Starting /dee2/code/volunteer_pipeline.sh ERR6133343 current disk space = 1548143902720 free memory = 1374636136 ERR6133343 SRAfilesize 289a43dab32e7a382dcf92580dd75088 ERR6133343.sra ERR6133343.sra file validated ERR6133343 is single end ERR6133343 is conventional basespace ERR6133343 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133343_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.152 37.0 37.0 37.0 33.0 37.0 2 36.61175 37.0 37.0 37.0 37.0 37.0 3 36.65325 37.0 37.0 37.0 37.0 37.0 4 36.41225 37.0 37.0 37.0 37.0 37.0 5 36.45 37.0 37.0 37.0 37.0 37.0 6 36.547 37.0 37.0 37.0 37.0 37.0 7 38.729 40.0 37.0 40.0 37.0 40.0 8 38.76375 40.0 37.0 40.0 37.0 40.0 9 38.788 40.0 37.0 40.0 37.0 40.0 10-11 38.7475 40.0 37.0 40.0 37.0 40.0 12-13 38.740125000000006 40.0 37.0 40.0 37.0 40.0 14-15 38.739625000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.709875 40.0 37.0 40.0 37.0 40.0 18-19 38.63275 40.0 37.0 40.0 37.0 40.0 20-21 38.585499999999996 40.0 37.0 40.0 37.0 40.0 22-23 38.515 40.0 37.0 40.0 37.0 40.0 24-25 38.37875 40.0 37.0 40.0 37.0 40.0 26-27 38.425749999999994 40.0 37.0 40.0 37.0 40.0 28-29 38.4615 40.0 37.0 40.0 37.0 40.0 30-31 38.38 40.0 37.0 40.0 37.0 40.0 32-33 38.245875 40.0 37.0 40.0 37.0 40.0 34-35 38.085625 40.0 37.0 40.0 37.0 40.0 36-37 38.016375 40.0 37.0 40.0 37.0 40.0 38-39 37.976749999999996 40.0 37.0 40.0 37.0 40.0 40-41 37.856625 37.0 37.0 40.0 37.0 40.0 42-43 37.731624999999994 37.0 37.0 40.0 37.0 40.0 44-45 37.590875 37.0 37.0 40.0 37.0 40.0 46-47 37.448375 37.0 37.0 40.0 35.0 40.0 48-49 37.273875000000004 37.0 37.0 40.0 33.0 40.0 50-51 37.133875 37.0 37.0 40.0 33.0 40.0 52-53 37.016875 37.0 37.0 38.5 33.0 40.0 54-55 36.769125 37.0 37.0 37.0 33.0 40.0 56-57 36.716375 37.0 37.0 37.0 33.0 40.0 58-59 36.582625 37.0 37.0 37.0 33.0 40.0 60-61 36.468625 37.0 37.0 37.0 33.0 38.5 62-63 36.2675 37.0 37.0 37.0 33.0 37.0 64-65 36.157624999999996 37.0 37.0 37.0 33.0 37.0 66-67 36.022375 37.0 37.0 37.0 33.0 37.0 68-69 35.199749999999995 35.0 35.0 37.0 33.0 37.0 70-71 35.41027809415338 37.0 35.0 37.0 33.0 37.0 72-73 35.893021041889696 37.0 37.0 37.0 33.0 37.0 74-75 35.81514769243246 37.0 37.0 37.0 33.0 37.0 76-77 35.78723025291944 37.0 37.0 37.0 33.0 37.0 78-79 35.810686221629965 37.0 37.0 37.0 33.0 37.0 80-81 35.74405172719719 37.0 37.0 37.0 33.0 37.0 82-83 35.60272615379243 37.0 37.0 37.0 33.0 37.0 84-85 35.603535094334504 37.0 37.0 37.0 33.0 37.0 86-87 35.57331378299121 37.0 33.0 37.0 33.0 37.0 88-89 35.5741935483871 37.0 35.0 37.0 33.0 37.0 90-91 35.50557184750733 37.0 35.0 37.0 33.0 37.0 92-93 35.345454545454544 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 3.0 21 2.0 22 2.0 23 2.0 24 5.0 25 6.0 26 9.0 27 7.0 28 10.0 29 19.0 30 24.0 31 31.0 32 68.0 33 67.0 34 85.0 35 185.0 36 793.0 37 1237.0 38 1342.0 39 103.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.60930465232616 8.429214607303653 7.703851925962982 15.257628814407203 2 49.175000000000004 25.474999999999998 14.674999999999999 10.674999999999999 3 32.875 37.15 16.1 13.875000000000002 4 32.0 26.825 20.0 21.175 5 25.5 27.3 26.325 20.875 6 21.675 32.75 26.974999999999998 18.6 7 34.675 25.874999999999996 21.75 17.7 8 28.725 28.475 25.4 17.4 9 25.474999999999998 26.325 28.175 20.025000000000002 10-11 26.387500000000003 26.987499999999997 26.775 19.85 12-13 25.412499999999998 28.050000000000004 27.500000000000004 19.037499999999998 14-15 22.725 28.762500000000003 28.8375 19.675 16-17 25.8125 29.425 23.5625 21.2 18-19 26.424999999999997 25.0375 27.35 21.1875 20-21 25.45 27.1375 25.95 21.462500000000002 22-23 29.4125 24.8625 24.45 21.275 24-25 25.8 26.450000000000003 27.5125 20.2375 26-27 26.474999999999998 25.0125 28.3375 20.175 28-29 25.2625 29.275000000000002 24.9375 20.525 30-31 26.887499999999996 26.4125 25.825 20.875 32-33 26.5125 26.3125 27.400000000000002 19.775000000000002 34-35 25.637500000000003 29.025000000000002 25.7375 19.6 36-37 25.7875 26.875 24.65 22.6875 38-39 26.144036009002253 25.756439109777446 26.894223555888974 21.205301325331334 40-41 26.400000000000002 26.137500000000003 26.1 21.3625 42-43 25.924999999999997 30.575000000000003 24.349999999999998 19.15 44-45 22.6 29.7125 27.3625 20.325 46-47 25.4375 27.700000000000003 26.0625 20.8 48-49 24.2 26.987499999999997 28.3625 20.45 50-51 23.05 29.325000000000003 27.35 20.275000000000002 52-53 23.9875 29.812499999999996 26.387500000000003 19.8125 54-55 23.8375 30.112499999999997 27.2625 18.787499999999998 56-57 24.887500000000003 27.375 27.05 20.6875 58-59 23.7625 28.8625 26.6625 20.7125 60-61 26.0125 27.5125 26.7125 19.7625 62-63 22.2625 31.85 27.875 18.0125 64-65 22.67383691845923 31.953476738369186 26.900950475237618 18.471735867933965 66-67 25.05 30.887500000000003 25.5125 18.55 68-69 24.0375 29.1125 25.937500000000004 20.9125 70-71 25.367878254307634 28.81398566218086 25.70745818136084 20.110677902150673 72-73 26.753313601853044 28.297516407154806 26.586024964612022 18.36314502638013 74-75 24.459300039323633 27.841132520644905 27.854240398479487 19.845327041551972 76-77 23.479188900747065 28.281750266808963 27.374599786552828 20.86446104589114 78-79 24.363143631436316 28.211382113821138 27.967479674796746 19.4579945799458 80-81 24.419247787610622 31.95519911504425 25.48396017699115 18.141592920353983 82-83 22.82871357498223 28.315565031982942 26.979388770433548 21.87633262260128 84-85 23.722149410222805 27.42099898063201 27.843308577253534 21.013543031891654 86-87 23.73900293255132 28.95894428152493 26.59824046920821 20.703812316715542 88-89 22.038123167155423 33.60703812316716 25.117302052785924 19.237536656891496 90-91 25.410557184750733 30.29325513196481 25.63049853372434 18.665689149560116 92-93 22.243401759530794 34.98533724340176 23.225806451612904 19.545454545454547 >>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 0.5 18 1.0 19 0.5 20 0.0 21 0.5 22 4.5 23 8.5 24 9.0 25 8.5 26 13.0 27 21.0 28 27.0 29 30.0 30 35.5 31 41.0 32 44.0 33 58.0 34 71.5 35 92.0 36 126.0 37 172.0 38 189.0 39 173.0 40 194.0 41 205.0 42 203.5 43 210.0 44 187.5 45 179.0 46 172.5 47 159.5 48 162.5 49 175.5 50 171.5 51 166.0 52 172.0 53 173.5 54 166.0 55 138.5 56 114.5 57 102.5 58 77.0 59 37.5 60 19.5 61 21.5 62 21.5 63 17.0 64 14.0 65 14.5 66 14.5 67 11.5 68 16.0 69 17.5 70 9.5 71 4.0 72 3.0 73 1.0 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 0.05 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 0.025 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 0.05 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 49.0 71 49.0 72 33.0 73 39.0 74 31.0 75 36.0 76 30.0 77 25.0 78 36.0 79 36.0 80 40.0 81 53.0 82 51.0 83 35.0 84 47.0 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 3410.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 71.475 #Duplication Level Percentage of deduplicated Percentage of total 1 89.50682056663169 63.975 2 4.686953480237845 6.7 3 1.6789087093389297 3.5999999999999996 4 1.1892270024484084 3.4000000000000004 5 0.5946135012242042 2.125 6 0.4547044421126268 1.95 7 0.38474991255683805 1.925 8 0.13990905911157747 0.8 9 0.27981811822315494 1.7999999999999998 >10 1.0842952081147255 13.725000000000001 >50 0.0 0.0 >100 0.0 0.0 >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 41 1.0250000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 39 0.975 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 32 0.8 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 31 0.775 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 27 0.675 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 25 0.625 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 23 0.575 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 22 0.5499999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 21 0.525 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 20 0.5 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 15 0.375 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 15 0.375 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 12 0.3 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 11 0.27499999999999997 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 11 0.27499999999999997 No Hit GCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGA 11 0.27499999999999997 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 10 0.25 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 10 0.25 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 10 0.25 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 10 0.25 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 9 0.22499999999999998 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 9 0.22499999999999998 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 9 0.22499999999999998 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 9 0.22499999999999998 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 9 0.22499999999999998 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 9 0.22499999999999998 No Hit CAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTAT 8 0.2 No Hit GAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAGA 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 8 0.2 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 7 0.17500000000000002 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 7 0.17500000000000002 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 7 0.17500000000000002 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 7 0.17500000000000002 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 7 0.17500000000000002 No Hit AGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCG 7 0.17500000000000002 No Hit GCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATC 7 0.17500000000000002 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 7 0.17500000000000002 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 7 0.17500000000000002 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit GTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCCGCT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 6 0.15 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 6 0.15 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 6 0.15 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit CAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGT 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTT 5 0.125 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 5 0.125 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 5 0.125 No Hit GAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGC 5 0.125 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit ATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAAT 5 0.125 No Hit CGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATG 5 0.125 No Hit TATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAA 5 0.125 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit AAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTT 5 0.125 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 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 0.037500000000000006 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.225 0.0 0.0 0.0 0.0 36-37 0.225 0.0 0.0 0.0 0.0 38-39 0.2375 0.0 0.0 0.0 0.0 40-41 0.2625 0.0 0.0 0.0 0.0 42-43 0.275 0.0 0.0 0.0 0.0 44-45 0.275 0.0 0.0 0.0 0.0 46-47 0.275 0.0 0.0 0.0 0.0 48-49 0.275 0.0 0.0 0.0 0.0 50-51 0.275 0.0 0.0 0.0 0.0 52-53 0.275 0.0 0.0 0.0 0.0 54-55 0.275 0.0 0.0 0.0 0.0 56-57 0.275 0.0 0.0 0.0 0.0 58-59 0.275 0.0 0.0 0.0 0.0 60-61 0.275 0.0 0.0 0.0 0.0 62-63 0.275 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.275 0.0 0.0 0.0 0.0 68-69 0.275 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.3 0.0 0.0 0.0 0.0 74-75 0.3 0.0 0.0 0.0 0.0 76-77 0.3 0.0 0.0 0.0 0.0 78-79 0.3 0.0 0.0 0.0 0.0 80-81 0.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 20 0.002907886 64.21875 2 GCAATAC 20 0.002907886 64.21875 7 GGGAGAG 20 0.002907886 64.21875 1 CAATACA 20 0.002907886 64.21875 8 GAGCAAT 20 0.002907886 64.21875 5 AGAGCAA 20 0.002907886 64.21875 4 GAGAGCA 20 0.002907886 64.21875 3 AGCAATA 20 0.002907886 64.21875 6 AATACAA 25 0.007036667 51.375004 9 AGCCGAA 20 6.133027E-4 45.666668 74-75 GTAGCCG 20 6.339982E-4 45.364243 72-73 CAGTAGC 20 6.552444E-4 45.06579 70-71 TCCAGTA 20 6.552444E-4 45.06579 68-69 AGTCCAG 20 7.459535E-4 43.910255 66-67 GGTTGAG 20 8.4635866E-4 42.8125 38-39 GCTAGGC 20 8.4635866E-4 42.8125 26-27 GCGGTTG 20 8.4635866E-4 42.8125 36-37 ATGGCTA 20 8.4635866E-4 42.8125 58-59 TGCTGCT 20 8.4635866E-4 42.8125 22-23 CGAAGCG 20 8.4635866E-4 42.8125 32-33 >>END_MODULE Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23752 READS because READLEN < 1 Read 23752 spots for ERR6133343.sra Written 23752 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra Rejected 23733 READS because READLEN < 1 Read 23733 spots for ERR6133343.sra Written 23733 spots for ERR6133343.sra SRR ids: ['ERR6133343.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_tyil_8nj ERR6133343.sra spots: 474679 blocks: [[1, 23733], [23734, 47466], [47467, 71199], [71200, 94932], [94933, 118665], [118666, 142398], [142399, 166131], [166132, 189864], [189865, 213597], [213598, 237330], [237331, 261063], [261064, 284796], [284797, 308529], [308530, 332262], [332263, 355995], [355996, 379728], [379729, 403461], [403462, 427194], [427195, 450927], [450928, 474679]] ERR6133343 file size 102353 ERR6133343 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 ERR6133343 ERR6133343_1.fastq Input file: ERR6133343_1.fastq trimmed: ERR6133343-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 01:04:03 2024 >> started Sat Dec 7 01:04:03 2024 >> done (0.612s) 474679 reads processed; of these: 48 ( 0.01%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 474631 (99.99%) reads available; of these: 3750 ( 0.79%) trimmed reads available after processing 470881 (99.21%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 19 6 0.00% 20 3 0.00% 21 2 0.00% 22 6 0.00% 23 5 0.00% 24 2 0.00% 25 3 0.00% 26 4 0.00% 27 2 0.00% 28 3 0.00% 29 85 0.02% 30 4 0.00% 31 4 0.00% 32 13 0.00% 33 802 0.17% 34 6 0.00% 35 8 0.00% 36 9 0.00% 37 7 0.00% 38 16 0.00% 39 10 0.00% 40 28 0.01% 41 7 0.00% 42 1 0.00% 43 8 0.00% 44 6 0.00% 45 7 0.00% 46 2 0.00% 47 2 0.00% 48 5 0.00% 49 5 0.00% 50 5 0.00% 51 23 0.00% 52 9 0.00% 53 6 0.00% 54 3 0.00% 55 3 0.00% 56 3 0.00% 57 5 0.00% 58 8 0.00% 59 7 0.00% 60 6 0.00% 61 7 0.00% 62 2 0.00% 63 1 0.00% 64 0 0.00% 65 6 0.00% 66 4 0.00% 67 4 0.00% 68 8 0.00% 69 24 0.01% 70 5178 1.09% 71 4469 0.94% 72 4874 1.03% 73 4542 0.96% 74 4448 0.94% 75 4218 0.89% 76 3719 0.78% 77 4062 0.86% 78 4275 0.90% 79 4820 1.02% 80 4317 0.91% 81 5512 1.16% 82 5925 1.25% 83 5245 1.11% 84 5760 1.21% 85 20 0.00% 86 37 0.01% 87 41 0.01% 88 50 0.01% 89 104 0.02% 90 175 0.04% 91 393 0.08% 92 1265 0.27% 93 399977 84.27% 474631 reads passed initial QC criterion=sequence-density sequence-density=5.66 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=17 prefix-density=5.72 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=283.07 fanout-score-rank=1 prefix-density=6.06 prefix-fanout=1.1 sequence=TAATGAAATTGAAATTATTAAGTAAAGTGCAAATACAAATAAAGAAACAACTTTGCTGACCATGATAGATTTTTATCTAGGCGGAAGAGTCCTCTTAATATTTATCTAATCTTATATAGGTTTCAGTATATTGAAATAGAAAGATAAAATAGAAGAGAGAGGATAGGCTCATTACTTAAAAAAAAGATATGGAAATAGCCATAGC 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 01:04:32 Started mapping on | Dec 07 01:04:32 Finished on | Dec 07 01:04:36 Mapping speed, Million of reads per hour | 427.17 Number of input reads | 474631 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 219486 Uniquely mapped reads % | 46.24% Average mapped length | 89.08 Number of splices: Total | 6465 Number of splices: Annotated (sjdb) | 5180 Number of splices: GT/AG | 5992 Number of splices: GC/AG | 188 Number of splices: AT/AC | 16 Number of splices: Non-canonical | 269 Mismatch rate per base, % | 0.57% Deletion rate per base | 0.05% Deletion average length | 1.83 Insertion rate per base | 0.04% Insertion average length | 2.05 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 209182 % of reads mapped to multiple loci | 44.07% Number of reads mapped to too many loci | 28410 % of reads mapped to too many loci | 5.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.43% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 45963 45963 45963 N_multimapping 209182 209182 209182 N_noFeature 16718 18898 209498 N_ambiguous 9125 1314 46 UnstrandedReadsAssigned:193643 PositiveStrandReadsAssigned:199274 NegativeStrandReadsAssigned:9942 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133343 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: ERR6133343-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 474,631 reads, 319,996 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 877 rounds 52973 ERR6133343.ke.tsv 35125 ERR6133343.se.tsv 88098 total ==> ERR6133343.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 5 15.8883 PNS24243 293 194 0 0 KQK14069 1603 1504 5 14.4938 KQK14071 474 375 0 0 ==> ERR6133343.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 1 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 0 BRADI_1g74790v3 0 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 ERR6133343 completed mapping pipeline successfully