Starting /dee2/code/volunteer_pipeline.sh ERR6133555 current disk space = 1544454864896 free memory = 1478421452 ERR6133555 SRAfilesize b103e8550fcccca0fa9ad45183e66f41 ERR6133555.sra ERR6133555.sra file validated ERR6133555 is single end ERR6133555 is conventional basespace ERR6133555 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133555_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.646 33.0 33.0 37.0 27.0 37.0 2 35.98975 37.0 37.0 37.0 33.0 37.0 3 35.1845 37.0 33.0 37.0 33.0 37.0 4 35.284 37.0 37.0 37.0 33.0 37.0 5 35.29075 37.0 37.0 37.0 33.0 37.0 6 35.61075 37.0 37.0 37.0 33.0 37.0 7 37.38175 37.0 37.0 40.0 33.0 40.0 8 37.37825 37.0 37.0 40.0 33.0 40.0 9 37.41125 37.0 37.0 40.0 33.0 40.0 10-11 37.485625 37.0 37.0 40.0 33.0 40.0 12-13 37.420874999999995 37.0 37.0 40.0 33.0 40.0 14-15 37.405375 37.0 37.0 40.0 33.0 40.0 16-17 37.303250000000006 37.0 37.0 40.0 33.0 40.0 18-19 37.182625 37.0 37.0 40.0 33.0 40.0 20-21 37.01025 37.0 37.0 40.0 33.0 40.0 22-23 37.033625 37.0 37.0 40.0 33.0 40.0 24-25 37.087999999999994 37.0 37.0 40.0 33.0 40.0 26-27 37.135625 37.0 37.0 40.0 33.0 40.0 28-29 37.01475000000001 37.0 37.0 40.0 33.0 40.0 30-31 36.962125 37.0 37.0 40.0 33.0 40.0 32-33 36.756625 37.0 37.0 40.0 33.0 40.0 34-35 36.6845 37.0 37.0 40.0 33.0 40.0 36-37 36.365625 37.0 37.0 40.0 33.0 40.0 38-39 36.316625 37.0 37.0 40.0 33.0 40.0 40-41 36.042125 37.0 37.0 40.0 33.0 40.0 42-43 36.01725 37.0 37.0 40.0 33.0 40.0 44-45 35.722375 37.0 35.0 38.5 33.0 40.0 46-47 35.406375 37.0 33.0 37.0 33.0 40.0 48-49 35.399125 37.0 33.0 37.0 33.0 40.0 50-51 35.30825 37.0 33.0 37.0 33.0 40.0 52-53 35.037875 37.0 33.0 37.0 33.0 40.0 54-55 35.00675 37.0 33.0 37.0 33.0 37.0 56-57 34.93375 37.0 33.0 37.0 33.0 37.0 58-59 34.257 37.0 33.0 37.0 27.0 37.0 60-61 34.402125 37.0 33.0 37.0 27.0 37.0 62-63 34.286625 37.0 33.0 37.0 27.0 37.0 64-65 34.339 37.0 33.0 37.0 27.0 37.0 66-67 34.354625 37.0 33.0 37.0 27.0 37.0 68-69 33.585125 35.0 33.0 37.0 27.0 37.0 70-71 33.700876001001 35.0 33.0 37.0 27.0 37.0 72-73 34.10299594273209 37.0 33.0 37.0 27.0 37.0 74-75 34.04629623081193 37.0 33.0 37.0 27.0 37.0 76-77 33.98525820053492 37.0 33.0 37.0 27.0 37.0 78-79 34.05742116478224 37.0 33.0 37.0 27.0 37.0 80-81 33.93575625044153 37.0 33.0 37.0 27.0 37.0 82-83 33.883141235848925 37.0 33.0 37.0 27.0 37.0 84-85 33.9054753141361 37.0 33.0 37.0 27.0 37.0 86-87 33.79708663429594 37.0 33.0 37.0 27.0 37.0 88-89 33.736647073856375 37.0 33.0 37.0 27.0 37.0 90-91 33.59238435982622 37.0 33.0 37.0 27.0 37.0 92-93 33.457321748019424 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 16.0 21 18.0 22 14.0 23 13.0 24 22.0 25 44.0 26 44.0 27 37.0 28 54.0 29 61.0 30 84.0 31 128.0 32 126.0 33 158.0 34 260.0 35 452.0 36 950.0 37 965.0 38 546.0 39 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.35 2.5250000000000004 2.85 6.275 2 75.075 15.5 5.949999999999999 3.4750000000000005 3 37.824999999999996 37.85 13.100000000000001 11.225 4 33.375 28.799999999999997 18.725 19.1 5 26.125 29.625 26.375 17.875 6 20.7 38.125 23.825 17.349999999999998 7 39.5 28.325 16.375 15.8 8 28.9 32.05 22.325 16.725 9 25.7 30.675 27.0 16.625 10-11 24.875 28.299999999999997 28.5875 18.2375 12-13 27.900000000000002 27.3875 26.5 18.212500000000002 14-15 20.1 33.275 27.487499999999997 19.1375 16-17 24.462500000000002 32.0375 22.85 20.65 18-19 24.2625 26.950000000000003 28.3875 20.4 20-21 26.0125 25.624999999999996 28.237499999999997 20.125 22-23 28.549999999999997 22.3125 28.1 21.0375 24-25 25.2 25.1875 27.787499999999998 21.825 26-27 25.2125 24.2875 31.2375 19.2625 28-29 26.125 27.650000000000002 26.9625 19.2625 30-31 28.675 24.6 26.487500000000004 20.2375 32-33 24.3875 26.8125 27.075 21.725 34-35 23.538981354023274 30.021273933174818 25.328494556375926 21.111250156425978 36-37 24.928116014501814 25.278159769971246 27.015876984623077 22.777847230903863 38-39 29.062500000000004 25.087500000000002 27.8875 17.962500000000002 40-41 27.817385866166354 23.939962476547844 26.85428392745466 21.388367729831145 42-43 25.10015022533801 29.081121682523786 25.187781672508763 20.630946419629446 44-45 23.139462163852407 26.59161976235147 29.9437148217636 20.32520325203252 46-47 25.678209776222026 24.315539442430303 27.11588948618577 22.890361295161895 48-49 25.722145804676757 24.0090033762661 28.83581343003626 21.433037389020885 50-51 24.2 26.9625 27.9125 20.925 52-53 24.31181181181181 27.264764764764767 25.425425425425423 22.997997997998 54-55 24.349999999999998 27.3 28.1875 20.1625 56-57 26.75 25.7625 27.6375 19.85 58-59 23.5125 25.087500000000002 28.975 22.425 60-61 26.125 25.05 27.675 21.15 62-63 22.1 26.700000000000003 32.25 18.95 64-65 22.475 29.5 28.6375 19.3875 66-67 25.412499999999998 27.825 26.1625 20.599999999999998 68-69 20.65 27.250000000000004 27.287499999999998 24.8125 70-71 23.06153076538269 28.38919459729865 26.725862931465734 21.823411705852926 72-73 27.06295460245799 23.5766240280913 29.13217958364685 20.228241785803863 74-75 23.947732127151653 27.591405955522053 29.249905767056163 19.210956150270135 76-77 22.72784570780285 24.65649817219211 28.135635951090382 24.48002016891466 78-79 24.769483390173043 25.691549829480863 29.304029304029307 20.234937476316787 80-81 22.554485554992397 30.82868727825646 28.547896604156108 18.068930562595035 82-83 23.699936427209153 25.352828989192627 29.09090909090909 21.85632549268913 84-85 23.709759836484416 23.77363311190598 31.09351047521717 21.423096576392435 86-87 21.581906465627394 27.383082034244826 30.334781497572195 20.700230002555582 88-89 19.67799642218247 28.07308970099668 31.012011244569383 21.23690263225147 90-91 26.935854842831585 26.616406848964992 27.293636595962177 19.154101712241246 92-93 21.952466138512648 28.034755941732687 29.836442627140304 20.17633529261436 >>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 0.0 17 5.5 18 6.0 19 1.0 20 1.0 21 3.5 22 4.0 23 3.0 24 3.5 25 4.0 26 8.5 27 8.5 28 10.5 29 17.0 30 22.0 31 33.5 32 52.0 33 71.0 34 79.5 35 81.0 36 94.0 37 129.5 38 188.0 39 182.5 40 169.0 41 176.5 42 197.0 43 234.5 44 202.0 45 183.0 46 209.5 47 204.5 48 167.5 49 144.0 50 139.5 51 153.5 52 147.5 53 131.5 54 166.5 55 145.0 56 79.5 57 68.5 58 65.5 59 52.5 60 37.0 61 31.0 62 29.0 63 29.5 64 30.0 65 29.0 66 24.0 67 18.0 68 20.5 69 18.5 70 9.0 71 5.0 72 7.0 73 7.0 74 2.5 75 1.0 76 1.5 77 1.0 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 0.11249999999999999 36-37 0.0125 38-39 0.0 40-41 0.0625 42-43 0.15 44-45 0.0625 46-47 0.0125 48-49 0.0375 50-51 0.0 52-53 0.1 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 4.0 71 7.0 72 4.0 73 2.0 74 7.0 75 8.0 76 3.0 77 3.0 78 7.0 79 5.0 80 8.0 81 6.0 82 7.0 83 14.0 84 2.0 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 3913.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.6 #Duplication Level Percentage of deduplicated Percentage of total 1 91.88179347826086 67.625 2 4.211956521739131 6.2 3 1.3926630434782608 3.075 4 0.6793478260869565 2.0 5 0.33967391304347827 1.25 6 0.2377717391304348 1.05 7 0.1358695652173913 0.7000000000000001 8 0.16983695652173914 1.0 9 0.0 0.0 >10 0.8491847826086956 11.275 >50 0.06793478260869565 2.9250000000000003 >100 0.033967391304347824 2.9000000000000004 >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 116 2.9000000000000004 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 63 1.575 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 54 1.35 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 48 1.2 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 35 0.8750000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 26 0.65 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 26 0.65 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 25 0.625 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 24 0.6 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 23 0.575 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 21 0.525 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 19 0.475 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 18 0.44999999999999996 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 16 0.4 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 16 0.4 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 15 0.375 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 14 0.35000000000000003 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 13 0.325 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 13 0.325 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 12 0.3 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 11 0.27499999999999997 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 10 0.25 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 8 0.2 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 8 0.2 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 7 0.17500000000000002 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 6 0.15 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 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 0.0125 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.1125 0.0 0.0 0.0 0.0 38-39 0.2 0.0 0.0 0.0 0.0 40-41 0.2 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.2 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.21250000000000002 0.0 0.0 0.0 0.0 52-53 0.225 0.0 0.0 0.0 0.0 54-55 0.225 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.225 0.0 0.0 0.0 0.0 60-61 0.225 0.0 0.0 0.0 0.0 62-63 0.225 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.225 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 40 1.2732926E-11 86.775 2 GCAATAC 35 4.765752E-10 86.775 7 GGGAGAG 45 0.0 86.775 1 CAATACA 35 4.765752E-10 86.775 8 GAGCAAT 35 4.765752E-10 86.775 5 GAGAGCA 40 1.2732926E-11 86.775 3 AATACAA 35 4.765752E-10 86.775 9 AGCAATA 35 4.765752E-10 86.775 6 AGAGCAA 45 3.6379788E-11 77.13333 4 GGAGGAG 25 0.0066749183 52.065002 1 AGTAGCC 35 1.2316377E-7 43.936707 70-71 CAGTAGC 35 1.2316377E-7 43.936707 70-71 TAGCCGA 35 1.2316377E-7 43.936707 72-73 CATCACT 35 1.2316377E-7 43.936707 82-83 ATCACTA 35 1.2316377E-7 43.936707 84-85 CGAAAGC 35 1.2316377E-7 43.936707 76-77 AGCATCA 35 1.2316377E-7 43.936707 80-81 CACTAGC 35 1.2316377E-7 43.936707 86-87 TCACTAG 35 1.2316377E-7 43.936707 84-85 ACTAGCT 35 1.2316377E-7 43.936707 86-87 >>END_MODULE Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290099 READS because READLEN < 1 Read 290099 spots for ERR6133555.sra Written 290099 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra Rejected 290098 READS because READLEN < 1 Read 290098 spots for ERR6133555.sra Written 290098 spots for ERR6133555.sra SRR ids: ['ERR6133555.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ttkf92gh ERR6133555.sra spots: 5801961 blocks: [[1, 290098], [290099, 580196], [580197, 870294], [870295, 1160392], [1160393, 1450490], [1450491, 1740588], [1740589, 2030686], [2030687, 2320784], [2320785, 2610882], [2610883, 2900980], [2900981, 3191078], [3191079, 3481176], [3481177, 3771274], [3771275, 4061372], [4061373, 4351470], [4351471, 4641568], [4641569, 4931666], [4931667, 5221764], [5221765, 5511862], [5511863, 5801961]] ERR6133555 file size 1285640 ERR6133555 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 ERR6133555 ERR6133555_1.fastq Input file: ERR6133555_1.fastq trimmed: ERR6133555-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 08:31:53 2024 >> started Sat Dec 7 08:31:57 2024 >> done (3.307s) 5801961 reads processed; of these: 341 ( 0.01%) short reads filtered out after trimming by size control 139 ( 0.00%) empty reads filtered out after trimming by size control 5801481 (99.99%) reads available; of these: 126479 ( 2.18%) trimmed reads available after processing 5675002 (97.82%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 81 0.00% 20 28 0.00% 21 23 0.00% 22 25 0.00% 23 7 0.00% 24 13 0.00% 25 6 0.00% 26 22 0.00% 27 13 0.00% 28 34 0.00% 29 47 0.00% 30 42 0.00% 31 105 0.00% 32 134 0.00% 33 214 0.00% 34 263 0.00% 35 620 0.01% 36 13577 0.23% 37 210 0.00% 38 172 0.00% 39 225 0.00% 40 281 0.00% 41 229 0.00% 42 230 0.00% 43 193 0.00% 44 217 0.00% 45 184 0.00% 46 191 0.00% 47 222 0.00% 48 189 0.00% 49 170 0.00% 50 155 0.00% 51 222 0.00% 52 132 0.00% 53 94 0.00% 54 92 0.00% 55 94 0.00% 56 75 0.00% 57 70 0.00% 58 63 0.00% 59 43 0.00% 60 42 0.00% 61 53 0.00% 62 4 0.00% 63 6 0.00% 64 10 0.00% 65 9 0.00% 66 8 0.00% 67 21 0.00% 68 40 0.00% 69 121 0.00% 70 8851 0.15% 71 7836 0.14% 72 7993 0.14% 73 7382 0.13% 74 7777 0.13% 75 7858 0.14% 76 6901 0.12% 77 7468 0.13% 78 8611 0.15% 79 9663 0.17% 80 8879 0.15% 81 10806 0.19% 82 12423 0.21% 83 11173 0.19% 84 10103 0.17% 85 219 0.00% 86 456 0.01% 87 745 0.01% 88 1398 0.02% 89 2714 0.05% 90 6065 0.10% 91 18561 0.32% 92 74879 1.29% 93 5543364 95.55% 5801481 reads passed initial QC criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=35 prefix-density=0.51 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=21 fanout-score=54.91 fanout-score-rank=1 prefix-density=0.89 prefix-fanout=1.9 sequence=TGCTGCAGCAGCTTAATTTGCATGCCAGGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCT Started job on | Dec 07 08:32:14 Started mapping on | Dec 07 08:32:14 Finished on | Dec 07 08:32:21 Mapping speed, Million of reads per hour | 2983.62 Number of input reads | 5801481 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3647192 Uniquely mapped reads % | 62.87% Average mapped length | 92.21 Number of splices: Total | 202663 Number of splices: Annotated (sjdb) | 172688 Number of splices: GT/AG | 196616 Number of splices: GC/AG | 3961 Number of splices: AT/AC | 87 Number of splices: Non-canonical | 1999 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.82 Insertion rate per base | 0.02% Insertion average length | 2.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1990267 % of reads mapped to multiple loci | 34.31% Number of reads mapped to too many loci | 57386 % of reads mapped to too many loci | 0.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.78% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 164022 164022 164022 N_multimapping 1990267 1990267 1990267 N_noFeature 280659 315950 3489334 N_ambiguous 142603 19994 511 UnstrandedReadsAssigned:3223930 PositiveStrandReadsAssigned:3311248 NegativeStrandReadsAssigned:157347 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133555 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: ERR6133555-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,801,481 reads, 4,530,140 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,000 rounds 52973 ERR6133555.ke.tsv 35125 ERR6133555.se.tsv 88098 total ==> ERR6133555.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 109 22.8476 PNS24243 293 194 0 0 KQK14069 1603 1504 75 14.3411 KQK14071 474 375 0 0 ==> ERR6133555.se.tsv <== BRADI_1g14170v3 76 BRADI_1g53295v3 12 BRADI_1g59795v3 33 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 33 BRADI_1g74790v3 19 BRADI_1g09890v3 0 BRADI_1g77505v3 82 BRADI_1g48960v3 0 ERR6133555 completed mapping pipeline successfully