Starting /dee2/code/volunteer_pipeline.sh ERR6133416 current disk space = 1547272044544 free memory = 1457742984 ERR6133416 SRAfilesize e543ea963a37e0ba1592fbf06eadceb3 ERR6133416.sra ERR6133416.sra file validated ERR6133416 is single end ERR6133416 is conventional basespace ERR6133416 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133416_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 47 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.229 33.0 27.0 33.0 15.0 37.0 2 34.05875 37.0 33.0 37.0 27.0 37.0 3 33.6725 37.0 33.0 37.0 27.0 37.0 4 33.28375 37.0 33.0 37.0 22.0 37.0 5 33.529 37.0 33.0 37.0 22.0 37.0 6 33.444 37.0 33.0 37.0 22.0 37.0 7 34.9985 37.0 33.0 37.0 27.0 40.0 8 35.01225 37.0 33.0 37.0 27.0 40.0 9 35.151 37.0 33.0 37.0 33.0 40.0 10-11 35.115875 37.0 33.0 37.0 30.0 40.0 12-13 34.944 37.0 33.0 37.0 27.0 40.0 14-15 34.8465 37.0 33.0 37.0 27.0 40.0 16-17 34.525999999999996 37.0 33.0 37.0 27.0 40.0 18-19 34.354124999999996 37.0 33.0 37.0 27.0 40.0 20-21 33.7415 37.0 33.0 37.0 24.5 40.0 22-23 33.363875 37.0 33.0 37.0 22.0 40.0 24-25 33.187625 35.0 33.0 37.0 22.0 40.0 26-27 33.124375 35.0 33.0 37.0 22.0 40.0 28-29 32.629 33.0 33.0 37.0 22.0 40.0 30-31 32.67275 33.0 33.0 37.0 22.0 40.0 32-33 31.898875000000004 33.0 30.0 37.0 22.0 40.0 34-35 30.784375 33.0 27.0 37.0 15.0 40.0 36-37 30.554000000000002 33.0 27.0 37.0 15.0 37.0 38-39 31.145000000000003 33.0 27.0 37.0 22.0 37.0 40-41 30.703125 33.0 27.0 37.0 15.0 38.5 42-43 30.720625 33.0 27.0 37.0 15.0 37.0 44-45 30.32 33.0 27.0 37.0 15.0 37.0 46-47 29.856375 33.0 27.0 37.0 15.0 37.0 48-49 29.704875 33.0 27.0 37.0 15.0 37.0 50-51 29.106125 33.0 24.5 37.0 15.0 37.0 52-53 29.1275 33.0 27.0 37.0 15.0 37.0 54-55 29.275 33.0 27.0 37.0 15.0 37.0 56-57 28.6665 33.0 27.0 33.0 15.0 37.0 58-59 28.332375 33.0 27.0 33.0 15.0 37.0 60-61 28.163625 33.0 27.0 33.0 15.0 37.0 62-63 27.851625 33.0 22.0 33.0 15.0 37.0 64-65 27.483625 33.0 24.5 33.0 15.0 37.0 66-67 27.0635 33.0 22.0 33.0 15.0 37.0 68-69 26.086875 27.0 18.5 33.0 10.5 35.0 70-71 28.176048052842475 33.0 27.0 33.0 15.0 37.0 72-73 28.71211376963064 33.0 27.0 33.0 15.0 37.0 74-75 28.62073914548713 33.0 27.0 33.0 15.0 37.0 76-77 28.48460862334251 33.0 27.0 33.0 15.0 37.0 78-79 27.38862558815587 33.0 24.5 33.0 10.5 37.0 80-81 26.51916270573591 33.0 22.0 33.0 6.0 37.0 82-83 25.74042594929896 33.0 22.0 33.0 2.0 37.0 84-85 25.203888655189303 33.0 18.5 33.0 2.0 37.0 86-87 24.315301391035547 33.0 15.0 33.0 2.0 37.0 88-89 23.800231839258114 30.0 10.5 33.0 2.0 35.0 90-91 22.76249356002061 27.0 2.0 33.0 2.0 33.0 92-93 21.1617722823287 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 122.0 21 144.0 22 139.0 23 179.0 24 186.0 25 214.0 26 196.0 27 212.0 28 258.0 29 255.0 30 230.0 31 242.0 32 316.0 33 276.0 34 307.0 35 322.0 36 235.0 37 137.0 38 30.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 75.02499999999999 7.35 6.425 11.200000000000001 2 61.25000000000001 18.4 11.675 8.674999999999999 3 43.225 29.725 15.7 11.35 4 24.55 41.125 17.349999999999998 16.975 5 37.7 23.925 21.575 16.8 6 15.475 48.25 21.25 15.024999999999999 7 44.725 22.275 18.6 14.399999999999999 8 22.825 21.25 21.525 34.4 9 20.575 41.425 21.7 16.3 10-11 18.462500000000002 32.0125 33.6 15.925 12-13 18.925 32.45 22.7 25.924999999999997 14-15 18.0375 42.9375 22.525000000000002 16.5 16-17 29.862499999999997 23.275000000000002 20.200000000000003 26.6625 18-19 28.349999999999998 19.625 34.4625 17.5625 20-21 29.4 21.4125 32.9125 16.275000000000002 22-23 32.5625 18.025 31.8125 17.599999999999998 24-25 21.1125 19.412499999999998 32.4375 27.037499999999998 26-27 29.45 20.5 24.725 25.324999999999996 28-29 20.5 31.45 31.6 16.45 30-31 41.9125 20.4875 21.4 16.2 32-33 30.612499999999997 20.6375 22.2125 26.5375 34-35 20.349999999999998 42.65 20.8 16.2 36-37 30.312499999999996 21.2 21.425 27.0625 38-39 41.3875 19.375 21.675 17.5625 40-41 21.462500000000002 19.8625 42.2125 16.4625 42-43 30.3 33.887499999999996 20.1625 15.65 44-45 29.9 21.875 31.2625 16.9625 46-47 31.075000000000003 19.7 21.575 27.650000000000002 48-49 29.75 19.6125 23.599999999999998 27.037499999999998 50-51 19.3 31.912499999999998 22.55 26.237500000000004 52-53 19.662499999999998 22.125 20.8 37.4125 54-55 19.287499999999998 20.549999999999997 32.6 27.5625 56-57 29.775000000000002 31.112499999999997 21.987499999999997 17.125 58-59 18.8875 31.75 31.724999999999998 17.6375 60-61 39.875 21.325 21.925 16.875 62-63 17.75 22.8125 33.6625 25.775 64-65 18.475 44.1 21.4 16.025 66-67 30.4 32.5125 20.7875 16.3 68-69 19.425 21.3625 31.412499999999998 27.800000000000004 70-71 19.729763543100212 31.827849368197175 21.719004128612536 26.72338296009008 72-73 30.31293200955134 21.503079049893177 32.33630765363831 15.847681286917178 74-75 29.528254288597378 31.886982845610497 23.183652875882945 15.401109989909182 76-77 19.61528726904581 19.640597317134905 22.930903568716783 37.81321184510251 78-79 29.95438418651799 30.157121135326914 23.91028890015205 15.97820577800304 80-81 19.030657677140315 44.54903956239664 21.89288894542679 14.527413815036255 82-83 29.042988741044013 22.070112589559876 20.893039918116685 27.993858751279426 84-85 18.461340537758907 29.267978901325097 33.70641965778979 18.564260903126208 86-87 17.86450283359093 33.565172591447705 21.354971664090673 27.21535291087068 88-89 17.259144770736732 23.72488408037094 32.122617207624934 26.89335394126739 90-91 29.121586810922206 32.30293663060278 21.87017001545595 16.705306543019063 92-93 17.8902627511592 24.871200412158682 31.504379185986604 25.734157650695515 >>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 0.5 17 3.5 18 4.5 19 1.5 20 1.0 21 2.0 22 3.0 23 3.0 24 2.5 25 3.5 26 4.0 27 6.5 28 15.5 29 21.5 30 19.5 31 22.5 32 28.5 33 34.0 34 43.0 35 48.0 36 78.0 37 142.0 38 187.5 39 183.0 40 161.5 41 161.0 42 173.5 43 179.5 44 160.0 45 135.5 46 131.0 47 121.5 48 105.0 49 100.0 50 101.5 51 115.5 52 140.5 53 199.5 54 452.5 55 463.0 56 182.0 57 98.0 58 88.5 59 58.0 60 26.0 61 21.5 62 24.0 63 14.0 64 12.0 65 11.5 66 8.0 67 7.5 68 5.5 69 4.5 70 5.0 71 5.0 72 3.0 73 1.0 74 1.0 75 0.5 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 0.0 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 7.0 71 10.0 72 9.0 73 6.0 74 8.0 75 7.0 76 4.0 77 2.0 78 2.0 79 10.0 80 9.0 81 12.0 82 12.0 83 11.0 84 9.0 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 3882.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 64.1 #Duplication Level Percentage of deduplicated Percentage of total 1 92.74570982839313 59.45 2 3.3541341653666144 4.3 3 0.9750390015600624 1.875 4 0.6630265210608425 1.7000000000000002 5 0.46801872074883 1.5 6 0.19500780031201248 0.75 7 0.15600624024961 0.7000000000000001 8 0.19500780031201248 1.0 9 0.0390015600624025 0.22499999999999998 >10 1.1700468018720749 11.450000000000001 >50 0.0 0.0 >100 0.0 0.0 >500 0.0390015600624025 17.05 >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 682 17.05 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 30 0.75 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 27 0.675 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 24 0.6 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 22 0.5499999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 21 0.525 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 20 0.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 18 0.44999999999999996 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 18 0.44999999999999996 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 17 0.42500000000000004 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 17 0.42500000000000004 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 14 0.35000000000000003 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 14 0.35000000000000003 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 13 0.325 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 13 0.325 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 13 0.325 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGGGCCGC 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCAGC 11 0.27499999999999997 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 11 0.27499999999999997 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 11 0.27499999999999997 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 11 0.27499999999999997 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 10 0.25 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 8 0.2 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGCGTGCCGC 6 0.15 No Hit CAACAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAG 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGA 6 0.15 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCA 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit AGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAA 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit CTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGAT 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGAGGTTGAGTGCCGC 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit GGGAGAGCAATACAAGCTTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 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 0.0125 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 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 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 GGAGAGC 105 0.0 57.65 2 GCAATAC 105 0.0 57.65 7 GGGAGAG 105 0.0 57.65 1 CAATACA 105 0.0 57.65 8 GAGCAAT 105 0.0 57.65 5 AGAGCAA 105 0.0 57.65 4 GAGAGCA 105 0.0 57.65 3 AATACAA 110 0.0 55.02955 9 AGCAATA 110 0.0 55.02955 6 CATCACT 60 0.0 44.922077 82-83 AGCATCA 65 0.0 44.922077 80-81 TCACTAG 60 0.0 44.922077 84-85 ACTAGCT 65 0.0 44.922077 86-87 ATCACTA 60 1.8189894E-12 41.17857 84-85 CACTAGC 60 1.8189894E-12 41.17857 86-87 GCATCAC 60 1.8189894E-12 41.17857 82-83 AAGCATC 70 0.0 38.50464 80-81 AAAGCAT 80 0.0 36.49919 78-79 CGAAAGC 80 0.0 35.80175 76-77 GCCGAAA 80 0.0 35.575157 74-75 >>END_MODULE Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72033 READS because READLEN < 1 Read 72033 spots for ERR6133416.sra Written 72033 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra Rejected 72022 READS because READLEN < 1 Read 72022 spots for ERR6133416.sra Written 72022 spots for ERR6133416.sra SRR ids: ['ERR6133416.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4j76djfa ERR6133416.sra spots: 1440451 blocks: [[1, 72022], [72023, 144044], [144045, 216066], [216067, 288088], [288089, 360110], [360111, 432132], [432133, 504154], [504155, 576176], [576177, 648198], [648199, 720220], [720221, 792242], [792243, 864264], [864265, 936286], [936287, 1008308], [1008309, 1080330], [1080331, 1152352], [1152353, 1224374], [1224375, 1296396], [1296397, 1368418], [1368419, 1440451]] ERR6133416 file size 317477 ERR6133416 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 ERR6133416 ERR6133416_1.fastq Input file: ERR6133416_1.fastq trimmed: ERR6133416-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 03:57:17 2024 >> started Sat Dec 7 03:57:18 2024 >> done (1.061s) 1440451 reads processed; of these: 21 ( 0.00%) short reads filtered out after trimming by size control 2 ( 0.00%) empty reads filtered out after trimming by size control 1440428 (100.00%) reads available; of these: 392767 (27.27%) trimmed reads available after processing 1047661 (72.73%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 0 0.00% 21 1 0.00% 22 2 0.00% 23 1 0.00% 24 1 0.00% 25 1 0.00% 26 0 0.00% 27 0 0.00% 28 3 0.00% 29 35 0.00% 30 1 0.00% 31 3 0.00% 32 2 0.00% 33 0 0.00% 34 2 0.00% 35 0 0.00% 36 0 0.00% 37 3 0.00% 38 4 0.00% 39 3 0.00% 40 9 0.00% 41 5 0.00% 42 0 0.00% 43 7 0.00% 44 11 0.00% 45 6 0.00% 46 28 0.00% 47 24 0.00% 48 57 0.00% 49 73 0.01% 50 110 0.01% 51 155 0.01% 52 218 0.02% 53 328 0.02% 54 530 0.04% 55 727 0.05% 56 935 0.06% 57 1395 0.10% 58 1044 0.07% 59 1340 0.09% 60 1696 0.12% 61 1981 0.14% 62 2204 0.15% 63 2401 0.17% 64 2525 0.18% 65 2694 0.19% 66 2790 0.19% 67 2903 0.20% 68 2378 0.17% 69 2207 0.15% 70 4746 0.33% 71 5701 0.40% 72 7325 0.51% 73 7628 0.53% 74 7932 0.55% 75 9244 0.64% 76 11095 0.77% 77 13011 0.90% 78 13221 0.92% 79 13338 0.93% 80 14235 0.99% 81 15602 1.08% 82 16788 1.17% 83 18357 1.27% 84 21995 1.53% 85 20488 1.42% 86 19738 1.37% 87 22666 1.57% 88 30444 2.11% 89 29365 2.04% 90 29863 2.07% 91 32601 2.26% 92 28940 2.01% 93 1015259 70.48% 1440428 reads passed initial QC criterion=sequence-density sequence-density=1.36 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=35 prefix-density=1.42 prefix-fanout=2.1 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.11 sequence-density-rank=31 fanout-score=220.03 fanout-score-rank=1 prefix-density=24.27 prefix-fanout=1.0 sequence=GCGGTTGAGTGACGCACCCTAGA Started job on | Dec 07 03:57:34 Started mapping on | Dec 07 03:57:34 Finished on | Dec 07 03:57:41 Mapping speed, Million of reads per hour | 740.79 Number of input reads | 1440428 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 527089 Uniquely mapped reads % | 36.59% Average mapped length | 89.25 Number of splices: Total | 31696 Number of splices: Annotated (sjdb) | 25551 Number of splices: GT/AG | 30787 Number of splices: GC/AG | 599 Number of splices: AT/AC | 37 Number of splices: Non-canonical | 273 Mismatch rate per base, % | 0.68% Deletion rate per base | 0.02% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 819473 % of reads mapped to multiple loci | 56.89% Number of reads mapped to too many loci | 23512 % of reads mapped to too many loci | 1.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.59% % of reads unmapped: other | 0.29% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 93866 93866 93866 N_multimapping 819473 819473 819473 N_noFeature 40219 45112 503552 N_ambiguous 21757 3095 89 UnstrandedReadsAssigned:465113 PositiveStrandReadsAssigned:478882 NegativeStrandReadsAssigned:23448 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=87 echo kmer=83 ERR6133416 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: ERR6133416-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,440,428 reads, 802,002 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 868 rounds 52973 ERR6133416.ke.tsv 35125 ERR6133416.se.tsv 88098 total ==> ERR6133416.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 15 17.5998 PNS24243 293 194 0 0 KQK14069 1603 1504 4 4.28136 KQK14071 474 375 0 0 ==> ERR6133416.se.tsv <== BRADI_1g14170v3 4 BRADI_1g53295v3 7 BRADI_1g59795v3 14 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 14 BRADI_1g48960v3 0 ERR6133416 completed mapping pipeline successfully