Starting /dee2/code/volunteer_pipeline.sh ERR6133419 current disk space = 1547207639040 free memory = 1603596816 ERR6133419 SRAfilesize f180447633387da5aff556e6c555f9b0 ERR6133419.sra ERR6133419.sra file validated ERR6133419 is single end ERR6133419 is conventional basespace ERR6133419 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133419_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.43425 33.0 27.0 33.0 15.0 37.0 2 33.45625 33.0 33.0 37.0 27.0 37.0 3 33.96425 37.0 33.0 37.0 27.0 37.0 4 34.176 37.0 33.0 37.0 27.0 37.0 5 34.284 37.0 33.0 37.0 27.0 37.0 6 34.38675 37.0 33.0 37.0 27.0 37.0 7 35.397 37.0 33.0 40.0 27.0 40.0 8 35.36325 37.0 33.0 40.0 27.0 40.0 9 35.533 37.0 33.0 40.0 27.0 40.0 10-11 35.4915 37.0 33.0 40.0 30.0 40.0 12-13 35.478875 37.0 33.0 40.0 30.0 40.0 14-15 35.253874999999994 37.0 33.0 40.0 27.0 40.0 16-17 35.0215 37.0 33.0 38.5 27.0 40.0 18-19 34.900375 37.0 33.0 37.0 27.0 40.0 20-21 34.1315 37.0 33.0 37.0 27.0 40.0 22-23 33.948 37.0 33.0 37.0 24.5 40.0 24-25 33.487875 37.0 33.0 37.0 22.0 40.0 26-27 33.415 37.0 33.0 37.0 22.0 40.0 28-29 32.890874999999994 37.0 33.0 37.0 22.0 40.0 30-31 32.834625 37.0 33.0 37.0 22.0 40.0 32-33 32.54075 35.0 33.0 37.0 22.0 40.0 34-35 31.660874999999997 33.0 27.0 37.0 15.0 40.0 36-37 31.579375 33.0 27.0 37.0 18.5 40.0 38-39 31.5485 33.0 27.0 37.0 22.0 40.0 40-41 31.557625 33.0 27.0 37.0 22.0 40.0 42-43 31.219875000000002 33.0 27.0 37.0 15.0 40.0 44-45 31.175625 33.0 27.0 37.0 18.5 40.0 46-47 30.50425 33.0 27.0 37.0 15.0 37.0 48-49 30.308750000000003 33.0 27.0 37.0 15.0 37.0 50-51 29.76575 33.0 27.0 37.0 15.0 37.0 52-53 29.7485 33.0 27.0 37.0 15.0 37.0 54-55 29.362250000000003 33.0 27.0 37.0 15.0 37.0 56-57 28.7715 33.0 27.0 37.0 15.0 37.0 58-59 28.344749999999998 33.0 24.5 33.0 15.0 37.0 60-61 28.20075 33.0 27.0 33.0 15.0 37.0 62-63 27.695500000000003 33.0 22.0 33.0 15.0 37.0 64-65 26.914375 33.0 22.0 33.0 6.0 37.0 66-67 26.614 27.0 22.0 33.0 6.0 37.0 68-69 26.54925 27.0 22.0 33.0 10.5 35.0 70-71 28.259734437751003 33.0 27.0 33.0 15.0 37.0 72-73 28.795360166807633 33.0 27.0 33.0 15.0 37.0 74-75 28.716871680606484 33.0 27.0 33.0 15.0 37.0 76-77 28.263177988668804 33.0 27.0 33.0 15.0 37.0 78-79 27.898600243543225 33.0 27.0 33.0 15.0 37.0 80-81 27.278940433172664 33.0 27.0 33.0 6.0 37.0 82-83 26.313363466523334 33.0 22.0 33.0 4.0 37.0 84-85 25.375137530640547 33.0 18.5 33.0 2.0 37.0 86-87 24.342220399234346 30.0 15.0 33.0 2.0 37.0 88-89 23.747607328411267 30.0 15.0 33.0 2.0 37.0 90-91 22.681432868471425 27.0 4.0 33.0 2.0 37.0 92-93 21.27536231884058 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 98.0 21 90.0 22 113.0 23 138.0 24 183.0 25 190.0 26 223.0 27 264.0 28 260.0 29 271.0 30 255.0 31 270.0 32 286.0 33 267.0 34 299.0 35 303.0 36 277.0 37 181.0 38 31.0 39 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.72500000000001 6.550000000000001 7.025 17.7 2 49.275000000000006 25.75 15.024999999999999 9.950000000000001 3 28.4 40.300000000000004 18.975 12.325 4 28.499999999999996 26.650000000000002 22.875 21.975 5 23.95 25.85 29.975 20.225 6 19.875 32.324999999999996 28.4 19.400000000000002 7 29.575000000000003 29.925 22.925 17.575 8 24.825 30.275000000000002 28.375 16.525000000000002 9 22.55 27.150000000000002 30.049999999999997 20.25 10-11 22.9875 27.125 30.349999999999998 19.537499999999998 12-13 22.037499999999998 28.8875 30.4875 18.587500000000002 14-15 19.537499999999998 29.299999999999997 31.937500000000004 19.225 16-17 22.8125 29.825000000000003 25.025 22.3375 18-19 22.075 26.375 31.4875 20.0625 20-21 24.762500000000003 25.0625 28.512500000000003 21.6625 22-23 27.3 24.2375 27.400000000000002 21.0625 24-25 23.7625 27.9125 28.275 20.05 26-27 23.0 25.0625 31.587500000000002 20.349999999999998 28-29 24.25 27.525 29.075 19.15 30-31 24.3875 27.925 28.025 19.662499999999998 32-33 24.45 25.174999999999997 30.475 19.900000000000002 34-35 21.837500000000002 30.475 27.825 19.8625 36-37 23.8875 28.037499999999998 26.8125 21.2625 38-39 25.825 25.324999999999996 29.1625 19.6875 40-41 24.5375 24.837500000000002 28.3625 22.2625 42-43 25.6125 27.6125 27.675 19.1 44-45 21.2625 27.0625 31.2125 20.4625 46-47 23.674999999999997 27.075 28.1625 21.087500000000002 48-49 22.325 27.462500000000002 30.062499999999996 20.150000000000002 50-51 21.675 28.075 29.012500000000003 21.2375 52-53 23.7125 28.5625 27.3875 20.3375 54-55 22.85 28.025 30.9625 18.1625 56-57 24.7 27.987499999999997 28.050000000000004 19.2625 58-59 23.6625 27.5625 27.55 21.224999999999998 60-61 25.1 27.9125 28.262500000000003 18.725 62-63 20.962500000000002 29.175 29.7 20.1625 64-65 22.3 30.95 28.512500000000003 18.2375 66-67 23.5875 28.199999999999996 27.200000000000003 21.0125 68-69 21.6 28.962500000000002 27.187499999999996 22.25 70-71 23.822645290581164 28.907815631262523 26.528056112224448 20.741482965931866 72-73 23.030226381687115 27.507272037435182 29.556089540913117 19.90641203996459 74-75 24.37804565273147 27.3146960759169 29.340856629905105 18.966401641446527 76-77 22.356143079315707 28.602903058579578 27.190254017625715 21.850699844479003 78-79 22.217858078030897 26.839486776643103 30.269704111023827 20.672951034302173 80-81 21.92180251822399 31.954937044400268 27.886017229953612 18.237243207422136 82-83 20.85741163822067 28.342964655288267 28.799892487568872 21.99973121892219 84-85 22.154139433551197 24.645969498910674 31.045751633986928 22.154139433551197 86-87 21.79382007109653 28.35657642876675 27.72764561115669 22.121957888980038 88-89 20.617992890347278 29.13590374624009 29.928903472791905 20.317199890620728 90-91 23.21575061525841 29.163248564397048 26.606508066721357 21.014492753623188 92-93 20.399234345091603 33.16926442439158 26.825266611977028 19.606234618539787 >>END_MODULE >>Per sequence GC content warn #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 2.0 18 2.5 19 2.0 20 4.0 21 3.5 22 4.0 23 7.5 24 9.0 25 10.0 26 15.0 27 24.5 28 31.0 29 32.5 30 37.5 31 52.5 32 64.5 33 81.0 34 92.5 35 101.5 36 130.5 37 191.0 38 240.0 39 225.0 40 232.5 41 252.0 42 239.5 43 235.5 44 217.5 45 185.0 46 163.0 47 155.0 48 141.5 49 139.5 50 129.5 51 92.5 52 88.5 53 104.0 54 121.5 55 119.0 56 95.5 57 91.0 58 64.0 59 30.0 60 21.5 61 16.5 62 14.5 63 16.0 64 14.0 65 12.0 66 12.5 67 13.0 68 16.5 69 14.5 70 7.5 71 4.0 72 3.0 73 1.5 74 0.5 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 0.0 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 16.0 71 17.0 72 27.0 73 33.0 74 16.0 75 22.0 76 22.0 77 19.0 78 18.0 79 27.0 80 21.0 81 26.0 82 31.0 83 18.0 84 30.0 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 3657.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.55000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 91.24748490945674 68.025 2 4.527162977867203 6.75 3 1.1066398390342052 2.475 4 0.9725016767270288 2.9000000000000004 5 0.4359490274983233 1.625 6 0.30181086519114686 1.35 7 0.1676727028839705 0.8750000000000001 8 0.2012072434607646 1.2 9 0.1341381623071764 0.8999999999999999 >10 0.8718980549966466 12.375 >50 0.0335345405767941 1.525 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 61 1.525 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 44 1.0999999999999999 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 41 1.0250000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 41 1.0250000000000001 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 39 0.975 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 30 0.75 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 29 0.7250000000000001 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 26 0.65 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 21 0.525 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 18 0.44999999999999996 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 18 0.44999999999999996 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 16 0.4 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 14 0.35000000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 13 0.325 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 12 0.3 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 12 0.3 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 11 0.27499999999999997 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 10 0.25 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 10 0.25 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 10 0.25 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 9 0.22499999999999998 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 9 0.22499999999999998 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 8 0.2 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 8 0.2 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 8 0.2 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 8 0.2 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 8 0.2 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 8 0.2 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 7 0.17500000000000002 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 7 0.17500000000000002 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 6 0.15 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGC 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit TGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATA 5 0.125 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 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 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 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 TTCAATT 55 1.2119326E-6 47.147728 4 TCAATTT 55 1.2119326E-6 47.147728 5 AATTTCA 60 2.207942E-6 43.21875 7 CAATTTC 60 2.207942E-6 43.21875 6 TTTCAAC 60 2.207942E-6 43.21875 9 GATTCAA 60 2.207942E-6 43.21875 2 ATTTCAA 60 2.207942E-6 43.21875 8 ATTCAAT 60 2.207942E-6 43.21875 3 GGATTCA 65 3.8309972E-6 39.89423 1 TTCAACC 70 1.0711046E-6 24.696428 10-11 CAACCAA 70 1.0711046E-6 24.696428 12-13 ACCAATC 70 1.0711046E-6 24.696428 14-15 ATCTTGG 75 1.2357159E-6 24.263159 80-81 TGGTATG 75 1.2357159E-6 24.263159 84-85 CTTGGTA 75 1.2357159E-6 24.263159 82-83 TAATCTT 75 1.2357159E-6 24.263159 78-79 AGTTGAT 65 1.7685723E-5 23.271635 24-25 CTGTAGT 65 1.7685723E-5 23.271635 20-21 CAATCTG 75 1.9542258E-6 23.05 16-17 GTATGGA 80 2.1682135E-6 22.74671 86-87 >>END_MODULE Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76056 READS because READLEN < 1 Read 76056 spots for ERR6133419.sra Written 76056 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra Rejected 76039 READS because READLEN < 1 Read 76039 spots for ERR6133419.sra Written 76039 spots for ERR6133419.sra SRR ids: ['ERR6133419.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_pgviyz2n ERR6133419.sra spots: 1520797 blocks: [[1, 76039], [76040, 152078], [152079, 228117], [228118, 304156], [304157, 380195], [380196, 456234], [456235, 532273], [532274, 608312], [608313, 684351], [684352, 760390], [760391, 836429], [836430, 912468], [912469, 988507], [988508, 1064546], [1064547, 1140585], [1140586, 1216624], [1216625, 1292663], [1292664, 1368702], [1368703, 1444741], [1444742, 1520797]] ERR6133419 file size 332462 ERR6133419 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 ERR6133419 ERR6133419_1.fastq Input file: ERR6133419_1.fastq trimmed: ERR6133419-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 04:30:08 2024 >> started Sat Dec 7 04:30:09 2024 >> done (0.959s) 1520797 reads processed; of these: 26 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 1520768 (100.00%) reads available; of these: 379323 (24.94%) trimmed reads available after processing 1141445 (75.06%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 16 0.00% 20 15 0.00% 21 4 0.00% 22 13 0.00% 23 2 0.00% 24 3 0.00% 25 3 0.00% 26 3 0.00% 27 2 0.00% 28 13 0.00% 29 44 0.00% 30 2 0.00% 31 7 0.00% 32 16 0.00% 33 11 0.00% 34 1 0.00% 35 5 0.00% 36 5 0.00% 37 9 0.00% 38 17 0.00% 39 23 0.00% 40 50 0.00% 41 17 0.00% 42 15 0.00% 43 32 0.00% 44 30 0.00% 45 43 0.00% 46 49 0.00% 47 84 0.01% 48 114 0.01% 49 141 0.01% 50 180 0.01% 51 295 0.02% 52 336 0.02% 53 453 0.03% 54 590 0.04% 55 831 0.05% 56 1168 0.08% 57 1726 0.11% 58 1199 0.08% 59 1425 0.09% 60 1740 0.11% 61 2004 0.13% 62 2096 0.14% 63 2234 0.15% 64 2454 0.16% 65 2585 0.17% 66 2586 0.17% 67 2581 0.17% 68 2583 0.17% 69 2666 0.18% 70 10918 0.72% 71 11025 0.72% 72 12683 0.83% 73 13463 0.89% 74 13513 0.89% 75 14784 0.97% 76 14823 0.97% 77 16112 1.06% 78 17166 1.13% 79 18581 1.22% 80 19158 1.26% 81 22664 1.49% 82 24540 1.61% 83 24650 1.62% 84 26993 1.77% 85 19066 1.25% 86 20083 1.32% 87 22048 1.45% 88 25107 1.65% 89 28006 1.84% 90 29595 1.95% 91 32540 2.14% 92 27091 1.78% 93 1023631 67.31% 1520768 reads passed initial QC criterion=sequence-density sequence-density=3.60 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=26 prefix-density=3.70 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=23.00 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=2.9 sequence=TGAAGAAATTAGAGTGCTCAAAGCAAGCCATCGCTCTGGATACATTAGCATGGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGT 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 04:30:21 Started mapping on | Dec 07 04:30:23 Finished on | Dec 07 04:30:29 Mapping speed, Million of reads per hour | 912.46 Number of input reads | 1520768 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 645862 Uniquely mapped reads % | 42.47% Average mapped length | 88.34 Number of splices: Total | 19413 Number of splices: Annotated (sjdb) | 15179 Number of splices: GT/AG | 18257 Number of splices: GC/AG | 495 Number of splices: AT/AC | 18 Number of splices: Non-canonical | 643 Mismatch rate per base, % | 0.90% Deletion rate per base | 0.05% Deletion average length | 1.77 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 715026 % of reads mapped to multiple loci | 47.02% Number of reads mapped to too many loci | 65990 % of reads mapped to too many loci | 4.34% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.41% % of reads unmapped: other | 0.76% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 159880 159880 159880 N_multimapping 715026 715026 715026 N_noFeature 65238 73627 615894 N_ambiguous 26692 5095 164 UnstrandedReadsAssigned:553932 PositiveStrandReadsAssigned:567140 NegativeStrandReadsAssigned:29804 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133419 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: ERR6133419-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,520,768 reads, 1,046,029 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,064 rounds 52973 ERR6133419.ke.tsv 35125 ERR6133419.se.tsv 88098 total ==> ERR6133419.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 5.53532 PNS24243 293 194 0 0 KQK14069 1603 1504 83 69.8515 KQK14071 474 375 0 0 ==> ERR6133419.se.tsv <== BRADI_1g14170v3 81 BRADI_1g53295v3 7 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 9 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 5 BRADI_1g48960v3 0 ERR6133419 completed mapping pipeline successfully