Starting /dee2/code/volunteer_pipeline.sh ERR6133327 current disk space = 1548172931072 free memory = 1599790808 ERR6133327 SRAfilesize 5142c558fd80265c2d2aaff82a3d4469 ERR6133327.sra ERR6133327.sra file validated ERR6133327 is single end ERR6133327 is conventional basespace ERR6133327 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133327_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.2295 37.0 37.0 37.0 33.0 37.0 2 36.6365 37.0 37.0 37.0 37.0 37.0 3 36.5715 37.0 37.0 37.0 37.0 37.0 4 36.249 37.0 37.0 37.0 33.0 37.0 5 36.298 37.0 37.0 37.0 37.0 37.0 6 36.43425 37.0 37.0 37.0 37.0 37.0 7 38.59225 40.0 37.0 40.0 37.0 40.0 8 38.66975 40.0 37.0 40.0 37.0 40.0 9 38.72425 40.0 37.0 40.0 37.0 40.0 10-11 38.69475 40.0 37.0 40.0 37.0 40.0 12-13 38.6495 40.0 37.0 40.0 37.0 40.0 14-15 38.626 40.0 37.0 40.0 37.0 40.0 16-17 38.596625 40.0 37.0 40.0 37.0 40.0 18-19 38.53037500000001 40.0 37.0 40.0 37.0 40.0 20-21 38.442750000000004 40.0 37.0 40.0 37.0 40.0 22-23 38.380125 40.0 37.0 40.0 37.0 40.0 24-25 38.319375 40.0 37.0 40.0 37.0 40.0 26-27 38.361999999999995 40.0 37.0 40.0 37.0 40.0 28-29 38.405625 40.0 37.0 40.0 37.0 40.0 30-31 38.31725 40.0 37.0 40.0 37.0 40.0 32-33 38.232875 40.0 37.0 40.0 37.0 40.0 34-35 38.072625 40.0 37.0 40.0 37.0 40.0 36-37 37.979625 40.0 37.0 40.0 37.0 40.0 38-39 37.893 40.0 37.0 40.0 37.0 40.0 40-41 37.785250000000005 38.5 37.0 40.0 37.0 40.0 42-43 37.7 37.0 37.0 40.0 35.0 40.0 44-45 37.574124999999995 37.0 37.0 40.0 33.0 40.0 46-47 37.440875 37.0 37.0 40.0 33.0 40.0 48-49 37.262249999999995 37.0 37.0 40.0 33.0 40.0 50-51 37.06375 37.0 37.0 40.0 33.0 40.0 52-53 36.927875 37.0 37.0 38.5 33.0 40.0 54-55 36.871750000000006 37.0 37.0 37.0 33.0 40.0 56-57 36.733374999999995 37.0 37.0 37.0 33.0 40.0 58-59 36.496375 37.0 37.0 37.0 33.0 40.0 60-61 36.425250000000005 37.0 37.0 37.0 33.0 38.5 62-63 36.241 37.0 37.0 37.0 33.0 37.0 64-65 36.0985 37.0 37.0 37.0 33.0 37.0 66-67 36.026125 37.0 37.0 37.0 33.0 37.0 68-69 35.025000000000006 35.0 35.0 37.0 33.0 37.0 70-71 35.286870286576175 37.0 33.0 37.0 33.0 37.0 72-73 35.74831231760117 37.0 37.0 37.0 33.0 37.0 74-75 35.5108256409779 37.0 37.0 37.0 33.0 37.0 76-77 35.58215711235477 37.0 37.0 37.0 33.0 37.0 78-79 35.6253400639059 37.0 37.0 37.0 33.0 37.0 80-81 35.59073380625687 37.0 37.0 37.0 33.0 37.0 82-83 35.45317856304038 37.0 33.0 37.0 33.0 37.0 84-85 35.461569193905625 37.0 33.0 37.0 33.0 37.0 86-87 35.43692819517605 37.0 33.0 37.0 33.0 37.0 88-89 35.45023565289715 37.0 33.0 37.0 33.0 37.0 90-91 35.355281397283065 37.0 33.0 37.0 33.0 37.0 92-93 35.22650401996118 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 7.0 22 3.0 23 6.0 24 7.0 25 7.0 26 9.0 27 10.0 28 15.0 29 17.0 30 26.0 31 44.0 32 55.0 33 65.0 34 110.0 35 184.0 36 838.0 37 1159.0 38 1366.0 39 70.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.19154788697175 8.477119279819954 8.752188047011753 16.579144786196547 2 49.3 25.5 14.975 10.225 3 33.45 35.625 15.875 15.049999999999999 4 29.575000000000003 28.825 21.65 19.950000000000003 5 25.35 27.975 26.200000000000003 20.474999999999998 6 19.55 38.45 24.25 17.75 7 36.65 26.474999999999998 20.875 16.0 8 26.6 27.150000000000002 25.15 21.099999999999998 9 25.4 30.575000000000003 26.275 17.75 10-11 24.712500000000002 28.762500000000003 27.9125 18.6125 12-13 24.2 29.5 25.687500000000004 20.6125 14-15 21.5625 31.137500000000003 28.1625 19.1375 16-17 26.0375 28.925 23.6625 21.375 18-19 26.325 24.5625 28.812500000000004 20.3 20-21 26.4125 25.387500000000003 28.3625 19.8375 22-23 27.775 23.8625 27.3875 20.974999999999998 24-25 24.6875 25.337500000000002 27.85 22.125 26-27 26.0 24.575 28.050000000000004 21.375 28-29 24.775 27.3625 27.525 20.3375 30-31 28.825 25.587500000000002 25.387500000000003 20.200000000000003 32-33 27.462500000000002 24.6 26.2875 21.65 34-35 23.7875 30.9375 25.424999999999997 19.85 36-37 26.8125 26.187500000000004 22.775000000000002 24.224999999999998 38-39 28.57857232154019 24.590573821727716 25.965745718214777 20.865108138517314 40-41 26.087500000000002 25.112499999999997 28.625 20.175 42-43 26.775 30.9875 24.3125 17.925 44-45 24.075 27.85 27.787499999999998 20.2875 46-47 27.9375 25.2125 24.6875 22.162499999999998 48-49 26.1 25.3 27.250000000000004 21.349999999999998 50-51 22.825 29.099999999999998 27.025 21.05 52-53 24.975 27.275 25.2 22.55 54-55 23.6375 26.1625 27.625 22.575 56-57 26.4125 28.0875 26.075 19.425 58-59 23.3125 29.6625 26.85 20.175 60-61 28.3375 26.2875 25.25 20.125 62-63 23.1875 27.8375 28.7375 20.2375 64-65 22.755688922230558 33.44586146536634 25.30632658164541 18.49212303075769 66-67 24.415551943992998 31.87898487310914 24.6530816352044 19.05238154769346 68-69 22.6375 27.6 26.7125 23.05 70-71 25.670594133868136 28.12735021308599 24.880922536976684 21.32113311606919 72-73 28.010670731707314 25.927337398373986 27.820121951219512 18.241869918699187 74-75 27.333677153171738 27.84940691077875 27.114492006188755 17.702423929860753 76-77 23.512526096033405 24.37369519832985 26.918058455114824 25.19572025052192 78-79 27.771171885321706 27.440877262518164 26.50284053375611 18.285110318404016 80-81 23.82034487367999 34.260125651650846 25.11696297286459 16.802566501804574 82-83 24.48896710437255 27.358873697035328 25.030458914308923 23.1217002842832 84-85 23.005796301407674 26.469776428374274 29.05051062655258 21.47391664366547 86-87 22.01275298031605 31.092320487940118 24.743554200166344 22.151372331577488 88-89 20.252287219295813 31.272525644579986 27.432769614638204 21.042417521485998 90-91 25.33961741059052 31.646797892985862 23.85639035209315 19.15719434433047 92-93 19.725533684502356 33.90629331854727 25.977266426393125 20.39090657055725 >>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 1.5 19 2.0 20 1.5 21 1.5 22 2.0 23 3.5 24 5.0 25 6.5 26 10.5 27 14.5 28 22.5 29 25.5 30 22.5 31 29.5 32 44.5 33 55.0 34 63.0 35 82.5 36 111.5 37 146.5 38 182.5 39 177.5 40 190.5 41 200.0 42 201.5 43 226.5 44 196.5 45 162.0 46 151.0 47 144.5 48 132.0 49 121.0 50 136.0 51 177.5 52 194.5 53 210.0 54 260.5 55 216.0 56 122.5 57 95.5 58 77.0 59 43.0 60 23.0 61 19.0 62 15.0 63 13.5 64 13.0 65 13.5 66 8.5 67 5.0 68 13.0 69 15.0 70 6.0 71 1.0 72 1.5 73 2.0 74 1.0 75 0.0 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 0.025 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 0.0125 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 0.025 66-67 0.0125 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 0.013798813302056023 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 22.0 71 25.0 72 34.0 73 29.0 74 24.0 75 23.0 76 22.0 77 25.0 78 23.0 79 24.0 80 17.0 81 21.0 82 35.0 83 36.0 84 33.0 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 3607.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 68.525 #Duplication Level Percentage of deduplicated Percentage of total 1 89.20102152499088 61.12499999999999 2 5.107624954396206 7.000000000000001 3 1.897117840204305 3.9 4 0.8391098139365194 2.3 5 0.7661437431594309 2.625 6 0.5472455308281649 2.25 7 0.2553812477198103 1.225 8 0.1459321415541773 0.8 9 0.1459321415541773 0.8999999999999999 >10 1.0580080262677856 13.55 >50 0.0 0.0 >100 0.036483035388544326 4.324999999999999 >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 173 4.324999999999999 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 42 1.05 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 36 0.8999999999999999 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 36 0.8999999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 33 0.8250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 25 0.625 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 25 0.625 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 24 0.6 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 20 0.5 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 20 0.5 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 20 0.5 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 15 0.375 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 15 0.375 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 12 0.3 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 12 0.3 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 11 0.27499999999999997 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 11 0.27499999999999997 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 10 0.25 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 10 0.25 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 10 0.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 10 0.25 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 9 0.22499999999999998 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 9 0.22499999999999998 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 9 0.22499999999999998 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 9 0.22499999999999998 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 8 0.2 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 8 0.2 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 7 0.17500000000000002 No Hit AGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGA 7 0.17500000000000002 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 7 0.17500000000000002 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 7 0.17500000000000002 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 6 0.15 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 6 0.15 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 6 0.15 No Hit GGGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 6 0.15 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 6 0.15 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 6 0.15 No Hit GTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGA 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 6 0.15 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit CAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGG 5 0.125 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit GAGGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGG 5 0.125 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 5 0.125 No Hit CAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAA 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit CGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGA 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 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCACTA 25 2.1998705E-5 48.692856 84-85 AGCATCA 25 2.1998705E-5 48.692856 80-81 CACTAGC 25 2.1998705E-5 48.692856 86-87 ACTAGCT 25 2.1998705E-5 48.692856 86-87 GCATCAC 25 2.1998705E-5 48.692856 82-83 CATCACT 30 6.459166E-5 40.57738 82-83 TCACTAG 30 6.459166E-5 40.57738 84-85 GCAATAC 55 7.845628E-5 38.732956 7 GGGAGAG 55 7.845628E-5 38.732956 1 CAATACA 55 7.845628E-5 38.732956 8 AGAGCAA 55 7.845628E-5 38.732956 4 GAGAGCA 55 7.845628E-5 38.732956 3 AGCAATA 55 7.845628E-5 38.732956 6 GGAGAGC 60 1.3101513E-4 35.505207 2 GAGCAAT 60 1.3101513E-4 35.505207 5 AATACAA 60 1.3101513E-4 35.505207 9 AAGCATC 35 1.601587E-4 34.780617 80-81 AAAGCAT 35 1.7435019E-4 34.29075 78-79 CGAAAGC 40 4.6941492E-4 28.983843 76-77 CCGAAAG 40 4.6941492E-4 28.983843 76-77 >>END_MODULE Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67155 READS because READLEN < 1 Read 67155 spots for ERR6133327.sra Written 67155 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra Rejected 67142 READS because READLEN < 1 Read 67142 spots for ERR6133327.sra Written 67142 spots for ERR6133327.sra SRR ids: ['ERR6133327.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_tsybh0ty ERR6133327.sra spots: 1342853 blocks: [[1, 67142], [67143, 134284], [134285, 201426], [201427, 268568], [268569, 335710], [335711, 402852], [402853, 469994], [469995, 537136], [537137, 604278], [604279, 671420], [671421, 738562], [738563, 805704], [805705, 872846], [872847, 939988], [939989, 1007130], [1007131, 1074272], [1074273, 1141414], [1141415, 1208556], [1208557, 1275698], [1275699, 1342853]] ERR6133327 file size 292517 ERR6133327 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 ERR6133327 ERR6133327_1.fastq Input file: ERR6133327_1.fastq trimmed: ERR6133327-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 00:44:13 2024 >> started Sat Dec 7 00:44:14 2024 >> done (0.895s) 1342853 reads processed; of these: 83 ( 0.01%) short reads filtered out after trimming by size control 2 ( 0.00%) empty reads filtered out after trimming by size control 1342768 (99.99%) reads available; of these: 8253 ( 0.61%) trimmed reads available after processing 1334515 (99.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 20 0.00% 20 11 0.00% 21 10 0.00% 22 6 0.00% 23 5 0.00% 24 3 0.00% 25 6 0.00% 26 8 0.00% 27 8 0.00% 28 23 0.00% 29 181 0.01% 30 4 0.00% 31 12 0.00% 32 30 0.00% 33 14 0.00% 34 11 0.00% 35 36 0.00% 36 7 0.00% 37 7 0.00% 38 9 0.00% 39 38 0.00% 40 53 0.00% 41 11 0.00% 42 5 0.00% 43 14 0.00% 44 15 0.00% 45 8 0.00% 46 13 0.00% 47 7 0.00% 48 14 0.00% 49 8 0.00% 50 20 0.00% 51 40 0.00% 52 12 0.00% 53 4 0.00% 54 2 0.00% 55 8 0.00% 56 13 0.00% 57 21 0.00% 58 13 0.00% 59 9 0.00% 60 16 0.00% 61 19 0.00% 62 0 0.00% 63 8 0.00% 64 8 0.00% 65 3 0.00% 66 17 0.00% 67 21 0.00% 68 15 0.00% 69 41 0.00% 70 9414 0.70% 71 8595 0.64% 72 9287 0.69% 73 8549 0.64% 74 8391 0.62% 75 7873 0.59% 76 7770 0.58% 77 8405 0.63% 78 8593 0.64% 79 9103 0.68% 80 9120 0.68% 81 11770 0.88% 82 12344 0.92% 83 10326 0.77% 84 12313 0.92% 85 49 0.00% 86 65 0.00% 87 122 0.01% 88 151 0.01% 89 252 0.02% 90 540 0.04% 91 1190 0.09% 92 3926 0.29% 93 1193725 88.90% 1342768 reads passed initial QC criterion=sequence-density sequence-density=5.04 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=27 prefix-density=5.09 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=35.71 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=3.1 sequence=TTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATGTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACC 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 00:44:28 Started mapping on | Dec 07 00:44:28 Finished on | Dec 07 00:44:32 Mapping speed, Million of reads per hour | 1208.49 Number of input reads | 1342768 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 592902 Uniquely mapped reads % | 44.16% Average mapped length | 89.98 Number of splices: Total | 22557 Number of splices: Annotated (sjdb) | 18018 Number of splices: GT/AG | 21146 Number of splices: GC/AG | 511 Number of splices: AT/AC | 35 Number of splices: Non-canonical | 865 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.67 Insertion rate per base | 0.03% Insertion average length | 1.52 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 657119 % of reads mapped to multiple loci | 48.94% Number of reads mapped to too many loci | 60618 % of reads mapped to too many loci | 4.51% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.19% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 92747 92747 92747 N_multimapping 657119 657119 657119 N_noFeature 51765 57582 567689 N_ambiguous 22432 3024 100 UnstrandedReadsAssigned:518705 PositiveStrandReadsAssigned:532296 NegativeStrandReadsAssigned:25113 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133327 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: ERR6133327-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,342,768 reads, 823,481 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 864 rounds 52973 ERR6133327.ke.tsv 35125 ERR6133327.se.tsv 88098 total ==> ERR6133327.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 13 15.3774 PNS24243 293 194 0 0 KQK14069 1603 1504 7 7.55343 KQK14071 474 375 0 0 ==> ERR6133327.se.tsv <== BRADI_1g14170v3 7 BRADI_1g53295v3 0 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 8 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR6133327 completed mapping pipeline successfully