Starting /dee2/code/volunteer_pipeline.sh ERR6133417 current disk space = 1547255205888 free memory = 1474890916 ERR6133417 SRAfilesize d722fd3e9542fbd1380cfe06753cd98c ERR6133417.sra ERR6133417.sra file validated ERR6133417 is single end ERR6133417 is conventional basespace ERR6133417 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133417_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 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.80825 33.0 27.0 33.0 15.0 37.0 2 33.827 37.0 33.0 37.0 27.0 37.0 3 33.60175 37.0 33.0 37.0 27.0 37.0 4 33.59825 37.0 33.0 37.0 27.0 37.0 5 33.698 37.0 33.0 37.0 27.0 37.0 6 33.6695 37.0 33.0 37.0 22.0 37.0 7 34.9185 37.0 33.0 37.0 27.0 40.0 8 34.8785 37.0 33.0 37.0 27.0 40.0 9 35.11375 37.0 33.0 37.0 27.0 40.0 10-11 35.135999999999996 37.0 33.0 37.0 27.0 40.0 12-13 34.9525 37.0 33.0 37.0 27.0 40.0 14-15 34.9 37.0 33.0 37.0 27.0 40.0 16-17 34.522 37.0 33.0 37.0 27.0 40.0 18-19 34.555625 37.0 33.0 37.0 27.0 40.0 20-21 33.647999999999996 37.0 33.0 37.0 22.0 40.0 22-23 33.444125 37.0 33.0 37.0 22.0 40.0 24-25 33.197 37.0 33.0 37.0 22.0 40.0 26-27 32.9765 37.0 33.0 37.0 22.0 40.0 28-29 32.472 33.0 33.0 37.0 22.0 40.0 30-31 32.576125000000005 33.0 33.0 37.0 22.0 40.0 32-33 31.8725 33.0 30.0 37.0 18.5 40.0 34-35 30.967374999999997 33.0 27.0 37.0 15.0 40.0 36-37 30.612625 33.0 27.0 37.0 15.0 37.0 38-39 31.166625 33.0 27.0 37.0 22.0 37.0 40-41 30.904625 33.0 27.0 37.0 22.0 37.0 42-43 30.602875 33.0 27.0 37.0 15.0 37.0 44-45 30.173000000000002 33.0 27.0 37.0 15.0 37.0 46-47 29.81125 33.0 27.0 37.0 15.0 37.0 48-49 29.57875 33.0 27.0 37.0 15.0 37.0 50-51 29.165625 33.0 27.0 37.0 15.0 37.0 52-53 29.075375 33.0 27.0 37.0 15.0 37.0 54-55 29.09975 33.0 27.0 37.0 15.0 37.0 56-57 28.21475 33.0 24.5 33.0 15.0 37.0 58-59 28.087875 33.0 27.0 33.0 15.0 37.0 60-61 28.0265 33.0 27.0 33.0 15.0 37.0 62-63 27.57375 33.0 22.0 33.0 15.0 37.0 64-65 27.155124999999998 33.0 22.0 33.0 15.0 37.0 66-67 26.874499999999998 30.0 22.0 33.0 10.5 37.0 68-69 26.096375000000002 27.0 22.0 33.0 10.5 35.0 70-71 27.99127603905859 33.0 27.0 33.0 15.0 35.0 72-73 28.513378419337727 33.0 27.0 33.0 15.0 37.0 74-75 28.372451315847808 33.0 27.0 33.0 15.0 37.0 76-77 28.269302590564898 33.0 27.0 33.0 15.0 37.0 78-79 27.26280678503789 33.0 24.5 33.0 10.5 37.0 80-81 26.417947514704387 33.0 22.0 33.0 6.0 37.0 82-83 25.76850942244548 33.0 22.0 33.0 2.0 37.0 84-85 25.38949397392766 33.0 22.0 33.0 2.0 37.0 86-87 24.400938477580816 30.0 15.0 33.0 2.0 35.0 88-89 23.63242961418144 30.0 10.5 33.0 2.0 35.0 90-91 22.341240875912412 27.0 2.0 33.0 2.0 33.0 92-93 21.00469238790407 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 117.0 21 107.0 22 152.0 23 194.0 24 183.0 25 197.0 26 212.0 27 261.0 28 240.0 29 258.0 30 258.0 31 283.0 32 303.0 33 282.0 34 277.0 35 288.0 36 243.0 37 123.0 38 22.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 77.35 5.625 4.95 12.075 2 60.575 20.724999999999998 11.625 7.074999999999999 3 38.125 34.25 15.475 12.15 4 27.0 33.025 19.525000000000002 20.45 5 31.25 23.925 27.075 17.75 6 16.725 40.575 25.025 17.675 7 38.875 26.474999999999998 18.35 16.3 8 23.625 26.6 25.15 24.625 9 21.175 36.25 24.85 17.724999999999998 10-11 21.1625 29.15 32.025 17.6625 12-13 20.2625 32.4125 25.5 21.825 14-15 18.087500000000002 38.1375 25.137500000000003 18.637500000000003 16-17 25.912499999999998 26.937499999999996 21.875 25.275 18-19 25.687500000000004 23.0375 33.4625 17.8125 20-21 27.237499999999997 21.9 32.4125 18.45 22-23 30.4875 20.549999999999997 29.5375 19.425 24-25 20.849999999999998 25.087500000000002 29.6875 24.375 26-27 27.0875 21.712500000000002 28.6875 22.5125 28-29 21.925 30.049999999999997 31.025000000000002 17.0 30-31 33.900000000000006 23.0375 23.6875 19.375 32-33 28.6125 20.5 26.6 24.2875 34-35 20.1125 37.7875 23.75 18.35 36-37 27.825 24.2 23.3125 24.6625 38-39 35.4125 21.224999999999998 25.074999999999996 18.2875 40-41 23.1625 23.1375 35.625 18.075 42-43 28.0625 30.8 24.2 16.9375 44-45 26.950000000000003 22.650000000000002 31.85 18.55 46-47 28.475 24.099999999999998 23.7875 23.6375 48-49 27.825 22.475 25.674999999999997 24.025 50-51 20.65 30.675 24.55 24.125 52-53 22.075 23.849999999999998 23.3125 30.7625 54-55 21.45 22.787499999999998 32.737500000000004 23.025000000000002 56-57 28.65 29.575000000000003 22.95 18.825 58-59 21.3625 29.9625 29.299999999999997 19.375 60-61 33.5125 23.6625 25.2875 17.5375 62-63 19.675 24.5625 32.824999999999996 22.9375 64-65 18.912499999999998 39.550000000000004 25.275 16.2625 66-67 27.150000000000002 31.2625 23.6125 17.974999999999998 68-69 19.15 24.625 30.337500000000002 25.887500000000003 70-71 21.215911933950462 30.24768576432324 24.293219914936202 24.243182386790092 72-73 27.314989320266363 24.12363362231436 30.59429576579972 17.96708129161955 74-75 27.86553772273474 29.129280930114998 26.197396688992796 16.807784658157463 76-77 21.14213197969543 22.601522842639593 24.758883248730964 31.497461928934012 78-79 26.157377885473792 29.906899630149216 25.774773625813037 18.16094885856396 80-81 20.463567678319887 40.28684850813165 22.947880650531438 16.30170316301703 82-83 24.34278350515464 24.8840206185567 23.646907216494846 27.12628865979381 84-85 20.58785277669398 26.089218363896478 32.77409285992977 20.548835999479774 86-87 19.408237747653807 31.8169968717414 24.15276329509906 24.622002085505734 88-89 17.570385818561 25.391032325338898 31.00886339937435 26.029718456725753 90-91 27.919708029197082 30.213764337851927 24.035453597497394 17.831074035453597 92-93 18.117831074035454 29.26225234619395 29.092805005213762 23.52711157455683 >>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 2.0 18 2.5 19 1.5 20 2.0 21 3.5 22 4.0 23 5.0 24 5.5 25 5.5 26 9.5 27 14.0 28 15.0 29 13.0 30 23.0 31 30.5 32 38.5 33 46.5 34 44.5 35 60.0 36 105.0 37 171.0 38 221.5 39 206.0 40 197.0 41 195.0 42 190.5 43 210.0 44 193.0 45 169.5 46 158.5 47 128.0 48 105.0 49 116.5 50 114.0 51 102.0 52 109.0 53 144.5 54 315.0 55 331.5 56 161.0 57 115.5 58 85.0 59 43.5 60 30.0 61 23.0 62 14.0 63 11.0 64 10.0 65 10.0 66 8.5 67 5.5 68 7.0 69 13.5 70 12.0 71 6.0 72 4.5 73 2.5 74 1.5 75 0.5 76 0.0 77 0.5 78 0.5 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 0.0 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 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 6.0 71 10.0 72 9.0 73 13.0 74 11.0 75 5.0 76 12.0 77 8.0 78 11.0 79 7.0 80 7.0 81 12.0 82 18.0 83 18.0 84 17.0 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 3836.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 64.725 #Duplication Level Percentage of deduplicated Percentage of total 1 91.8115102356122 59.425 2 3.5921205098493627 4.65 3 1.3904982618771726 2.7 4 0.656624179219776 1.7000000000000002 5 0.5793742757821553 1.875 6 0.2317497103128621 0.8999999999999999 7 0.27037466203167243 1.225 8 0.27037466203167243 1.4000000000000001 9 0.1544998068752414 0.8999999999999999 >10 0.9269988412514484 11.475 >50 0.0772499034376207 3.25 >100 0.03862495171881035 10.5 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 420 10.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 78 1.95 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 52 1.3 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 47 1.175 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 39 0.975 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 32 0.8 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 28 0.7000000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 26 0.65 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 20 0.5 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 20 0.5 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 19 0.475 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 18 0.44999999999999996 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 18 0.44999999999999996 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 17 0.42500000000000004 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 17 0.42500000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 17 0.42500000000000004 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 16 0.4 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 16 0.4 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 15 0.375 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 14 0.35000000000000003 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 14 0.35000000000000003 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 11 0.27499999999999997 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 11 0.27499999999999997 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 11 0.27499999999999997 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 10 0.25 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 9 0.22499999999999998 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 9 0.22499999999999998 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 9 0.22499999999999998 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 9 0.22499999999999998 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 8 0.2 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 8 0.2 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 8 0.2 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 8 0.2 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 7 0.17500000000000002 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GAAAACGGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAG 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 5 0.125 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit CAACCTGGCGAACTGAAACATCTTAGTAGCCAGAGGAAAAGAAAGCAAAA 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGG 5 0.125 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCAGC 5 0.125 No Hit GTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGT 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGCGTGCCGC 5 0.125 No Hit GAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCC 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 5 0.125 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 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 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 60 3.5845005E-8 50.261456 1 GCAATAC 70 1.9626896E-9 49.235714 7 CAATACA 70 1.9626896E-9 49.235714 8 AATACAA 70 1.9626896E-9 49.235714 9 GGAGAGC 65 6.737355E-8 46.395195 2 GAGCAAT 65 6.737355E-8 46.395195 5 AGAGCAA 65 6.737355E-8 46.395195 4 GAGAGCA 65 6.737355E-8 46.395195 3 AGCAATA 65 6.737355E-8 46.395195 6 ACTAGCT 50 3.6281563E-8 36.278946 86-87 CACTAGC 60 4.485628E-9 34.011513 86-87 GCATCAC 70 5.293259E-10 32.39192 82-83 GCGGTTG 60 7.514245E-9 32.310936 36-37 CGAAGCG 60 7.514245E-9 32.310936 32-33 AAGCGGT 60 7.514245E-9 32.310936 34-35 ATCACTA 65 9.804353E-9 31.39524 84-85 GGTTGAG 70 9.331416E-10 30.772322 38-39 GAGTGCC 70 9.331416E-10 30.772322 42-43 TGCTGCT 70 9.331416E-10 30.772322 22-23 TTGAGTG 70 9.331416E-10 30.772322 40-41 >>END_MODULE Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67472 READS because READLEN < 1 Read 67472 spots for ERR6133417.sra Written 67472 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra Rejected 67455 READS because READLEN < 1 Read 67455 spots for ERR6133417.sra Written 67455 spots for ERR6133417.sra SRR ids: ['ERR6133417.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7g5kpnz8 ERR6133417.sra spots: 1349117 blocks: [[1, 67455], [67456, 134910], [134911, 202365], [202366, 269820], [269821, 337275], [337276, 404730], [404731, 472185], [472186, 539640], [539641, 607095], [607096, 674550], [674551, 742005], [742006, 809460], [809461, 876915], [876916, 944370], [944371, 1011825], [1011826, 1079280], [1079281, 1146735], [1146736, 1214190], [1214191, 1281645], [1281646, 1349117]] ERR6133417 file size 296583 ERR6133417 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 ERR6133417 ERR6133417_1.fastq Input file: ERR6133417_1.fastq trimmed: ERR6133417-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 04:14:16 2024 >> started Sat Dec 7 04:14:17 2024 >> done (1.106s) 1349117 reads processed; of these: 12 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 1349105 (100.00%) reads available; of these: 361379 (26.79%) trimmed reads available after processing 987726 (73.21%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 19 8 0.00% 20 1 0.00% 21 2 0.00% 22 2 0.00% 23 3 0.00% 24 1 0.00% 25 0 0.00% 26 0 0.00% 27 0 0.00% 28 2 0.00% 29 15 0.00% 30 0 0.00% 31 1 0.00% 32 4 0.00% 33 1 0.00% 34 1 0.00% 35 1 0.00% 36 0 0.00% 37 2 0.00% 38 3 0.00% 39 9 0.00% 40 14 0.00% 41 2 0.00% 42 8 0.00% 43 10 0.00% 44 13 0.00% 45 11 0.00% 46 35 0.00% 47 36 0.00% 48 47 0.00% 49 82 0.01% 50 144 0.01% 51 155 0.01% 52 221 0.02% 53 370 0.03% 54 493 0.04% 55 681 0.05% 56 874 0.06% 57 1352 0.10% 58 1031 0.08% 59 1231 0.09% 60 1532 0.11% 61 1807 0.13% 62 1876 0.14% 63 2017 0.15% 64 2327 0.17% 65 2485 0.18% 66 2533 0.19% 67 2635 0.20% 68 2249 0.17% 69 2129 0.16% 70 5486 0.41% 71 6165 0.46% 72 7628 0.57% 73 8429 0.62% 74 8625 0.64% 75 9766 0.72% 76 10515 0.78% 77 12261 0.91% 78 12685 0.94% 79 13343 0.99% 80 14584 1.08% 81 16690 1.24% 82 18127 1.34% 83 18749 1.39% 84 22272 1.65% 85 18399 1.36% 86 18948 1.40% 87 21104 1.56% 88 26800 1.99% 89 26622 1.97% 90 27907 2.07% 91 30620 2.27% 92 26688 1.98% 93 938236 69.55% 1349105 reads passed initial QC criterion=sequence-density sequence-density=2.64 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=30 prefix-density=2.71 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.13 sequence-density-rank=23 fanout-score=124.53 fanout-score-rank=1 prefix-density=15.45 prefix-fanout=1.0 sequence=GATGGCTAAAGCCCAGTAGCCGA 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 04:14:33 Started mapping on | Dec 07 04:14:33 Finished on | Dec 07 04:14:41 Mapping speed, Million of reads per hour | 607.10 Number of input reads | 1349105 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 470202 Uniquely mapped reads % | 34.85% Average mapped length | 89.04 Number of splices: Total | 23477 Number of splices: Annotated (sjdb) | 18918 Number of splices: GT/AG | 22500 Number of splices: GC/AG | 430 Number of splices: AT/AC | 33 Number of splices: Non-canonical | 514 Mismatch rate per base, % | 0.82% Deletion rate per base | 0.04% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 1.81 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 777746 % of reads mapped to multiple loci | 57.65% Number of reads mapped to too many loci | 39478 % of reads mapped to too many loci | 2.93% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.07% % of reads unmapped: other | 0.50% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 101157 101157 101157 N_multimapping 777746 777746 777746 N_noFeature 47226 51998 449695 N_ambiguous 18807 3031 93 UnstrandedReadsAssigned:404169 PositiveStrandReadsAssigned:415173 NegativeStrandReadsAssigned:20414 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=87 echo kmer=83 ERR6133417 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: ERR6133417-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,349,105 reads, 803,063 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 862 rounds 52973 ERR6133417.ke.tsv 35125 ERR6133417.se.tsv 88098 total ==> ERR6133417.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 12 13.9697 PNS24243 293 194 0 0 KQK14069 1603 1504 5 5.30984 KQK14071 474 375 0 0 ==> ERR6133417.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 6 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 1 BRADI_1g09890v3 0 BRADI_1g77505v3 6 BRADI_1g48960v3 0 ERR6133417 completed mapping pipeline successfully