 37.0 37.0 37.0 37.0 37.0 8 36.1725 37.0 37.0 37.0 37.0 37.0 9 36.2865 37.0 37.0 37.0 37.0 37.0 10-14 36.2741 37.0 37.0 37.0 37.0 37.0 15-19 36.2188 37.0 37.0 37.0 37.0 37.0 20-24 36.134 37.0 37.0 37.0 37.0 37.0 25-29 36.142 37.0 37.0 37.0 37.0 37.0 30-34 36.0948 37.0 37.0 37.0 37.0 37.0 35-39 36.0327 37.0 37.0 37.0 37.0 37.0 40-44 36.034000000000006 37.0 37.0 37.0 37.0 37.0 45-49 35.9777 37.0 37.0 37.0 37.0 37.0 50-54 35.944900000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.0289 37.0 37.0 37.0 37.0 37.0 60-64 35.9811 37.0 37.0 37.0 37.0 37.0 65-69 35.8795 37.0 37.0 37.0 37.0 37.0 70-74 35.852700000000006 37.0 37.0 37.0 37.0 37.0 75-79 35.8944 37.0 37.0 37.0 37.0 37.0 80-84 35.8373 37.0 37.0 37.0 37.0 37.0 85-89 35.8206 37.0 37.0 37.0 37.0 37.0 90-94 35.792199999999994 37.0 37.0 37.0 37.0 37.0 95-99 35.853899999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.7633 37.0 37.0 37.0 37.0 37.0 105-109 35.7387 37.0 37.0 37.0 37.0 37.0 110-114 35.642700000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.659000000000006 37.0 37.0 37.0 37.0 37.0 120-124 35.5323 37.0 37.0 37.0 37.0 37.0 125-129 35.4611 37.0 37.0 37.0 37.0 37.0 130-134 35.394099999999995 37.0 37.0 37.0 34.6 37.0 135-139 35.388149999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.1574 37.0 37.0 37.0 32.2 37.0 145-149 34.82505 37.0 37.0 37.0 25.0 37.0 150-151 34.42725 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 3.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 2.0 13 8.0 14 5.0 15 3.0 16 0.0 17 2.0 18 2.0 19 7.0 20 0.0 21 3.0 22 9.0 23 6.0 24 5.0 25 8.0 26 7.0 27 9.0 28 18.0 29 10.0 30 21.0 31 41.0 32 64.0 33 85.0 34 175.0 35 544.0 36 2710.0 37 252.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.27646763672855 22.05218263923733 8.780732563973908 25.89061716006021 2 31.674999999999997 21.45 25.3 21.575 3 24.75 24.4 28.65 22.2 4 24.8 31.525 20.150000000000002 23.525 5 29.25 32.05 18.2 20.5 6 21.8 37.3 19.025 21.875 7 23.799999999999997 20.275000000000002 34.599999999999994 21.325 8 24.45 23.849999999999998 23.05 28.65 9 23.150000000000002 21.7 27.625 27.525 10-14 26.165 25.55 23.575 24.709999999999997 15-19 26.729999999999997 25.34 23.955000000000002 23.974999999999998 20-24 27.047047047047045 25.310310310310307 23.513513513513516 24.12912912912913 25-29 26.326326326326328 25.51051051051051 24.314314314314313 23.84884884884885 30-34 26.25125125125125 25.640640640640637 23.86886886886887 24.23923923923924 35-39 25.730730730730734 26.3013013013013 23.60860860860861 24.35935935935936 40-44 25.935935935935934 26.001001001001 23.8988988988989 24.164164164164166 45-49 26.216216216216214 25.435435435435434 24.244244244244246 24.104104104104103 50-54 25.995995995995997 25.725725725725724 24.424424424424423 23.853853853853852 55-59 27.192192192192195 25.305305305305303 23.293293293293292 24.20920920920921 60-64 26.38138138138138 25.745745745745747 23.773773773773772 24.0990990990991 65-69 26.986589271417134 25.555444355484386 24.0242193755004 23.433746997598078 70-74 27.507507507507505 25.785785785785787 23.413413413413416 23.293293293293292 75-79 27.05205205205205 25.265265265265263 24.094094094094093 23.58858858858859 80-84 27.507507507507505 25.83083083083083 24.15915915915916 22.5025025025025 85-89 26.641641641641638 25.890890890890887 24.31931931931932 23.14814814814815 90-94 26.75175175175175 25.62062062062062 25.005005005005003 22.62262262262262 95-99 27.05205205205205 25.005005005005003 24.654654654654653 23.28828828828829 100-104 27.17217217217217 25.640640640640637 23.7987987987988 23.38838838838839 105-109 26.346346346346344 26.09109109109109 24.054054054054056 23.50850850850851 110-114 27.78778778778779 25.41041041041041 23.663663663663666 23.138138138138135 115-119 28.203203203203202 25.350350350350347 23.86886886886887 22.57757757757758 120-124 27.842842842842842 26.096096096096094 23.428428428428425 22.63263263263263 125-129 28.43843843843844 26.981981981981985 22.67267267267267 21.906906906906904 130-134 28.87175893482831 25.893482831114223 23.04534988487336 22.189408349184102 135-139 28.990439961960057 26.347665048300716 23.099254216927775 21.562640772811452 140-144 29.334334334334333 26.386386386386384 23.18818818818819 21.09109109109109 145-149 29.3858551479053 25.146403723910105 23.995194954702438 21.472546173482158 150-151 31.364205256570717 24.330413016270338 23.57947434292866 20.72590738423029 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.5 7 0.5 8 0.0 9 0.5 10 1.0 11 1.0 12 0.5 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 1.5 20 2.0 21 3.0 22 2.5 23 0.5 24 0.5 25 0.5 26 1.0 27 2.0 28 2.5 29 4.5 30 10.0 31 11.5 32 9.5 33 13.0 34 16.5 35 31.5 36 40.0 37 47.0 38 74.0 39 96.5 40 117.0 41 135.0 42 158.5 43 171.0 44 166.0 45 170.0 46 167.5 47 167.0 48 179.5 49 190.0 50 170.0 51 146.0 52 130.0 53 130.0 54 133.0 55 123.5 56 109.5 57 100.5 58 94.0 59 85.0 60 76.5 61 76.5 62 87.0 63 71.5 64 54.5 65 45.0 66 43.0 67 48.5 68 48.0 69 43.0 70 44.5 71 37.5 72 23.0 73 18.5 74 18.5 75 11.5 76 6.0 77 4.0 78 1.5 79 2.0 80 1.5 81 1.5 82 1.0 83 0.5 84 0.5 85 0.0 86 0.5 87 0.5 88 0.0 89 0.5 90 1.0 91 0.5 92 1.0 93 2.5 94 1.5 95 0.5 96 0.5 97 0.0 98 0.5 99 1.5 100 2.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.35000000000000003 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.1 25-29 0.1 30-34 0.1 35-39 0.1 40-44 0.1 45-49 0.1 50-54 0.1 55-59 0.1 60-64 0.1 65-69 0.08 70-74 0.1 75-79 0.1 80-84 0.1 85-89 0.1 90-94 0.1 95-99 0.1 100-104 0.1 105-109 0.1 110-114 0.1 115-119 0.1 120-124 0.1 125-129 0.1 130-134 0.11 135-139 0.105 140-144 0.1 145-149 0.105 150-151 0.125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.95 #Duplication Level Percentage of deduplicated Percentage of total 1 73.59277275886032 52.949999999999996 2 17.92911744266852 25.8 3 5.6636553161918 12.225 4 2.0847810979847115 6.0 5 0.4864489228630994 1.7500000000000002 6 0.13898540653231412 0.6 7 0.03474635163307853 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.06949270326615706 0.5 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GCAAGAGCTTGGTATGGTTGGACCTCAACAACAACCAACTCAATGGGTCA 10 0.25 No Hit GTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTTAACACATGCAA 10 0.25 No Hit CACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTT 7 0.17500000000000002 No Hit GGCCACCATGTCGAGCGGCTGCGGCAACTGCGACTGCGCTGACAAGACCC 6 0.15 No Hit GTCGTATGCTGGGTAGCCTCGGCCTTGACAACATTGGAAACCTGGTTGGC 6 0.15 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit AGAACCTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGG 6 0.15 No Hit CGGAGTTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGC 5 0.125 No Hit GCACGGAGCTCACTACCCGGTCCGTTGCTGCCAAGTATAGCAGCAACGGC 5 0.125 No Hit ATACCATTTGATTCTTTAGCGTTTTCTTCAATCATCGTCACCTTGAGGAT 5 0.125 No Hit ATTCTAGACGCCGTCGTTATCCCGTTTCCTGATGCCGAAGCTGGGGAAGT 5 0.125 No Hit TGTGAGGATGGTTCTGGAAGAAATCATATCACATACACAGACACTTGTAC 5 0.125 No Hit ATCACAACAGAATAAGCCAAGCATTTTCGCTTGTGAAGCAAAACAGGCGC 5 0.125 No Hit TGGTAGGCGATTTGTCTCTCTTTACTGCTCTGCACTGTTATTTTTTTCCT 5 0.125 No Hit AGTACTTTGATCCTGAAGATGCTGCTGATGCAAAATACTATATGGATGGG 5 0.125 No Hit CCTCACAGTTGAGGAGGCAATGGGAAAATCATTGGTAACAGATCTTATCT 5 0.125 No Hit CTGAGTGCTTGATGTAGTTACAAAGTGTTGATTTTCCAGATCATATTCTA 5 0.125 No Hit GGGTGAGTCAGGGCCTAAGATCAGGCCGAAAGGCGTAGTCGATGGACAAC 5 0.125 No Hit AGCTAAAGAAGGTTCTGTGCATGGGTGTTGCTGTGGGTAACTTGTCGATG 5 0.125 No Hit GTTTGAGACTGCACTTGTTACTACGGAGATTGGTAAATGGAACAAGATAA 5 0.125 No Hit GCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAG 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 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.25 0.0 0.0 0.0 0.0 62-63 0.325 0.0 0.0 0.0 0.0 64-65 0.325 0.0 0.0 0.0 0.0 66-67 0.35 0.0 0.0 0.0 0.0 68-69 0.35 0.0 0.0 0.0 0.0 70-71 0.35 0.0 0.0 0.0 0.0 72-73 0.375 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.425 0.0 0.0 0.0 0.0 78-79 0.5 0.0 0.0 0.0 0.0 80-81 0.6499999999999999 0.0 0.0 0.0 0.0 82-83 0.8875 0.0 0.0 0.0 0.0 84-85 1.125 0.0 0.0 0.0 0.0 86-87 1.3375 0.0 0.0 0.0 0.0 88-89 1.5375 0.0 0.0 0.0 0.0 90-91 1.6625 0.0 0.0 0.0 0.0 92-93 1.7875 0.0 0.0 0.0 0.0 94-95 2.0374999999999996 0.0 0.0 0.0 0.0 96-97 2.5375 0.0 0.0 0.0 0.0 98-99 3.0 0.0 0.0 0.0 0.0 100-101 3.375 0.0 0.0 0.0 0.0 102-103 3.9000000000000004 0.0 0.0 0.0 0.0 104-105 4.675 0.0 0.0 0.0 0.0 106-107 5.1375 0.0 0.0 0.0 0.0 108-109 5.525 0.0 0.0 0.0 0.0 110-111 6.1 0.0 0.0 0.0 0.0 112-113 6.6625 0.0 0.0 0.0 0.0 114-115 7.275 0.0 0.0 0.0 0.0 116-117 8.075 0.0 0.0 0.0 0.0 118-119 8.75 0.0 0.0 0.0 0.0 120-121 9.2 0.0 0.0 0.0 0.0 122-123 9.7375 0.0 0.0 0.0 0.0 124-125 10.3 0.0 0.0 0.0 0.0 126-127 11.1625 0.0 0.0 0.0 0.0 128-129 11.7875 0.0 0.0 0.0 0.0 130-131 12.425 0.0 0.0 0.0 0.0 132-133 12.912500000000001 0.0 0.0 0.0 0.0 134-135 13.9 0.0 0.0 0.0 0.0 136-137 14.8125 0.0 0.0 0.0 0.0 138-139 15.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGTG 10 0.006830828 145.0 145 TCGTTAA 10 0.006830828 145.0 2 GGGGGGG 95 1.00806574E-7 16.789474 140-144 >>END_MODULE Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243841 spots for SRR13165353.sra Written 1243841 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra Read 1243829 spots for SRR13165353.sra Written 1243829 spots for SRR13165353.sra SRR ids: ['SRR13165353.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_89p_76c1 SRR13165353.sra spots: 24876592 blocks: [[1, 1243829], [1243830, 2487658], [2487659, 3731487], [3731488, 4975316], [4975317, 6219145], [6219146, 7462974], [7462975, 8706803], [8706804, 9950632], [9950633, 11194461], [11194462, 12438290], [12438291, 13682119], [13682120, 14925948], [14925949, 16169777], [16169778, 17413606], [17413607, 18657435], [18657436, 19901264], [19901265, 21145093], [21145094, 22388922], [22388923, 23632751], [23632752, 24876592]] SRR13165353 file size 8432453 SRR13165353 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 SRR13165353 SRR13165353_1.fastq SRR13165353_2.fastq Input file: SRR13165353_1.fastq Paired file: SRR13165353_2.fastq trimmed: SRR13165353-trimmed-pair1.fastq, SRR13165353-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 15:50:36 2024 >> started Sat Dec 7 15:51:04 2024 >> done (27.877s) 24876592 read pairs processed; of these: 455 ( 0.00%) short read pairs filtered out after trimming by size control 37083 ( 0.15%) empty read pairs filtered out after trimming by size control 24839054 (99.85%) read pairs available; of these: 5000639 (20.13%) trimmed read pairs available after processing 19838415 (79.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 28 0.00% 20 27 0.00% 21 30 0.00% 22 37 0.00% 23 23 0.00% 24 46 0.00% 25 56 0.00% 26 88 0.00% 27 61 0.00% 28 74 0.00% 29 77 0.00% 30 93 0.00% 31 108 0.00% 32 99 0.00% 33 114 0.00% 34 89 0.00% 35 137 0.00% 36 127 0.00% 37 135 0.00% 38 154 0.00% 39 161 0.00% 40 164 0.00% 41 185 0.00% 42 216 0.00% 43 255 0.00% 44 265 0.00% 45 268 0.00% 46 294 0.00% 47 328 0.00% 48 370 0.00% 49 411 0.00% 50 488 0.00% 51 520 0.00% 52 626 0.00% 53 723 0.00% 54 753 0.00% 55 849 0.00% 56 932 0.00% 57 1055 0.00% 58 1243 0.01% 59 1327 0.01% 60 1602 0.01% 61 1917 0.01% 62 2110 0.01% 63 2385 0.01% 64 2648 0.01% 65 2783 0.01% 66 3077 0.01% 67 3379 0.01% 68 3950 0.02% 69 4202 0.02% 70 4662 0.02% 71 5224 0.02% 72 6177 0.02% 73 6925 0.03% 74 7738 0.03% 75 8384 0.03% 76 9276 0.04% 77 9726 0.04% 78 10994 0.04% 79 12471 0.05% 80 13159 0.05% 81 14939 0.06% 82 16250 0.07% 83 17892 0.07% 84 20641 0.08% 85 21702 0.09% 86 24082 0.10% 87 25150 0.10% 88 27115 0.11% 89 28118 0.11% 90 29942 0.12% 91 32160 0.13% 92 33704 0.14% 93 36617 0.15% 94 38901 0.16% 95 41631 0.17% 96 43405 0.17% 97 45659 0.18% 98 47162 0.19% 99 49818 0.20% 100 50708 0.20% 101 52479 0.21% 102 54154 0.22% 103 55512 0.22% 104 57762 0.23% 105 58913 0.24% 106 61360 0.25% 107 62124 0.25% 108 65108 0.26% 109 66992 0.27% 110 66584 0.27% 111 68321 0.28% 112 70816 0.29% 113 69372 0.28% 114 73425 0.30% 115 75319 0.30% 116 76528 0.31% 117 77474 0.31% 118 79229 0.32% 119 79620 0.32% 120 83027 0.33% 121 81727 0.33% 122 82834 0.33% 123 85982 0.35% 124 86376 0.35% 125 88428 0.36% 126 88549 0.36% 127 89338 0.36% 128 89650 0.36% 129 92103 0.37% 130 91409 0.37% 131 93364 0.38% 132 93745 0.38% 133 94032 0.38% 134 93064 0.37% 135 95276 0.38% 136 96662 0.39% 137 96391 0.39% 138 96379 0.39% 139 97326 0.39% 140 98482 0.40% 141 99167 0.40% 142 100272 0.40% 143 100176 0.40% 144 101318 0.41% 145 102121 0.41% 146 103472 0.42% 147 108055 0.44% 148 105132 0.42% 149 107138 0.43% 150 107110 0.43% 151 19838415 79.87% 24839054 reads passed initial QC criterion=sequence-density sequence-density=0.91 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=20 prefix-density=0.90 prefix-fanout=2.1 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCTTCGGTCGAGTGCTCGAACTTGCTTAGGAAGAAGATTAAGCTGAAGGCTTCTAGGCTTGTGTGTGCTTCTT criterion=fanout-score sequence-density=0.05 sequence-density-rank=27 fanout-score=17.09 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=4.2 sequence=GCTTCCTTGACAGCAAGCTCAGATGGGCCGTTGGGGATGCTGACGACAGTGCGCCACTTGGCGAAGCGGGCGCCTTGCTGGTAGTAGGCTGCCTCACGGGAGGCAAGGCCATCAAGACCTTGGCACCATGACTCGTCGTTGGAACCAACGAGTGGCACAAGACCCTTGTCAACCTTGATGCCGGGAACGATTCCCTGCTCGACAAGGATGTCAACAATCTTCTTGCCATCAACAGTCGATTGGTAGAGGGTCTCCTCGAAGAGGATAGCACCAGAGATGTAATTTCCCAGGCCTGGTGGAGTGACAAGGAGGGTACGGTAAGCCTGGCGGTTAGCCTCAGTGTTCTCAAGGCCAATCGAGTCAAGTCTCTTTCCACAGGTAGCATTGGACTCATCCATGGCTAGGATGCCCCTTCCTGGTGATGCGATGGTTTTCGCGGTCTTGACAAGTTCATCAGCGTATGCGCTGGCACGGACAACCATGGAGACGGTCATCTGCTTGGGAGTGGCAG criterion=sequence-density sequence-density=0.86 sequence-density-rank=1 fanout-score=2.17 fanout-score-rank=28 prefix-density=0.89 prefix-fanout=2.1 sequence=GGTGGTGCATGGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=37.30 fanout-score-rank=1 prefix-density=0.32 prefix-fanout=2.8 sequence=GCAGCAGCCATTACTTGATCATCTGAAAAATCTTAATCCAGATCAGACCAAGCAGAGCAGAGATGTCTGCTACCTTCTCGTCCACCGTCGGAGCTCCGGCTTCTACGCCAACCAGCTTCCTTGGGAAGAAGCTCAAGAAGCAGGTGACCTCGGCCGTGAACTACCATGGCAAGAGCACCAAGGCCAACAGATTCACAGTCATGGCCAAGGAGGTGGACGAGTCAAAGCAGACTGACCAGGACAGGTGGAAGGGCCTCGCCTACGATATCTCCGACGACCAGCAGGACATCACCAGGGGGAAGGGTATCGTCGACTCGCTCTTCCAGGCGCCCATGGGCGACGGTACCCACGTGGCCGTCCTCAGCTCCCAAGAGTACATCAGCCAGGGCCTAAGGAAGTACGACTTCGACAACA SRR13165353 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:52:17 Started mapping on | Dec 07 15:52:18 Finished on | Dec 07 15:56:23 Mapping speed, Million of reads per hour | 364.98 Number of input reads | 24839054 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 21160773 Uniquely mapped reads % | 85.19% Average mapped length | 289.48 Number of splices: Total | 20838090 Number of splices: Annotated (sjdb) | 19404029 Number of splices: GT/AG | 20551814 Number of splices: GC/AG | 242976 Number of splices: AT/AC | 8929 Number of splices: Non-canonical | 34371 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.55 Insertion rate per base | 0.01% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1060623 % of reads mapped to multiple loci | 4.27% Number of reads mapped to too many loci | 264708 % of reads mapped to too many loci | 1.07% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.05% % of reads unmapped: other | 4.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2617916 2617916 2617916 N_multimapping 1060623 1060623 1060623 N_noFeature 1370521 20552113 1540108 N_ambiguous 530328 3382 91967 UnstrandedReadsAssigned:19259924 PositiveStrandReadsAssigned:605278 NegativeStrandReadsAssigned:19528698 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR13165353 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR13165353-trimmed-pair1.fastq SRR13165353-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,839,054 reads, 20,064,852 reads pseudoaligned [quant] estimated average fragment length: 239.797 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,201 rounds 52973 SRR13165353.ke.tsv 35125 SRR13165353.se.tsv 88098 total ==> SRR13165353.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 697.761 0 0 PNS24247 1044 805.203 66.5524 5.66919 PNS24249 1928 1689.2 45.2304 1.83659 PNS24246 1044 805.203 66.5524 5.66919 PNS24248 1044 805.203 66.5524 5.66919 PNS24244 1471 1232.2 184.112 10.2486 PNS24243 293 112.477 0 0 KQK14069 1603 1364.2 2751.78 138.356 KQK14071 474 256.496 53.915 14.4176 ==> SRR13165353.se.tsv <== BRADI_1g14170v3 3007 BRADI_1g53295v3 129 BRADI_1g59795v3 642 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 476 BRADI_1g74790v3 541 BRADI_1g09890v3 0 BRADI_1g77505v3 259 BRADI_1g48960v3 0 SRR13165353 completed mapping pipeline successfully