Starting /dee2/code/volunteer_pipeline.sh ERR6133330 current disk space = 1548188667904 free memory = 1434103252 ERR6133330 SRAfilesize f5f129c2cac2e499b217e228b5b23eea ERR6133330.sra ERR6133330.sra file validated ERR6133330 is single end ERR6133330 is conventional basespace ERR6133330 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133330_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 36.23475 37.0 37.0 37.0 33.0 37.0 2 36.37475 37.0 37.0 37.0 37.0 37.0 3 36.3355 37.0 37.0 37.0 33.0 37.0 4 36.39775 37.0 37.0 37.0 37.0 37.0 5 36.483 37.0 37.0 37.0 37.0 37.0 6 36.50625 37.0 37.0 37.0 37.0 37.0 7 38.70575 40.0 37.0 40.0 37.0 40.0 8 38.733 40.0 37.0 40.0 37.0 40.0 9 38.81375 40.0 37.0 40.0 37.0 40.0 10-11 38.806875 40.0 37.0 40.0 37.0 40.0 12-13 38.81825 40.0 37.0 40.0 37.0 40.0 14-15 38.733000000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.67725 40.0 37.0 40.0 37.0 40.0 18-19 38.8225 40.0 37.0 40.0 37.0 40.0 20-21 38.529875 40.0 37.0 40.0 37.0 40.0 22-23 38.549 40.0 37.0 40.0 37.0 40.0 24-25 38.54925 40.0 37.0 40.0 37.0 40.0 26-27 38.520125 40.0 37.0 40.0 37.0 40.0 28-29 38.53975 40.0 37.0 40.0 37.0 40.0 30-31 38.44775 40.0 37.0 40.0 37.0 40.0 32-33 38.43625 40.0 37.0 40.0 37.0 40.0 34-35 38.443875 40.0 37.0 40.0 37.0 40.0 36-37 38.282 40.0 37.0 40.0 37.0 40.0 38-39 38.001125 40.0 37.0 40.0 37.0 40.0 40-41 37.902874999999995 40.0 37.0 40.0 37.0 40.0 42-43 37.8735 38.5 37.0 40.0 37.0 40.0 44-45 37.554 37.0 37.0 40.0 33.0 40.0 46-47 37.4105 37.0 37.0 40.0 33.0 40.0 48-49 37.31 37.0 37.0 40.0 33.0 40.0 50-51 37.09075 37.0 37.0 40.0 33.0 40.0 52-53 36.935625 37.0 37.0 40.0 33.0 40.0 54-55 36.715875 37.0 37.0 37.0 33.0 40.0 56-57 36.438500000000005 37.0 37.0 37.0 33.0 40.0 58-59 36.175375 37.0 37.0 37.0 33.0 40.0 60-61 36.043875 37.0 37.0 37.0 33.0 40.0 62-63 35.6295 37.0 33.0 37.0 33.0 37.0 64-65 35.21625 37.0 33.0 37.0 33.0 37.0 66-67 35.075625 37.0 33.0 37.0 33.0 37.0 68-69 33.783125 35.0 33.0 37.0 30.0 37.0 70-71 33.568789734269245 33.0 33.0 37.0 30.0 37.0 72-73 33.78818805425544 33.0 33.0 37.0 30.0 37.0 74-75 33.69541203106112 33.0 33.0 37.0 30.0 37.0 76-77 33.647766203227064 33.0 33.0 37.0 30.0 37.0 78-79 33.02246907924874 33.0 33.0 37.0 27.0 37.0 80-81 32.71026053947391 33.0 33.0 37.0 27.0 37.0 82-83 32.77790136779254 33.0 33.0 37.0 27.0 37.0 84-85 32.22831493157755 33.0 33.0 35.0 27.0 37.0 86-87 32.186058839120065 33.0 33.0 33.0 27.0 37.0 88-89 32.15345878611185 33.0 33.0 35.0 27.0 37.0 90-91 31.10522130930294 33.0 30.0 33.0 24.5 37.0 92-93 30.243175192154784 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 4.0 22 4.0 23 5.0 24 8.0 25 6.0 26 8.0 27 13.0 28 17.0 29 17.0 30 33.0 31 50.0 32 75.0 33 94.0 34 204.0 35 598.0 36 1138.0 37 1484.0 38 225.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 61.875 10.975 13.850000000000001 13.3 2 39.35 27.1 19.7 13.850000000000001 3 25.525 35.625 20.075000000000003 18.775 4 27.0 28.799999999999997 20.625 23.575 5 23.925 27.85 28.225 20.0 6 17.525 40.849999999999994 25.3 16.325 7 36.5 25.6 22.725 15.174999999999999 8 27.625 27.800000000000004 26.35 18.224999999999998 9 24.825 28.525 25.95 20.7 10-11 23.7875 29.275000000000002 28.275 18.6625 12-13 22.5625 29.099999999999998 27.800000000000004 20.5375 14-15 25.837500000000002 29.15 27.725 17.2875 16-17 24.462500000000002 28.3625 26.687499999999996 20.4875 18-19 22.8875 25.650000000000002 31.637500000000003 19.825 20-21 26.087500000000002 25.137500000000003 28.575 20.200000000000003 22-23 28.65 22.45 29.462500000000002 19.4375 24-25 25.1875 26.0 28.237499999999997 20.575 26-27 25.5125 26.9625 28.787499999999998 18.7375 28-29 22.9375 27.0125 29.012500000000003 21.0375 30-31 26.987499999999997 24.525 28.325 20.1625 32-33 25.137500000000003 26.825 28.512500000000003 19.525000000000002 34-35 22.575 29.862499999999997 26.387500000000003 21.175 36-37 23.825 28.050000000000004 25.525 22.6 38-39 25.825 23.674999999999997 28.525 21.975 40-41 23.575 27.0625 29.375 19.9875 42-43 26.7625 29.849999999999998 25.7125 17.675 44-45 23.775 28.5875 28.000000000000004 19.6375 46-47 27.224999999999998 25.387500000000003 27.6375 19.75 48-49 25.324999999999996 24.625 29.125 20.925 50-51 21.912499999999998 29.099999999999998 28.625 20.3625 52-53 24.825 27.1 27.0 21.075 54-55 26.775 24.9 28.212500000000002 20.1125 56-57 24.887500000000003 27.85 28.625 18.637500000000003 58-59 22.825 28.0625 30.375000000000004 18.7375 60-61 25.7875 29.4 26.450000000000003 18.3625 62-63 21.7375 28.95 30.225 19.0875 64-65 22.7125 31.374999999999996 26.625 19.287499999999998 66-67 22.6375 31.2875 27.5625 18.512500000000003 68-69 21.337500000000002 28.000000000000004 28.799999999999997 21.8625 70-71 22.16798097383903 29.76592815120791 28.401552134184506 19.664538740768556 72-73 25.522012578616355 25.849056603773583 31.18238993710692 17.446540880503143 74-75 23.611286853093763 28.495508034923446 29.12817917246615 18.76502593951664 76-77 20.602501914730663 23.72989532805719 29.435792698493746 26.23181005871841 78-79 27.88276128037023 25.337446972618586 28.654068646355572 18.125723100655613 80-81 25.604551920341397 30.815983447562395 26.6778740462951 16.901590585801113 82-83 23.03979125896934 27.749510763209393 28.193085453359423 21.01761252446184 84-85 20.242968440512346 25.089132444209696 35.13799022844316 19.529908886834807 86-87 20.97800159024649 29.035250463821892 28.452160084813144 21.534587861118474 88-89 20.037105751391465 31.566392790882585 28.14736284124039 20.249138616485553 90-91 22.157434402332363 30.32069970845481 29.313543599257883 18.208322289954943 92-93 20.964749536178108 32.50728862973761 27.657036840710308 18.870924993373972 >>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 1.5 16 1.5 17 2.0 18 3.5 19 2.0 20 0.5 21 4.0 22 6.5 23 6.0 24 7.0 25 7.5 26 10.0 27 17.0 28 24.0 29 25.0 30 25.0 31 33.0 32 45.5 33 51.5 34 59.5 35 83.5 36 153.0 37 235.5 38 228.5 39 175.5 40 217.5 41 260.0 42 250.5 43 255.5 44 212.5 45 157.0 46 147.5 47 137.0 48 129.0 49 146.5 50 186.0 51 220.5 52 171.5 53 136.5 54 171.0 55 125.0 56 59.0 57 55.0 58 37.5 59 19.0 60 19.5 61 16.0 62 10.5 63 6.5 64 3.5 65 3.0 66 2.5 67 2.0 68 2.0 69 1.0 70 0.0 71 0.0 72 0.0 73 0.0 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 0.0 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 0.012651821862348178 76-77 0.012763241863433313 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 11.0 71 8.0 72 12.0 73 9.0 74 16.0 75 16.0 76 21.0 77 13.0 78 9.0 79 10.0 80 17.0 81 13.0 82 25.0 83 20.0 84 27.0 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 3773.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.95 #Duplication Level Percentage of deduplicated Percentage of total 1 92.14732453092425 66.3 2 4.065323141070188 5.8500000000000005 3 1.0771369006254343 2.325 4 0.7644197359277276 2.1999999999999997 5 0.4864489228630994 1.7500000000000002 6 0.17373175816539263 0.75 7 0.17373175816539263 0.8750000000000001 8 0.13898540653231412 0.8 9 0.10423905489923557 0.675 >10 0.7644197359277276 10.2 >50 0.03474635163307853 2.3 >100 0.06949270326615706 5.975 >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 120 3.0 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 119 2.9749999999999996 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 92 2.3 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 33 0.8250000000000001 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 29 0.7250000000000001 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 29 0.7250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 28 0.7000000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 26 0.65 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 26 0.65 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 23 0.575 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 19 0.475 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 19 0.475 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 15 0.375 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 15 0.375 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 15 0.375 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 15 0.375 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 14 0.35000000000000003 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 13 0.325 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 13 0.325 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 12 0.3 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 12 0.3 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 10 0.25 No Hit AATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTAT 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 9 0.22499999999999998 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 9 0.22499999999999998 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 8 0.2 No Hit ATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAG 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 7 0.17500000000000002 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 7 0.17500000000000002 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 7 0.17500000000000002 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 7 0.17500000000000002 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit TAATTAAGAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAA 5 0.125 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit GCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGT 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit AAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTA 5 0.125 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.07500000000000001 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 15 9.165171E-4 85.899994 2 GCAATAC 15 9.165171E-4 85.899994 7 CAATACA 15 9.165171E-4 85.899994 8 GAGCAAT 15 9.165171E-4 85.899994 5 AGAGCAA 15 9.165171E-4 85.899994 4 GAGAGCA 15 9.165171E-4 85.899994 3 AATACAA 15 9.165171E-4 85.899994 9 AGCAATA 15 9.165171E-4 85.899994 6 AATCTGG 20 0.0028711539 64.424995 9 TAGGAAT 20 0.0028711539 64.424995 5 AGTAGGA 20 0.0028711539 64.424995 3 AGGAATC 20 0.0028711539 64.424995 6 GGGAGAG 20 0.0028711539 64.424995 1 TAGTAGG 20 0.0028711539 64.424995 2 GAATCTG 20 0.0028711539 64.424995 8 GTAGGAA 20 0.0028711539 64.424995 4 GGAATCT 20 0.0028711539 64.424995 7 GTAGTAG 20 0.0028711539 64.424995 1 AAAAAAA 25 0.001810243 36.650665 86-87 >>END_MODULE Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40954 READS because READLEN < 1 Read 40954 spots for ERR6133330.sra Written 40954 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra Rejected 40950 READS because READLEN < 1 Read 40950 spots for ERR6133330.sra Written 40950 spots for ERR6133330.sra SRR ids: ['ERR6133330.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qvc25e2o ERR6133330.sra spots: 819004 blocks: [[1, 40950], [40951, 81900], [81901, 122850], [122851, 163800], [163801, 204750], [204751, 245700], [245701, 286650], [286651, 327600], [327601, 368550], [368551, 409500], [409501, 450450], [450451, 491400], [491401, 532350], [532351, 573300], [573301, 614250], [614251, 655200], [655201, 696150], [696151, 737100], [737101, 778050], [778051, 819004]] ERR6133330 file size 179317 ERR6133330 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 ERR6133330 ERR6133330_1.fastq Input file: ERR6133330_1.fastq trimmed: ERR6133330-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 00:49:49 2024 >> started Sat Dec 7 00:49:49 2024 >> done (0.642s) 819004 reads processed; of these: 166 ( 0.02%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 818831 (99.98%) reads available; of these: 12376 ( 1.51%) trimmed reads available after processing 806455 (98.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 14 0.00% 20 11 0.00% 21 7 0.00% 22 10 0.00% 23 6 0.00% 24 12 0.00% 25 4 0.00% 26 4 0.00% 27 6 0.00% 28 20 0.00% 29 17 0.00% 30 6 0.00% 31 8 0.00% 32 6 0.00% 33 10 0.00% 34 3 0.00% 35 6 0.00% 36 8 0.00% 37 7 0.00% 38 3 0.00% 39 12 0.00% 40 9 0.00% 41 8 0.00% 42 5 0.00% 43 0 0.00% 44 3 0.00% 45 2 0.00% 46 2 0.00% 47 2 0.00% 48 4 0.00% 49 2 0.00% 50 0 0.00% 51 7 0.00% 52 1 0.00% 53 5 0.00% 54 3 0.00% 55 1 0.00% 56 3 0.00% 57 3 0.00% 58 3 0.00% 59 3 0.00% 60 3 0.00% 61 5 0.00% 62 0 0.00% 63 1 0.00% 64 0 0.00% 65 0 0.00% 66 0 0.00% 67 3 0.00% 68 3 0.00% 69 10 0.00% 70 2375 0.29% 71 2295 0.28% 72 2337 0.29% 73 2464 0.30% 74 2356 0.29% 75 2497 0.30% 76 2430 0.30% 77 2580 0.32% 78 2628 0.32% 79 2711 0.33% 80 2669 0.33% 81 3346 0.41% 82 3245 0.40% 83 2949 0.36% 84 3430 0.42% 85 10 0.00% 86 13 0.00% 87 33 0.00% 88 80 0.01% 89 163 0.02% 90 425 0.05% 91 1510 0.18% 92 9544 1.17% 93 766467 93.61% 818831 reads passed initial QC criterion=sequence-density sequence-density=0.96 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=19 prefix-density=0.96 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.05 sequence-density-rank=18 fanout-score=28.68 fanout-score-rank=1 prefix-density=0.21 prefix-fanout=6.3 sequence=AAAAAAAGATTTTGAATCTGCCTTTTCCTTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATTTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACC Started job on | Dec 07 00:50:05 Started mapping on | Dec 07 00:50:05 Finished on | Dec 07 00:50:08 Mapping speed, Million of reads per hour | 982.60 Number of input reads | 818831 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 420720 Uniquely mapped reads % | 51.38% Average mapped length | 91.25 Number of splices: Total | 23244 Number of splices: Annotated (sjdb) | 18704 Number of splices: GT/AG | 22001 Number of splices: GC/AG | 510 Number of splices: AT/AC | 12 Number of splices: Non-canonical | 721 Mismatch rate per base, % | 0.49% Deletion rate per base | 0.05% Deletion average length | 1.82 Insertion rate per base | 0.02% Insertion average length | 1.71 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 368819 % of reads mapped to multiple loci | 45.04% Number of reads mapped to too many loci | 9044 % of reads mapped to too many loci | 1.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.39% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 29292 29292 29292 N_multimapping 368819 368819 368819 N_noFeature 32369 37097 402433 N_ambiguous 15710 2143 78 UnstrandedReadsAssigned:372641 PositiveStrandReadsAssigned:381480 NegativeStrandReadsAssigned:18209 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133330 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: ERR6133330-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 818,831 reads, 602,448 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 808 rounds 52973 ERR6133330.ke.tsv 35125 ERR6133330.se.tsv 88098 total ==> ERR6133330.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 9 14.3842 PNS24243 293 194 0 0 KQK14069 1603 1504 13 18.9536 KQK14071 474 375 0 0 ==> ERR6133330.se.tsv <== BRADI_1g14170v3 13 BRADI_1g53295v3 11 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 13 BRADI_1g48960v3 0 ERR6133330 completed mapping pipeline successfully