Starting /dee2/code/volunteer_pipeline.sh ERR6133414 current disk space = 1547266465792 free memory = 1599566580 ERR6133414 SRAfilesize d256fcbbc87f42885c43adaa2930d829 ERR6133414.sra ERR6133414.sra file validated ERR6133414 is single end ERR6133414 is conventional basespace ERR6133414 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133414_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 30.187 33.0 27.0 33.0 15.0 37.0 2 33.88925 37.0 33.0 37.0 27.0 37.0 3 33.46275 33.0 33.0 37.0 27.0 37.0 4 33.4225 37.0 33.0 37.0 22.0 37.0 5 33.615 37.0 33.0 37.0 22.0 37.0 6 33.63425 37.0 33.0 37.0 22.0 37.0 7 35.233 37.0 33.0 37.0 27.0 40.0 8 34.76525 37.0 33.0 37.0 27.0 40.0 9 35.13075 37.0 33.0 37.0 27.0 40.0 10-11 34.93675 37.0 33.0 37.0 27.0 40.0 12-13 34.8535 37.0 33.0 37.0 27.0 40.0 14-15 34.765625 37.0 33.0 37.0 27.0 40.0 16-17 34.605625 37.0 33.0 37.0 27.0 40.0 18-19 34.448625 37.0 33.0 37.0 27.0 40.0 20-21 33.863125 37.0 33.0 37.0 24.5 40.0 22-23 33.457875 37.0 33.0 37.0 22.0 40.0 24-25 33.302125000000004 37.0 33.0 37.0 24.5 40.0 26-27 33.162125 37.0 33.0 37.0 22.0 40.0 28-29 32.769999999999996 33.0 33.0 37.0 22.0 40.0 30-31 32.51925 33.0 33.0 37.0 22.0 40.0 32-33 32.204875 33.0 33.0 37.0 22.0 40.0 34-35 31.0015 33.0 27.0 37.0 15.0 40.0 36-37 30.818875 33.0 27.0 37.0 15.0 37.0 38-39 31.298125 33.0 27.0 37.0 22.0 37.0 40-41 30.69175 33.0 27.0 37.0 18.5 38.5 42-43 30.533749999999998 33.0 27.0 37.0 15.0 37.0 44-45 30.352125 33.0 27.0 37.0 15.0 37.0 46-47 30.0045 33.0 27.0 37.0 15.0 37.0 48-49 29.73275 33.0 27.0 37.0 15.0 37.0 50-51 29.192875 33.0 24.5 37.0 15.0 37.0 52-53 29.022375 33.0 27.0 37.0 15.0 37.0 54-55 29.31725 33.0 27.0 37.0 15.0 37.0 56-57 28.38825 33.0 24.5 33.0 15.0 37.0 58-59 28.250125 33.0 27.0 33.0 15.0 37.0 60-61 28.149875 33.0 27.0 33.0 15.0 37.0 62-63 27.793875 33.0 22.0 33.0 15.0 37.0 64-65 27.328125 33.0 22.0 33.0 10.5 37.0 66-67 27.08775 33.0 22.0 33.0 15.0 37.0 68-69 26.26875 27.0 22.0 33.0 10.5 35.0 70-71 28.23291478696742 33.0 27.0 33.0 15.0 37.0 72-73 28.423105304983864 33.0 27.0 33.0 15.0 37.0 74-75 28.479449100628102 33.0 27.0 33.0 15.0 37.0 76-77 28.39780085204461 33.0 27.0 33.0 15.0 37.0 78-79 27.390192222751416 33.0 24.5 33.0 10.5 37.0 80-81 26.454155449356165 33.0 22.0 33.0 6.0 37.0 82-83 25.80820885311969 33.0 22.0 33.0 2.0 37.0 84-85 25.394728123530996 33.0 22.0 33.0 2.0 37.0 86-87 24.280954879328434 33.0 15.0 33.0 2.0 37.0 88-89 23.432581322140607 30.0 10.5 33.0 2.0 35.0 90-91 22.40175760755509 27.0 2.0 33.0 2.0 35.0 92-93 20.79000524658972 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 110.0 21 122.0 22 140.0 23 167.0 24 193.0 25 224.0 26 230.0 27 251.0 28 231.0 29 248.0 30 272.0 31 271.0 32 259.0 33 274.0 34 266.0 35 318.0 36 237.0 37 164.0 38 23.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 76.75 6.2 5.55 11.5 2 61.150000000000006 19.125 12.15 7.575 3 41.199999999999996 33.525 14.45 10.825 4 26.3 36.575 19.375 17.75 5 33.650000000000006 23.5 25.7 17.150000000000002 6 16.475 45.35 22.825 15.35 7 40.050000000000004 23.200000000000003 20.724999999999998 16.025 8 24.3 23.549999999999997 22.85 29.299999999999997 9 23.474999999999998 37.65 22.1 16.775000000000002 10-11 19.025 31.9625 31.912499999999998 17.1 12-13 19.0625 31.937500000000004 24.85 24.15 14-15 18.55 39.675 24.8625 16.9125 16-17 27.3375 25.162499999999998 21.2625 26.237500000000004 18-19 27.187499999999996 21.9375 33.125 17.75 20-21 28.025 22.5125 31.85 17.6125 22-23 31.5125 20.5375 29.462500000000002 18.4875 24-25 21.0375 22.1375 30.862499999999997 25.9625 26-27 26.9125 21.525 27.975 23.5875 28-29 21.475 30.9 30.4625 17.1625 30-31 36.975 23.7125 21.825 17.4875 32-33 29.8375 20.7625 24.5125 24.887500000000003 34-35 20.3875 38.875 22.5125 18.224999999999998 36-37 28.5625 23.799999999999997 21.8 25.837500000000002 38-39 37.4 20.275000000000002 23.7625 18.5625 40-41 22.7625 22.3375 37.974999999999994 16.925 42-43 29.362500000000004 32.425 22.6375 15.575 44-45 27.5875 24.0375 31.0375 17.3375 46-47 28.3375 22.8625 22.95 25.85 48-49 27.650000000000002 22.7375 24.45 25.162499999999998 50-51 19.625 32.4 22.662499999999998 25.3125 52-53 20.95 24.2375 22.8625 31.95 54-55 19.8625 23.150000000000002 32.85 24.1375 56-57 27.800000000000004 30.45 23.1875 18.5625 58-59 20.974999999999998 30.337500000000002 29.275000000000002 19.412499999999998 60-61 35.462500000000006 22.575 23.575 18.387500000000003 62-63 18.224999999999998 24.425 33.0875 24.2625 64-65 17.5 41.1875 23.1 18.212500000000002 66-67 28.212500000000002 31.724999999999998 23.150000000000002 16.9125 68-69 19.7625 24.175 29.1875 26.875 70-71 21.151439299123904 29.374217772215268 23.92991239048811 25.544430538172712 72-73 28.618172665492068 23.319909388371507 31.135162345834384 16.926755600302037 74-75 28.09614168247944 32.06831119544592 23.46616065781151 16.369386464263126 76-77 21.126939709997455 21.750190791147293 23.734418722971252 33.388450775883996 78-79 27.61356365962892 30.671785028790786 24.17146513115803 17.543186180422264 80-81 20.559062218214606 41.69779724333376 22.877753445832795 14.865387092618834 82-83 27.532467532467532 24.103896103896105 21.83116883116883 26.532467532467535 84-85 20.24090075936109 27.76904948939513 31.82770358732653 20.162346163917256 86-87 19.491080797481636 32.0697796432319 23.491605456453303 24.947534102833156 88-89 18.769674711437563 25.35414480587618 31.492654774396645 24.38352570828961 90-91 27.452780692549844 32.279643231899264 22.193074501573975 18.074501573976914 92-93 18.166316894018887 27.30849947534103 30.535152151101784 23.990031479538303 >>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 5.0 18 6.5 19 2.5 20 1.5 21 2.5 22 3.5 23 5.5 24 7.5 25 7.0 26 10.0 27 14.0 28 17.5 29 19.0 30 27.0 31 39.0 32 37.5 33 42.0 34 52.0 35 56.0 36 84.5 37 156.0 38 202.0 39 189.5 40 177.5 41 164.5 42 178.0 43 202.0 44 164.0 45 141.0 46 147.5 47 128.0 48 103.5 49 106.5 50 109.0 51 111.0 52 140.5 53 197.5 54 385.0 55 378.0 56 165.5 57 108.5 58 87.0 59 44.5 60 24.5 61 26.5 62 22.0 63 14.0 64 12.5 65 9.0 66 5.5 67 5.0 68 8.0 69 10.0 70 5.0 71 1.0 72 1.0 73 0.5 74 0.0 75 0.5 76 0.5 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 0.0 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 10.0 71 12.0 72 10.0 73 11.0 74 9.0 75 10.0 76 14.0 77 12.0 78 9.0 79 15.0 80 13.0 81 17.0 82 16.0 83 16.0 84 14.0 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 3812.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 64.35 #Duplication Level Percentage of deduplicated Percentage of total 1 90.83139083139083 58.45 2 4.428904428904429 5.7 3 1.6705516705516703 3.225 4 0.7381507381507382 1.9 5 0.3108003108003108 1.0 6 0.27195027195027194 1.05 7 0.11655011655011654 0.525 8 0.34965034965034963 1.7999999999999998 9 0.03885003885003885 0.22499999999999998 >10 1.2043512043512044 13.625000000000002 >50 0.0 0.0 >100 0.03885003885003885 12.5 >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 500 12.5 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 42 1.05 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 37 0.9249999999999999 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 28 0.7000000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 28 0.7000000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 26 0.65 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 25 0.625 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 20 0.5 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 20 0.5 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 19 0.475 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 18 0.44999999999999996 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 16 0.4 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 15 0.375 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 14 0.35000000000000003 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 14 0.35000000000000003 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 14 0.35000000000000003 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 12 0.3 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 12 0.3 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 12 0.3 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 10 0.25 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 10 0.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 10 0.25 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 10 0.25 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 10 0.25 No Hit GTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGA 9 0.22499999999999998 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 6 0.15 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGGGCCGC 6 0.15 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit GCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGT 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGCGCCGC 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGGTGAGTGCCGC 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGGGCTGCTAGGCGAAGCGGTTGAGTGCCGC 5 0.125 No Hit TGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCA 5 0.125 No Hit CAACAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAG 5 0.125 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 5 0.125 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 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 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 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 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 90 0.0 62.5625 7 GGGAGAG 90 0.0 62.5625 1 CAATACA 90 0.0 62.5625 8 GAGCAAT 90 0.0 62.5625 5 AATACAA 90 0.0 62.5625 9 AGCAATA 90 0.0 62.5625 6 GGAGAGC 95 0.0 59.269733 2 AGAGCAA 95 0.0 59.269733 4 GAGAGCA 100 0.0 56.30625 3 CACTAGC 60 1.8189894E-12 40.72115 86-87 ACTAGCT 60 1.8189894E-12 40.72115 86-87 GCATCAC 60 1.8189894E-12 40.72115 82-83 CATCACT 55 4.9112714E-11 40.384617 82-83 ATCACTA 55 4.9112714E-11 40.384617 84-85 TCACTAG 55 4.9112714E-11 40.384617 84-85 TGCCGCA 70 0.0 37.124996 44-45 GCCGCAC 80 0.0 35.191406 46-47 AGCATCA 70 1.6370905E-11 34.903843 80-81 TGCTGCT 75 1.8189894E-12 34.65 22-23 CCGCACC 75 1.8189894E-12 34.65 46-47 >>END_MODULE Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152200 READS because READLEN < 1 Read 152200 spots for ERR6133414.sra Written 152200 spots for ERR6133414.sra Rejected 152217 READS because READLEN < 1 Read 152217 spots for ERR6133414.sra Written 152217 spots for ERR6133414.sra SRR ids: ['ERR6133414.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__yke570r ERR6133414.sra spots: 3044017 blocks: [[1, 152200], [152201, 304400], [304401, 456600], [456601, 608800], [608801, 761000], [761001, 913200], [913201, 1065400], [1065401, 1217600], [1217601, 1369800], [1369801, 1522000], [1522001, 1674200], [1674201, 1826400], [1826401, 1978600], [1978601, 2130800], [2130801, 2283000], [2283001, 2435200], [2435201, 2587400], [2587401, 2739600], [2739601, 2891800], [2891801, 3044017]] ERR6133414 file size 671398 ERR6133414 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 ERR6133414 ERR6133414_1.fastq Input file: ERR6133414_1.fastq trimmed: ERR6133414-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 03:58:52 2024 >> started Sat Dec 7 03:58:55 2024 >> done (2.587s) 3044017 reads processed; of these: 23 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 3043991 (100.00%) reads available; of these: 820588 (26.96%) trimmed reads available after processing 2223403 (73.04%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 14 0.00% 20 5 0.00% 21 2 0.00% 22 4 0.00% 23 3 0.00% 24 1 0.00% 25 0 0.00% 26 0 0.00% 27 1 0.00% 28 4 0.00% 29 41 0.00% 30 3 0.00% 31 6 0.00% 32 13 0.00% 33 4 0.00% 34 2 0.00% 35 3 0.00% 36 4 0.00% 37 5 0.00% 38 14 0.00% 39 26 0.00% 40 32 0.00% 41 24 0.00% 42 22 0.00% 43 24 0.00% 44 41 0.00% 45 47 0.00% 46 59 0.00% 47 97 0.00% 48 141 0.00% 49 198 0.01% 50 302 0.01% 51 373 0.01% 52 547 0.02% 53 777 0.03% 54 1146 0.04% 55 1520 0.05% 56 2063 0.07% 57 3189 0.10% 58 2372 0.08% 59 2711 0.09% 60 3429 0.11% 61 4031 0.13% 62 4346 0.14% 63 4747 0.16% 64 5220 0.17% 65 5582 0.18% 66 5925 0.19% 67 6245 0.21% 68 5272 0.17% 69 5133 0.17% 70 14269 0.47% 71 15256 0.50% 72 18780 0.62% 73 19521 0.64% 74 20563 0.68% 75 22860 0.75% 76 25584 0.84% 77 29780 0.98% 78 30178 0.99% 79 31841 1.05% 80 33968 1.12% 81 38763 1.27% 82 41721 1.37% 83 43146 1.42% 84 50673 1.66% 85 42415 1.39% 86 41811 1.37% 87 46901 1.54% 88 60950 2.00% 89 60544 1.99% 90 62555 2.06% 91 69137 2.27% 92 59964 1.97% 93 2097034 68.89% 3043991 reads passed initial QC criterion=sequence-density sequence-density=0.97 sequence-density-rank=1 fanout-score=5.49 fanout-score-rank=25 prefix-density=2.73 prefix-fanout=1.9 sequence=AGGCTAAATACAGGCGAGAGACCGATAGCG criterion=fanout-score sequence-density=0.14 sequence-density-rank=26 fanout-score=137.59 fanout-score-rank=1 prefix-density=19.22 prefix-fanout=1.0 sequence=AGGCGAAGCGGGTGAGTGCCGCA Started job on | Dec 07 03:59:08 Started mapping on | Dec 07 03:59:08 Finished on | Dec 07 03:59:16 Mapping speed, Million of reads per hour | 1369.80 Number of input reads | 3043991 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 1024377 Uniquely mapped reads % | 33.65% Average mapped length | 88.89 Number of splices: Total | 60409 Number of splices: Annotated (sjdb) | 47885 Number of splices: GT/AG | 58524 Number of splices: GC/AG | 1016 Number of splices: AT/AC | 53 Number of splices: Non-canonical | 816 Mismatch rate per base, % | 0.83% Deletion rate per base | 0.04% Deletion average length | 1.77 Insertion rate per base | 0.02% Insertion average length | 1.86 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1846643 % of reads mapped to multiple loci | 60.67% Number of reads mapped to too many loci | 72024 % of reads mapped to too many loci | 2.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.90% % of reads unmapped: other | 0.42% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 172971 172971 172971 N_multimapping 1846643 1846643 1846643 N_noFeature 97955 108505 979942 N_ambiguous 42784 8901 204 UnstrandedReadsAssigned:883638 PositiveStrandReadsAssigned:906971 NegativeStrandReadsAssigned:44231 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=87 echo kmer=83 ERR6133414 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: ERR6133414-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,043,991 reads, 1,782,127 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 876 rounds 52973 ERR6133414.ke.tsv 35125 ERR6133414.se.tsv 88098 total ==> ERR6133414.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 19 9.92464 PNS24243 293 194 0 0 KQK14069 1603 1504 8 3.81204 KQK14071 474 375 0 0 ==> ERR6133414.se.tsv <== BRADI_1g14170v3 8 BRADI_1g53295v3 14 BRADI_1g59795v3 14 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 25 BRADI_1g48960v3 0 ERR6133414 completed mapping pipeline successfully