Starting /dee2/code/volunteer_pipeline.sh ERR6133415 current disk space = 1547262689280 free memory = 1437450140 ERR6133415 SRAfilesize 7bbddfea11e564437bceca456ab1beb9 ERR6133415.sra ERR6133415.sra file validated ERR6133415 is single end ERR6133415 is conventional basespace ERR6133415 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133415_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 29.654 33.0 27.0 33.0 15.0 37.0 2 33.76675 37.0 33.0 37.0 27.0 37.0 3 33.55025 37.0 33.0 37.0 27.0 37.0 4 33.59325 37.0 33.0 37.0 27.0 37.0 5 33.87225 37.0 33.0 37.0 27.0 37.0 6 33.801 37.0 33.0 37.0 27.0 37.0 7 35.105 37.0 33.0 40.0 27.0 40.0 8 35.12625 37.0 33.0 40.0 27.0 40.0 9 35.27925 37.0 33.0 40.0 33.0 40.0 10-11 35.188500000000005 37.0 33.0 37.0 27.0 40.0 12-13 35.062250000000006 37.0 33.0 37.0 27.0 40.0 14-15 35.036249999999995 37.0 33.0 37.0 27.0 40.0 16-17 34.608625 37.0 33.0 37.0 27.0 40.0 18-19 34.6255 37.0 33.0 37.0 27.0 40.0 20-21 33.843625 37.0 33.0 37.0 24.5 40.0 22-23 33.685500000000005 37.0 33.0 37.0 24.5 40.0 24-25 33.436375 37.0 33.0 37.0 24.5 40.0 26-27 33.3145 37.0 33.0 37.0 22.0 40.0 28-29 32.670125 33.0 33.0 37.0 22.0 40.0 30-31 32.7655 33.0 33.0 37.0 22.0 40.0 32-33 32.25125 33.0 33.0 37.0 22.0 40.0 34-35 31.232374999999998 33.0 27.0 37.0 15.0 40.0 36-37 30.736 33.0 27.0 37.0 15.0 37.0 38-39 31.233249999999998 33.0 27.0 37.0 22.0 37.0 40-41 30.826375 33.0 27.0 37.0 15.0 38.5 42-43 30.714 33.0 27.0 37.0 15.0 38.5 44-45 30.504625 33.0 27.0 37.0 15.0 37.0 46-47 30.062375 33.0 27.0 37.0 15.0 37.0 48-49 29.7545 33.0 27.0 37.0 15.0 37.0 50-51 29.268875 33.0 27.0 37.0 15.0 37.0 52-53 29.223875 33.0 27.0 37.0 15.0 37.0 54-55 29.210375 33.0 27.0 37.0 15.0 37.0 56-57 28.560125 33.0 24.5 33.0 15.0 37.0 58-59 28.161 33.0 27.0 33.0 15.0 37.0 60-61 27.99375 33.0 24.5 33.0 15.0 37.0 62-63 27.6685 33.0 22.0 33.0 15.0 37.0 64-65 27.175375000000003 33.0 22.0 33.0 10.5 37.0 66-67 26.925625 33.0 22.0 33.0 15.0 37.0 68-69 25.94275 27.0 18.5 33.0 10.5 35.0 70-71 28.266650570318376 33.0 27.0 33.0 15.0 37.0 72-73 28.63730083692397 33.0 27.0 33.0 15.0 37.0 74-75 28.506651602350765 33.0 27.0 33.0 15.0 37.0 76-77 28.390793886014443 33.0 27.0 33.0 15.0 37.0 78-79 27.574261509575955 33.0 24.5 33.0 10.5 37.0 80-81 26.685675046466336 33.0 22.0 33.0 6.0 37.0 82-83 25.909214002313828 33.0 22.0 33.0 2.0 37.0 84-85 25.34656831573199 33.0 18.5 33.0 2.0 37.0 86-87 24.448777348777348 33.0 15.0 33.0 2.0 37.0 88-89 23.74839124839125 30.0 15.0 33.0 2.0 37.0 90-91 22.514028314028316 27.0 2.0 33.0 2.0 33.0 92-93 21.22741312741313 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 102.0 21 119.0 22 140.0 23 185.0 24 182.0 25 207.0 26 208.0 27 242.0 28 257.0 29 275.0 30 262.0 31 257.0 32 285.0 33 243.0 34 296.0 35 300.0 36 249.0 37 165.0 38 26.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 74.175 7.199999999999999 6.125 12.5 2 58.025000000000006 20.349999999999998 13.55 8.075000000000001 3 36.925000000000004 34.35 16.45 12.275 4 25.624999999999996 35.275 19.55 19.55 5 31.874999999999996 24.224999999999998 27.525 16.375 6 16.525000000000002 43.35 23.799999999999997 16.325 7 41.3 22.75 18.725 17.224999999999998 8 24.05 24.4 24.85 26.700000000000003 9 22.225 36.55 23.425 17.8 10-11 20.2875 30.112499999999997 31.874999999999996 17.724999999999998 12-13 19.5 31.4875 25.637500000000003 23.375 14-15 19.775000000000002 37.0625 25.412499999999998 17.75 16-17 27.5125 24.7875 22.4625 25.2375 18-19 25.6125 22.5625 34.475 17.349999999999998 20-21 27.400000000000002 22.775000000000002 31.8125 18.0125 22-23 30.012499999999996 20.4125 30.0875 19.4875 24-25 21.837500000000002 22.775000000000002 30.625000000000004 24.762500000000003 26-27 26.400000000000002 22.662499999999998 28.65 22.287499999999998 28-29 22.0125 29.775000000000002 30.775000000000002 17.4375 30-31 35.5 23.8875 22.8 17.8125 32-33 29.049999999999997 20.825 25.387500000000003 24.7375 34-35 20.0625 37.5 23.8375 18.6 36-37 27.762500000000003 25.05 21.712500000000002 25.474999999999998 38-39 36.1 20.4625 24.5 18.9375 40-41 22.925 22.900000000000002 36.35 17.825 42-43 27.712500000000002 32.7 22.1 17.4875 44-45 27.037499999999998 23.3 30.837500000000002 18.825 46-47 29.15 22.650000000000002 23.0625 25.137500000000003 48-49 26.937499999999996 21.9625 26.325 24.775 50-51 19.75 30.1875 25.2625 24.8 52-53 21.8875 24.2875 22.8875 30.9375 54-55 20.9875 23.0625 32.337500000000006 23.6125 56-57 27.6875 30.15 23.674999999999997 18.4875 58-59 21.349999999999998 30.875000000000004 29.012500000000003 18.7625 60-61 34.2625 24.4375 23.6875 17.6125 62-63 19.3125 24.5125 32.9 23.275000000000002 64-65 18.6875 40.1 24.125 17.0875 66-67 27.462500000000002 30.0875 24.5 17.95 68-69 19.875 25.4375 28.7 25.9875 70-71 21.154086869445486 29.803479784703967 24.371010138941042 24.671423206909502 72-73 27.539871907572522 24.22453849051865 30.491020971995482 17.74456862991335 74-75 27.335683706874843 31.251573910853693 24.792243767313018 16.62049861495845 76-77 21.494383440615927 21.178846396566957 25.14199166982204 32.18477849299507 78-79 26.329787234042552 29.989868287740627 25.265957446808514 18.414387031408307 80-81 19.819361404401477 40.42742653606412 24.106347792901666 15.646864266632743 82-83 26.502173357197652 24.993607772948096 22.398363589874712 26.105855279979544 84-85 19.606835410510087 26.840549916484647 32.86650391879738 20.68611075420789 86-87 20.0 31.11969111969112 23.487773487773488 25.392535392535393 88-89 18.53281853281853 24.98069498069498 31.45431145431146 25.03217503217503 90-91 26.962676962676962 30.48906048906049 24.221364221364222 18.326898326898327 92-93 19.07335907335907 28.095238095238095 29.575289575289577 23.256113256113256 >>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 4.0 19 1.0 20 0.5 21 3.0 22 4.5 23 3.5 24 5.5 25 7.5 26 7.5 27 13.5 28 21.0 29 22.0 30 26.5 31 34.0 32 38.0 33 42.0 34 43.0 35 51.0 36 94.5 37 183.5 38 230.0 39 194.5 40 198.5 41 203.0 42 183.5 43 189.5 44 173.0 45 142.0 46 132.0 47 131.5 48 106.5 49 88.0 50 100.5 51 123.0 52 126.0 53 157.5 54 333.5 55 344.5 56 166.5 57 117.0 58 90.5 59 53.5 60 35.5 61 22.5 62 15.0 63 10.5 64 11.5 65 8.5 66 5.0 67 7.0 68 9.5 69 11.5 70 8.0 71 4.0 72 2.5 73 0.5 74 1.5 75 1.5 76 1.0 77 1.0 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 11.0 71 5.0 72 5.0 73 5.0 74 6.0 75 2.0 76 9.0 77 6.0 78 6.0 79 11.0 80 7.0 81 9.0 82 14.0 83 6.0 84 13.0 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 3885.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 63.65 #Duplication Level Percentage of deduplicated Percentage of total 1 90.37706205813039 57.525000000000006 2 4.241948153967007 5.4 3 1.8460329929300863 3.5249999999999995 4 1.1390416339355853 2.9000000000000004 5 0.432050274941084 1.375 6 0.2749410840534171 1.05 7 0.2749410840534171 1.225 8 0.03927729772191674 0.2 9 0.15710919088766695 0.8999999999999999 >10 1.178318931657502 15.049999999999999 >50 0.0 0.0 >100 0.03927729772191674 10.85 >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 434 10.85 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 50 1.25 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 44 1.0999999999999999 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 37 0.9249999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 36 0.8999999999999999 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 26 0.65 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 23 0.575 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 22 0.5499999999999999 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 22 0.5499999999999999 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 21 0.525 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 21 0.525 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 21 0.525 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 19 0.475 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 19 0.475 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 19 0.475 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 19 0.475 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 19 0.475 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 18 0.44999999999999996 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 18 0.44999999999999996 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 16 0.4 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 15 0.375 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 14 0.35000000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 14 0.35000000000000003 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 14 0.35000000000000003 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 12 0.3 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 10 0.25 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 10 0.25 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 10 0.25 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 10 0.25 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 9 0.22499999999999998 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 7 0.17500000000000002 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 7 0.17500000000000002 No Hit CTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGAT 7 0.17500000000000002 No Hit TGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGGGCCGC 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 6 0.15 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 6 0.15 No Hit GAAAACGGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAG 6 0.15 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCAGC 5 0.125 No Hit GAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTA 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGA 5 0.125 No Hit GCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGT 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGT 5 0.125 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 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 0.025 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 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 50 9.094947E-11 69.6 1 GCAATAC 60 5.456968E-12 65.25 7 CAATACA 60 5.456968E-12 65.25 8 GAGCAAT 60 5.456968E-12 65.25 5 AATACAA 60 5.456968E-12 65.25 9 AGCAATA 60 5.456968E-12 65.25 6 GGAGAGC 60 4.5838533E-10 58.0 2 AGAGCAA 60 4.5838533E-10 58.0 4 GAGAGCA 70 1.8007995E-9 49.714283 3 CTAGGCG 55 6.366463E-11 39.545452 26-27 GTCCAGT 55 6.366463E-11 39.545452 66-67 TGCTAGG 55 6.366463E-11 39.545452 24-25 AGCGTTG 55 6.366463E-11 39.545452 14-15 CGTTGTG 55 6.366463E-11 39.545452 16-17 TAAAGTC 55 6.366463E-11 39.545452 62-63 GCCGAAA 55 6.366463E-11 39.545452 74-75 CAAGCGT 55 6.366463E-11 39.545452 12-13 AAGTCCA 55 6.366463E-11 39.545452 64-65 GTGCTGC 55 6.366463E-11 39.545452 20-21 CATCACT 50 1.1477823E-9 39.15 82-83 >>END_MODULE Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63777 READS because READLEN < 1 Rejected 63758 READS because READLEN < 1 Read 63777 spots for ERR6133415.sra Written 63777 spots for ERR6133415.sra Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra Rejected 63758 READS because READLEN < 1 Read 63758 spots for ERR6133415.sra Written 63758 spots for ERR6133415.sra SRR ids: ['ERR6133415.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_nmzku6va ERR6133415.sra spots: 1275179 blocks: [[1, 63758], [63759, 127516], [127517, 191274], [191275, 255032], [255033, 318790], [318791, 382548], [382549, 446306], [446307, 510064], [510065, 573822], [573823, 637580], [637581, 701338], [701339, 765096], [765097, 828854], [828855, 892612], [892613, 956370], [956371, 1020128], [1020129, 1083886], [1083887, 1147644], [1147645, 1211402], [1211403, 1275179]] ERR6133415 file size 280654 ERR6133415 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 ERR6133415 ERR6133415_1.fastq Input file: ERR6133415_1.fastq trimmed: ERR6133415-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 04:07:09 2024 >> started Sat Dec 7 04:07:11 2024 >> done (1.691s) 1275179 reads processed; of these: 9 ( 0.00%) short reads filtered out after trimming by size control 1 ( 0.00%) empty reads filtered out after trimming by size control 1275169 (100.00%) reads available; of these: 342584 (26.87%) trimmed reads available after processing 932585 (73.13%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 0 0.00% 21 1 0.00% 22 1 0.00% 23 1 0.00% 24 0 0.00% 25 1 0.00% 26 0 0.00% 27 1 0.00% 28 4 0.00% 29 2 0.00% 30 0 0.00% 31 0 0.00% 32 6 0.00% 33 1 0.00% 34 2 0.00% 35 2 0.00% 36 2 0.00% 37 3 0.00% 38 3 0.00% 39 6 0.00% 40 8 0.00% 41 8 0.00% 42 9 0.00% 43 7 0.00% 44 6 0.00% 45 13 0.00% 46 26 0.00% 47 38 0.00% 48 45 0.00% 49 69 0.01% 50 109 0.01% 51 134 0.01% 52 198 0.02% 53 366 0.03% 54 441 0.03% 55 630 0.05% 56 801 0.06% 57 1291 0.10% 58 976 0.08% 59 1173 0.09% 60 1501 0.12% 61 1701 0.13% 62 1899 0.15% 63 1944 0.15% 64 2235 0.18% 65 2428 0.19% 66 2318 0.18% 67 2525 0.20% 68 2243 0.18% 69 1933 0.15% 70 4449 0.35% 71 5179 0.41% 72 6414 0.50% 73 7015 0.55% 74 7375 0.58% 75 8293 0.65% 76 9468 0.74% 77 11021 0.86% 78 11460 0.90% 79 11822 0.93% 80 12643 0.99% 81 14588 1.14% 82 15843 1.24% 83 16852 1.32% 84 19498 1.53% 85 17701 1.39% 86 17453 1.37% 87 19823 1.55% 88 25318 1.99% 89 25953 2.04% 90 26281 2.06% 91 28884 2.27% 92 25591 2.01% 93 899127 70.51% 1275169 reads passed initial QC criterion=sequence-density sequence-density=1.93 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=33 prefix-density=1.99 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.13 sequence-density-rank=25 fanout-score=139.08 fanout-score-rank=1 prefix-density=18.22 prefix-fanout=1.0 sequence=CGAAGCGGTTGCGTGCCGCACCC Started job on | Dec 07 04:07:30 Started mapping on | Dec 07 04:07:30 Finished on | Dec 07 04:07:42 Mapping speed, Million of reads per hour | 382.55 Number of input reads | 1275169 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 429591 Uniquely mapped reads % | 33.69% Average mapped length | 89.16 Number of splices: Total | 25032 Number of splices: Annotated (sjdb) | 19643 Number of splices: GT/AG | 24072 Number of splices: GC/AG | 446 Number of splices: AT/AC | 36 Number of splices: Non-canonical | 478 Mismatch rate per base, % | 0.83% Deletion rate per base | 0.04% Deletion average length | 1.74 Insertion rate per base | 0.02% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 765228 % of reads mapped to multiple loci | 60.01% Number of reads mapped to too many loci | 30351 % of reads mapped to too many loci | 2.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.51% % of reads unmapped: other | 0.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 80350 80350 80350 N_multimapping 765228 765228 765228 N_noFeature 41321 45824 410464 N_ambiguous 17279 2625 89 UnstrandedReadsAssigned:370991 PositiveStrandReadsAssigned:381142 NegativeStrandReadsAssigned:19038 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=88 echo kmer=83 ERR6133415 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: ERR6133415-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,275,169 reads, 755,699 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 867 rounds 52973 ERR6133415.ke.tsv 35125 ERR6133415.se.tsv 88098 total ==> ERR6133415.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 6 7.37496 PNS24243 293 194 0 0 KQK14069 1603 1504 9 10.0915 KQK14071 474 375 0 0 ==> ERR6133415.se.tsv <== BRADI_1g14170v3 9 BRADI_1g53295v3 0 BRADI_1g59795v3 4 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 11 BRADI_1g48960v3 0 ERR6133415 completed mapping pipeline successfully