Starting /dee2/code/volunteer_pipeline.sh ERR6133358 current disk space = 1548253540352 free memory = 1597242924 ERR6133358 SRAfilesize bab0ae656455ff44775daf236c51d5ac ERR6133358.sra ERR6133358.sra file validated ERR6133358 is single end ERR6133358 is conventional basespace ERR6133358 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133358_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.45875 37.0 37.0 37.0 33.0 37.0 2 36.742 37.0 37.0 37.0 37.0 37.0 3 36.66775 37.0 37.0 37.0 37.0 37.0 4 36.36575 37.0 37.0 37.0 37.0 37.0 5 36.372 37.0 37.0 37.0 37.0 37.0 6 36.51875 37.0 37.0 37.0 37.0 37.0 7 38.7055 40.0 37.0 40.0 37.0 40.0 8 38.806 40.0 37.0 40.0 37.0 40.0 9 38.77825 40.0 37.0 40.0 37.0 40.0 10-11 38.761375 40.0 37.0 40.0 37.0 40.0 12-13 38.73075 40.0 37.0 40.0 37.0 40.0 14-15 38.753625 40.0 37.0 40.0 37.0 40.0 16-17 38.679 40.0 37.0 40.0 37.0 40.0 18-19 38.696 40.0 37.0 40.0 37.0 40.0 20-21 38.6405 40.0 37.0 40.0 37.0 40.0 22-23 38.539125 40.0 37.0 40.0 37.0 40.0 24-25 38.444625 40.0 37.0 40.0 37.0 40.0 26-27 38.40925 40.0 37.0 40.0 37.0 40.0 28-29 38.477000000000004 40.0 37.0 40.0 37.0 40.0 30-31 38.444874999999996 40.0 37.0 40.0 37.0 40.0 32-33 38.297250000000005 40.0 37.0 40.0 37.0 40.0 34-35 38.2605 40.0 37.0 40.0 37.0 40.0 36-37 38.15725 40.0 37.0 40.0 37.0 40.0 38-39 38.123875 40.0 37.0 40.0 37.0 40.0 40-41 37.99487499999999 40.0 37.0 40.0 37.0 40.0 42-43 37.85575 38.5 37.0 40.0 37.0 40.0 44-45 37.674 37.0 37.0 40.0 37.0 40.0 46-47 37.600125 37.0 37.0 40.0 37.0 40.0 48-49 37.448499999999996 37.0 37.0 40.0 35.0 40.0 50-51 37.288875000000004 37.0 37.0 40.0 33.0 40.0 52-53 37.100625 37.0 37.0 40.0 33.0 40.0 54-55 36.919124999999994 37.0 37.0 37.0 33.0 40.0 56-57 36.77975 37.0 37.0 37.0 33.0 40.0 58-59 36.559625 37.0 37.0 37.0 33.0 40.0 60-61 36.46875 37.0 37.0 37.0 33.0 40.0 62-63 36.251374999999996 37.0 37.0 37.0 33.0 37.0 64-65 36.139624999999995 37.0 37.0 37.0 33.0 37.0 66-67 36.091875 37.0 37.0 37.0 33.0 37.0 68-69 35.213625 37.0 35.0 37.0 33.0 37.0 70-71 35.32611649510419 37.0 35.0 37.0 33.0 37.0 72-73 35.81338178594747 37.0 37.0 37.0 33.0 37.0 74-75 35.775048571065994 37.0 37.0 37.0 33.0 37.0 76-77 35.80057605463446 37.0 37.0 37.0 33.0 37.0 78-79 35.79206646877131 37.0 37.0 37.0 33.0 37.0 80-81 35.76126642353816 37.0 37.0 37.0 33.0 37.0 82-83 35.60042779687913 37.0 37.0 37.0 33.0 37.0 84-85 35.58464385367711 37.0 37.0 37.0 33.0 37.0 86-87 35.50708556149733 37.0 37.0 37.0 33.0 37.0 88-89 35.60120320855615 37.0 37.0 37.0 33.0 37.0 90-91 35.47406417112299 37.0 37.0 37.0 33.0 37.0 92-93 35.35120320855615 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 3.0 21 1.0 22 6.0 23 4.0 24 8.0 25 14.0 26 5.0 27 8.0 28 16.0 29 17.0 30 35.0 31 45.0 32 43.0 33 54.0 34 93.0 35 175.0 36 720.0 37 1118.0 38 1585.0 39 50.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.025 7.025 7.85 16.1 2 51.125 27.1 13.200000000000001 8.575000000000001 3 29.775000000000002 38.074999999999996 17.599999999999998 14.549999999999999 4 30.525000000000002 26.325 21.375 21.775 5 25.624999999999996 26.85 25.825 21.7 6 20.424999999999997 34.55 28.000000000000004 17.025000000000002 7 34.4 27.700000000000003 20.974999999999998 16.925 8 29.4 28.95 25.374999999999996 16.275000000000002 9 24.349999999999998 26.424999999999997 28.599999999999998 20.625 10-11 24.1375 27.525 29.3875 18.95 12-13 24.025 28.6375 27.762500000000003 19.575 14-15 21.5625 28.1625 30.975 19.3 16-17 24.337500000000002 31.225 24.6 19.8375 18-19 23.05 26.8375 29.812499999999996 20.3 20-21 25.912499999999998 26.75 27.150000000000002 20.1875 22-23 28.5625 23.7375 26.787499999999998 20.9125 24-25 24.775 27.675 28.15 19.400000000000002 26-27 26.637499999999996 24.5375 28.537499999999998 20.2875 28-29 25.5125 26.825 27.6875 19.975 30-31 25.387500000000003 27.6875 27.725 19.2 32-33 24.6625 24.525 30.675 20.1375 34-35 22.325 30.7875 26.887499999999996 20.0 36-37 24.4875 26.9125 26.6625 21.9375 38-39 25.815726965870734 26.128266033254157 28.166020752594072 19.889986248281037 40-41 25.637500000000003 25.162499999999998 27.700000000000003 21.5 42-43 26.6 28.1 27.075 18.224999999999998 44-45 23.8875 26.987499999999997 28.825 20.3 46-47 25.362499999999997 26.5625 27.500000000000004 20.575 48-49 23.075000000000003 25.337500000000002 30.175 21.4125 50-51 22.1 26.674999999999997 30.2625 20.962500000000002 52-53 25.074999999999996 26.8125 27.8125 20.3 54-55 26.075 26.474999999999998 29.0875 18.3625 56-57 25.587500000000002 27.287499999999998 27.650000000000002 19.475 58-59 24.7375 27.1625 27.6375 20.4625 60-61 25.7 28.262500000000003 26.700000000000003 19.3375 62-63 21.75 30.049999999999997 29.875 18.325 64-65 22.06801700425106 30.657664416104026 29.26981745436359 18.00450112528132 66-67 23.95 28.449999999999996 27.5875 20.0125 68-69 21.925 27.8375 28.512500000000003 21.725 70-71 24.351747463359636 27.884254039834648 26.669171990479768 21.09482650632594 72-73 25.19536173430804 27.842198134610534 28.661457020418453 18.30098311066297 74-75 25.495678698525676 26.525165226232843 29.181494661921707 18.797661413319776 76-77 22.492634814909696 27.270398360445753 28.01332137825029 22.22364544639426 78-79 24.73173884938591 27.29153199741435 29.191984486102136 18.78474466709761 80-81 22.693462090565053 31.580321023098 26.503980164426466 19.22223672191048 82-83 21.44835773644638 28.4263289803456 29.125445191927184 20.999868091280835 84-85 21.641791044776117 26.239339019189767 31.236673773987206 20.88219616204691 86-87 22.31283422459893 28.58288770053476 27.31283422459893 21.79144385026738 88-89 20.922459893048128 30.080213903743314 28.943850267379677 20.053475935828878 90-91 23.20855614973262 29.010695187165776 27.459893048128343 20.32085561497326 92-93 20.989304812834224 30.628342245989305 28.475935828877002 19.906417112299465 >>END_MODULE >>Per sequence GC content warn #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 0.5 17 1.5 18 1.5 19 1.0 20 1.0 21 1.0 22 2.0 23 5.0 24 6.5 25 6.0 26 8.0 27 16.5 28 24.0 29 28.0 30 34.0 31 43.0 32 54.5 33 61.5 34 67.5 35 75.5 36 114.5 37 174.5 38 206.5 39 198.0 40 226.0 41 256.5 42 263.0 43 281.0 44 226.5 45 183.0 46 182.0 47 166.5 48 149.0 49 140.0 50 169.5 51 171.0 52 126.5 53 118.0 54 132.5 55 112.5 56 77.0 57 63.5 58 56.5 59 37.0 60 19.5 61 20.5 62 20.0 63 14.5 64 11.0 65 10.5 66 9.0 67 6.5 68 16.0 69 21.0 70 10.0 71 2.5 72 2.0 73 0.5 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 0.0 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 0.0125 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 0.025 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 17.0 71 8.0 72 16.0 73 17.0 74 16.0 75 16.0 76 13.0 77 17.0 78 25.0 79 14.0 80 19.0 81 22.0 82 19.0 83 17.0 84 24.0 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 3740.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.675 #Duplication Level Percentage of deduplicated Percentage of total 1 90.87207329487615 66.95 2 4.479131319986427 6.6000000000000005 3 1.323379708177808 2.9250000000000003 4 1.0858500169664065 3.2 5 0.4750593824228029 1.7500000000000002 6 0.3732609433322022 1.6500000000000001 7 0.1357312521208008 0.7000000000000001 8 0.23752969121140144 1.4000000000000001 9 0.3053953172718018 2.025 >10 0.6447234475738038 9.700000000000001 >50 0.0678656260604004 3.1 >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 fail #Sequence Count Percentage Possible Source TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 62 1.55 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 62 1.55 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 50 1.25 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 45 1.125 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 40 1.0 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 30 0.75 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 28 0.7000000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 23 0.575 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 18 0.44999999999999996 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 18 0.44999999999999996 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 16 0.4 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 16 0.4 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 15 0.375 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 15 0.375 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 12 0.3 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 10 0.25 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 10 0.25 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 10 0.25 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 10 0.25 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 10 0.25 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 9 0.22499999999999998 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 9 0.22499999999999998 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 9 0.22499999999999998 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 9 0.22499999999999998 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 8 0.2 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 7 0.17500000000000002 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 6 0.15 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 6 0.15 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTCC 6 0.15 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATC 5 0.125 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit CTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 40-41 0.0125 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350175 READS because READLEN < 1 Read 350175 spots for ERR6133358.sra Written 350175 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra Rejected 350171 READS because READLEN < 1 Read 350171 spots for ERR6133358.sra Written 350171 spots for ERR6133358.sra SRR ids: ['ERR6133358.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r6fa57a7 ERR6133358.sra spots: 7003424 blocks: [[1, 350171], [350172, 700342], [700343, 1050513], [1050514, 1400684], [1400685, 1750855], [1750856, 2101026], [2101027, 2451197], [2451198, 2801368], [2801369, 3151539], [3151540, 3501710], [3501711, 3851881], [3851882, 4202052], [4202053, 4552223], [4552224, 4902394], [4902395, 5252565], [5252566, 5602736], [5602737, 5952907], [5952908, 6303078], [6303079, 6653249], [6653250, 7003424]] ERR6133358 file size 1544800 ERR6133358 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 ERR6133358 ERR6133358_1.fastq Input file: ERR6133358_1.fastq trimmed: ERR6133358-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 Sat Dec 7 01:21:41 2024 >> started Sat Dec 7 01:21:46 2024 >> done (5.253s) 7003424 reads processed; of these: 531 ( 0.01%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 7002882 (99.99%) reads available; of these: 40995 ( 0.59%) trimmed reads available after processing 6961887 (99.41%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 25 0.00% 19 83 0.00% 20 49 0.00% 21 32 0.00% 22 32 0.00% 23 32 0.00% 24 24 0.00% 25 17 0.00% 26 31 0.00% 27 27 0.00% 28 36 0.00% 29 173 0.00% 30 25 0.00% 31 34 0.00% 32 60 0.00% 33 32 0.00% 34 16 0.00% 35 80 0.00% 36 24 0.00% 37 28 0.00% 38 33 0.00% 39 94 0.00% 40 134 0.00% 41 45 0.00% 42 16 0.00% 43 29 0.00% 44 40 0.00% 45 27 0.00% 46 17 0.00% 47 10 0.00% 48 21 0.00% 49 21 0.00% 50 21 0.00% 51 130 0.00% 52 28 0.00% 53 15 0.00% 54 13 0.00% 55 14 0.00% 56 17 0.00% 57 46 0.00% 58 26 0.00% 59 34 0.00% 60 36 0.00% 61 34 0.00% 62 15 0.00% 63 10 0.00% 64 27 0.00% 65 35 0.00% 66 44 0.00% 67 55 0.00% 68 119 0.00% 69 218 0.00% 70 24633 0.35% 71 23887 0.34% 72 26035 0.37% 73 24669 0.35% 74 23790 0.34% 75 22991 0.33% 76 22383 0.32% 77 24440 0.35% 78 25242 0.36% 79 26716 0.38% 80 26576 0.38% 81 35178 0.50% 82 36260 0.52% 83 31185 0.45% 84 37507 0.54% 85 262 0.00% 86 391 0.01% 87 593 0.01% 88 889 0.01% 89 1521 0.02% 90 2757 0.04% 91 6565 0.09% 92 22019 0.31% 93 6554109 93.59% 7002882 reads passed initial QC criterion=sequence-density sequence-density=2.56 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=29 prefix-density=2.58 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=42.39 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=7.0 sequence=TTTCCTTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATTTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACCAAAA 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: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:22:00 Started mapping on | Dec 07 01:22:00 Finished on | Dec 07 01:22:10 Mapping speed, Million of reads per hour | 2521.04 Number of input reads | 7002882 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3671821 Uniquely mapped reads % | 52.43% Average mapped length | 91.35 Number of splices: Total | 149815 Number of splices: Annotated (sjdb) | 125372 Number of splices: GT/AG | 142895 Number of splices: GC/AG | 2876 Number of splices: AT/AC | 114 Number of splices: Non-canonical | 3930 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 1.71 Insertion rate per base | 0.02% Insertion average length | 1.69 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2927718 % of reads mapped to multiple loci | 41.81% Number of reads mapped to too many loci | 250735 % of reads mapped to too many loci | 3.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.01% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 403343 403343 403343 N_multimapping 2927718 2927718 2927718 N_noFeature 306849 341360 3513399 N_ambiguous 146789 22808 628 UnstrandedReadsAssigned:3218183 PositiveStrandReadsAssigned:3307653 NegativeStrandReadsAssigned:157794 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133358 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: ERR6133358-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,002,882 reads, 5,050,776 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,051 rounds 52973 ERR6133358.ke.tsv 35125 ERR6133358.se.tsv 88098 total ==> ERR6133358.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 92 17.5721 PNS24243 293 194 0 0 KQK14069 1603 1504 61 10.6285 KQK14071 474 375 0 0 ==> ERR6133358.se.tsv <== BRADI_1g14170v3 61 BRADI_1g53295v3 40 BRADI_1g59795v3 42 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 48 BRADI_1g74790v3 56 BRADI_1g09890v3 0 BRADI_1g77505v3 103 BRADI_1g48960v3 0 ERR6133358 completed mapping pipeline successfully