Starting /dee2/code/volunteer_pipeline.sh ERR6133411 current disk space = 1547524263936 free memory = 1603316056 ERR6133411 SRAfilesize 43abbe4cc9fc5f4a0de469fe7357388b ERR6133411.sra ERR6133411.sra file validated ERR6133411 is single end ERR6133411 is conventional basespace ERR6133411 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133411_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.035 33.0 27.0 33.0 15.0 37.0 2 33.76375 37.0 33.0 37.0 27.0 37.0 3 33.79425 37.0 33.0 37.0 27.0 37.0 4 33.83175 37.0 33.0 37.0 27.0 37.0 5 34.09975 37.0 33.0 37.0 27.0 37.0 6 34.0675 37.0 33.0 37.0 27.0 37.0 7 35.3375 37.0 33.0 37.0 27.0 40.0 8 35.21425 37.0 33.0 40.0 27.0 40.0 9 35.5955 37.0 33.0 40.0 33.0 40.0 10-11 35.318124999999995 37.0 33.0 40.0 30.0 40.0 12-13 35.2755 37.0 33.0 38.5 30.0 40.0 14-15 35.1055 37.0 33.0 37.0 27.0 40.0 16-17 34.840625 37.0 33.0 37.0 27.0 40.0 18-19 34.6935 37.0 33.0 37.0 27.0 40.0 20-21 34.032125 37.0 33.0 37.0 24.5 40.0 22-23 34.016375 37.0 33.0 37.0 27.0 40.0 24-25 33.689750000000004 37.0 33.0 37.0 24.5 40.0 26-27 33.214375000000004 37.0 33.0 37.0 22.0 40.0 28-29 32.831374999999994 37.0 33.0 37.0 22.0 40.0 30-31 32.72725 33.0 33.0 37.0 22.0 40.0 32-33 32.292500000000004 33.0 30.0 37.0 22.0 40.0 34-35 31.55775 33.0 27.0 37.0 15.0 40.0 36-37 31.201625 33.0 27.0 37.0 15.0 38.5 38-39 31.499 33.0 27.0 37.0 22.0 40.0 40-41 31.331125 33.0 27.0 37.0 22.0 40.0 42-43 30.730875 33.0 27.0 37.0 15.0 40.0 44-45 30.578875 33.0 27.0 37.0 15.0 37.0 46-47 30.087 33.0 27.0 37.0 15.0 37.0 48-49 30.022624999999998 33.0 27.0 37.0 15.0 37.0 50-51 29.546 33.0 27.0 37.0 15.0 37.0 52-53 29.426625 33.0 27.0 37.0 15.0 37.0 54-55 29.250875 33.0 27.0 37.0 15.0 37.0 56-57 28.438375 33.0 27.0 33.0 15.0 37.0 58-59 28.4055 33.0 27.0 33.0 15.0 37.0 60-61 28.369 33.0 27.0 33.0 15.0 37.0 62-63 27.9375 33.0 22.0 33.0 15.0 37.0 64-65 27.083750000000002 30.0 22.0 33.0 10.5 37.0 66-67 26.64375 27.0 22.0 33.0 6.0 37.0 68-69 26.208875 27.0 22.0 33.0 10.5 35.0 70-71 28.092242924528303 33.0 27.0 33.0 15.0 37.0 72-73 28.423566846600185 33.0 27.0 33.0 15.0 37.0 74-75 28.468848815140994 33.0 27.0 33.0 15.0 37.0 76-77 28.189784185404704 33.0 27.0 33.0 15.0 37.0 78-79 27.353249005438272 33.0 24.5 33.0 6.0 37.0 80-81 26.429369352546345 33.0 22.0 33.0 6.0 37.0 82-83 25.751884088168524 33.0 22.0 33.0 2.0 37.0 84-85 25.137275200568638 33.0 22.0 33.0 2.0 37.0 86-87 24.279676985195152 30.0 15.0 33.0 2.0 37.0 88-89 23.409825033647376 30.0 10.5 33.0 2.0 35.0 90-91 22.05343203230148 27.0 2.0 33.0 2.0 33.0 92-93 20.74912516823688 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 92.0 21 119.0 22 151.0 23 163.0 24 171.0 25 195.0 26 198.0 27 256.0 28 237.0 29 296.0 30 243.0 31 272.0 32 292.0 33 289.0 34 295.0 35 289.0 36 236.0 37 173.0 38 33.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.4 8.674999999999999 8.475000000000001 14.45 2 50.175000000000004 23.5 14.975 11.35 3 34.5 34.725 18.15 12.625 4 25.7 32.5 21.6 20.200000000000003 5 27.400000000000002 25.3 28.249999999999996 19.05 6 17.25 40.275 25.474999999999998 17.0 7 36.075 26.3 21.0 16.625 8 24.175 25.95 24.725 25.15 9 21.0 33.625 26.724999999999998 18.65 10-11 21.7 29.175 31.387500000000003 17.7375 12-13 21.85 29.7375 26.05 22.3625 14-15 19.7375 34.25 27.487499999999997 18.525 16-17 25.05 27.250000000000004 24.3125 23.3875 18-19 24.4375 23.7375 32.675 19.15 20-21 25.087500000000002 24.525 30.65 19.7375 22-23 28.237499999999997 22.287499999999998 30.7375 18.7375 24-25 22.037499999999998 24.5375 29.775000000000002 23.65 26-27 26.387500000000003 23.5375 28.275 21.8 28-29 22.625 29.375 29.4 18.6 30-31 32.1125 23.8125 25.324999999999996 18.75 32-33 27.224999999999998 24.7375 25.5375 22.5 34-35 20.8125 33.7875 25.900000000000002 19.5 36-37 27.1125 25.275 24.45 23.1625 38-39 31.775 22.325 26.437500000000004 19.4625 40-41 23.05 23.9875 34.525 18.4375 42-43 27.275 30.1875 24.6125 17.925 44-45 25.3 25.15 30.7375 18.8125 46-47 27.6125 24.5625 25.224999999999998 22.6 48-49 25.337500000000002 24.0625 27.2625 23.3375 50-51 21.2 30.225 25.887500000000003 22.6875 52-53 21.462500000000002 26.6 24.2375 27.700000000000003 54-55 21.712500000000002 24.775 31.3 22.2125 56-57 26.025 29.675 26.137500000000003 18.1625 58-59 21.4 29.4875 30.3 18.8125 60-61 30.075000000000003 25.387500000000003 26.2875 18.25 62-63 19.7625 26.187500000000004 32.3875 21.6625 64-65 21.7 35.25 25.337500000000002 17.712500000000002 66-67 24.637500000000003 31.137500000000003 25.8 18.425 68-69 21.1875 24.2875 29.875 24.65 70-71 21.46708463949843 29.442006269592476 26.583072100313483 22.50783699059561 72-73 25.894550512074847 25.565811101277024 29.902642559109875 18.636995827538247 74-75 26.77797603874586 29.35253632424165 26.051491205709915 17.817996431302575 76-77 20.996395468589082 23.892893923789906 26.15859938208033 28.952111225540676 78-79 26.01795238714713 29.07506179263692 27.045661506439444 17.861324313776507 80-81 22.27481919789612 36.09467455621302 24.77317554240631 16.85733070348455 82-83 24.56163655685441 25.425079702444208 26.115834218916046 23.897449521785337 84-85 21.385420861860652 27.292253993824673 32.138542086186064 19.183783058128608 86-87 20.430686406460296 30.484522207267833 25.383580080753703 23.701211305518168 88-89 20.69986541049798 27.33512786002692 30.134589502018844 21.83041722745626 90-91 25.491251682368777 31.372812920592192 25.19515477792732 17.94078061911171 92-93 19.43472409152086 29.811574697173622 28.627187079407808 22.12651413189771 >>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 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 5.5 18 7.5 19 3.0 20 2.5 21 5.0 22 5.5 23 5.0 24 5.5 25 8.0 26 13.5 27 18.5 28 21.0 29 19.5 30 29.0 31 46.0 32 58.5 33 68.0 34 69.0 35 85.5 36 118.5 37 184.0 38 227.5 39 207.5 40 205.5 41 211.5 42 181.5 43 158.0 44 164.5 45 157.0 46 146.0 47 135.0 48 119.5 49 125.5 50 123.5 51 126.5 52 131.5 53 151.0 54 256.5 55 249.0 56 129.0 57 92.5 58 67.0 59 34.0 60 24.0 61 23.5 62 17.0 63 12.0 64 13.0 65 7.0 66 3.0 67 4.0 68 9.0 69 11.0 70 8.5 71 8.0 72 5.5 73 1.5 74 0.5 75 0.5 76 0.5 77 0.5 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 25.0 71 12.0 72 17.0 73 14.0 74 18.0 75 20.0 76 20.0 77 18.0 78 25.0 79 21.0 80 15.0 81 21.0 82 20.0 83 20.0 84 19.0 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 3715.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.1944539541253 67.325 2 3.560424512153372 5.2 3 1.4720985963711057 3.225 4 0.6846970215679562 2.0 5 0.5135227661759671 1.875 6 0.23964395754878468 1.05 7 0.20540910647038688 1.05 8 0.23964395754878468 1.4000000000000001 9 0.13693940431359122 0.8999999999999999 >10 0.7189318726463539 8.475000000000001 >50 0.0 0.0 >100 0.034234851078397806 7.5 >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 300 7.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 36 0.8999999999999999 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 23 0.575 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 21 0.525 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 21 0.525 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 20 0.5 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 20 0.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 19 0.475 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 18 0.44999999999999996 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 18 0.44999999999999996 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 15 0.375 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 13 0.325 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 12 0.3 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 12 0.3 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 11 0.27499999999999997 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 10 0.25 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 10 0.25 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 10 0.25 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 9 0.22499999999999998 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 9 0.22499999999999998 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 9 0.22499999999999998 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 9 0.22499999999999998 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 8 0.2 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 8 0.2 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 8 0.2 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 7 0.17500000000000002 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCA 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGACGCGGTTGAGTGCCGC 5 0.125 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 5 0.125 No Hit CAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAGGAA 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 5 0.125 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 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 0.0125 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 0.05 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 50 1.8189894E-12 77.94 2 GGGAGAG 50 1.8189894E-12 77.94 1 GCAATAC 60 0.0 72.166664 7 CAATACA 60 0.0 72.166664 8 GAGCAAT 60 0.0 72.166664 5 AATACAA 60 0.0 72.166664 9 AGCAATA 65 0.0 66.61539 6 AGAGCAA 60 5.456968E-12 64.95 4 GAGAGCA 65 1.2732926E-11 59.953846 3 CATCACT 55 4.9112714E-11 40.37296 82-83 ATCACTA 55 4.9112714E-11 40.37296 84-85 CACTAGC 55 4.9112714E-11 40.37296 86-87 TCACTAG 55 4.9112714E-11 40.37296 84-85 ACTAGCT 55 4.9112714E-11 40.37296 86-87 GCATCAC 55 4.9112714E-11 40.37296 82-83 AGCATCA 50 9.313226E-10 39.96923 80-81 AAGCATC 45 1.7329512E-8 39.47578 80-81 CCAGTAG 50 1.0586518E-9 39.46329 68-69 TCCAGTA 50 1.0586518E-9 39.46329 68-69 GTCCAGT 50 1.0586518E-9 39.46329 66-67 >>END_MODULE Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108821 READS because READLEN < 1 Read 108821 spots for ERR6133411.sra Written 108821 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra Rejected 108819 READS because READLEN < 1 Read 108819 spots for ERR6133411.sra Written 108819 spots for ERR6133411.sra SRR ids: ['ERR6133411.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ksmyhwmc ERR6133411.sra spots: 2176382 blocks: [[1, 108819], [108820, 217638], [217639, 326457], [326458, 435276], [435277, 544095], [544096, 652914], [652915, 761733], [761734, 870552], [870553, 979371], [979372, 1088190], [1088191, 1197009], [1197010, 1305828], [1305829, 1414647], [1414648, 1523466], [1523467, 1632285], [1632286, 1741104], [1741105, 1849923], [1849924, 1958742], [1958743, 2067561], [2067562, 2176382]] ERR6133411 file size 477692 ERR6133411 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 ERR6133411 ERR6133411_1.fastq Input file: ERR6133411_1.fastq trimmed: ERR6133411-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 03:34:36 2024 >> started Sat Dec 7 03:34:37 2024 >> done (1.214s) 2176382 reads processed; of these: 30 ( 0.00%) short reads filtered out after trimming by size control 5 ( 0.00%) empty reads filtered out after trimming by size control 2176347 (100.00%) reads available; of these: 574979 (26.42%) trimmed reads available after processing 1601368 (73.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 13 0.00% 20 9 0.00% 21 2 0.00% 22 4 0.00% 23 1 0.00% 24 2 0.00% 25 5 0.00% 26 2 0.00% 27 2 0.00% 28 23 0.00% 29 47 0.00% 30 3 0.00% 31 4 0.00% 32 13 0.00% 33 13 0.00% 34 4 0.00% 35 4 0.00% 36 8 0.00% 37 9 0.00% 38 14 0.00% 39 24 0.00% 40 34 0.00% 41 21 0.00% 42 23 0.00% 43 31 0.00% 44 32 0.00% 45 43 0.00% 46 59 0.00% 47 95 0.00% 48 146 0.01% 49 198 0.01% 50 252 0.01% 51 322 0.01% 52 477 0.02% 53 704 0.03% 54 987 0.05% 55 1207 0.06% 56 1707 0.08% 57 2516 0.12% 58 1813 0.08% 59 2176 0.10% 60 2586 0.12% 61 3039 0.14% 62 3428 0.16% 63 3722 0.17% 64 3848 0.18% 65 4187 0.19% 66 4284 0.20% 67 4448 0.20% 68 3882 0.18% 69 3906 0.18% 70 14315 0.66% 71 14495 0.67% 72 17150 0.79% 73 17648 0.81% 74 18358 0.84% 75 19741 0.91% 76 21066 0.97% 77 23707 1.09% 78 24547 1.13% 79 25685 1.18% 80 26784 1.23% 81 30600 1.41% 82 32417 1.49% 83 33677 1.55% 84 37860 1.74% 85 28656 1.32% 86 29615 1.36% 87 32803 1.51% 88 40349 1.85% 89 41862 1.92% 90 44079 2.03% 91 46910 2.16% 92 40952 1.88% 93 1462684 67.21% 2176347 reads passed initial QC criterion=sequence-density sequence-density=2.94 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=29 prefix-density=3.02 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.12 sequence-density-rank=20 fanout-score=95.70 fanout-score-rank=1 prefix-density=11.15 prefix-fanout=1.1 sequence=CCTAGATGGCTCAAGTCCAGTAG 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 03:34:51 Started mapping on | Dec 07 03:34:51 Finished on | Dec 07 03:34:57 Mapping speed, Million of reads per hour | 1305.81 Number of input reads | 2176347 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 892526 Uniquely mapped reads % | 41.01% Average mapped length | 88.46 Number of splices: Total | 38833 Number of splices: Annotated (sjdb) | 31655 Number of splices: GT/AG | 37504 Number of splices: GC/AG | 781 Number of splices: AT/AC | 47 Number of splices: Non-canonical | 501 Mismatch rate per base, % | 0.68% Deletion rate per base | 0.02% Deletion average length | 1.42 Insertion rate per base | 0.00% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1123552 % of reads mapped to multiple loci | 51.63% Number of reads mapped to too many loci | 63357 % of reads mapped to too many loci | 2.91% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.94% % of reads unmapped: other | 0.52% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 160269 160269 160269 N_multimapping 1123552 1123552 1123552 N_noFeature 75031 83822 853614 N_ambiguous 36014 5840 191 UnstrandedReadsAssigned:781481 PositiveStrandReadsAssigned:802864 NegativeStrandReadsAssigned:38721 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133411 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: ERR6133411-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,176,347 reads, 1,393,392 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 938 rounds 52973 ERR6133411.ke.tsv 35125 ERR6133411.se.tsv 88098 total ==> ERR6133411.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 14 9.56905 PNS24243 293 194 0 0 KQK14069 1603 1504 7 4.3646 KQK14071 474 375 0 0 ==> ERR6133411.se.tsv <== BRADI_1g14170v3 7 BRADI_1g53295v3 12 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 15 BRADI_1g48960v3 0 ERR6133411 completed mapping pipeline successfully