Starting /dee2/code/volunteer_pipeline.sh ERR6133547 current disk space = 1544515305472 free memory = 1595655344 ERR6133547 SRAfilesize 9b937df79b0913717db3c02f1f352e8a ERR6133547.sra ERR6133547.sra file validated ERR6133547 is single end ERR6133547 is conventional basespace ERR6133547 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133547_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 33.9935 37.0 33.0 37.0 33.0 37.0 2 36.02775 37.0 37.0 37.0 33.0 37.0 3 35.149 37.0 33.0 37.0 33.0 37.0 4 35.21025 37.0 37.0 37.0 33.0 37.0 5 35.198 37.0 37.0 37.0 33.0 37.0 6 35.654 37.0 37.0 37.0 33.0 37.0 7 37.3485 37.0 37.0 40.0 33.0 40.0 8 37.4165 37.0 37.0 40.0 33.0 40.0 9 37.4245 37.0 37.0 40.0 33.0 40.0 10-11 37.407250000000005 37.0 37.0 40.0 33.0 40.0 12-13 37.289 37.0 37.0 40.0 33.0 40.0 14-15 37.329499999999996 37.0 37.0 40.0 33.0 40.0 16-17 37.184625 37.0 37.0 40.0 33.0 40.0 18-19 37.14175 37.0 37.0 40.0 33.0 40.0 20-21 37.03175 37.0 37.0 40.0 33.0 40.0 22-23 36.94225 37.0 37.0 40.0 33.0 40.0 24-25 37.051125 37.0 37.0 40.0 33.0 40.0 26-27 36.981875 37.0 37.0 40.0 33.0 40.0 28-29 36.915 37.0 37.0 40.0 33.0 40.0 30-31 36.918125 37.0 37.0 40.0 33.0 40.0 32-33 36.747749999999996 37.0 37.0 40.0 33.0 40.0 34-35 36.5185 37.0 37.0 40.0 33.0 40.0 36-37 36.3455 37.0 37.0 40.0 33.0 40.0 38-39 36.30275 37.0 37.0 40.0 33.0 40.0 40-41 35.9845 37.0 37.0 40.0 33.0 40.0 42-43 35.9045 37.0 37.0 40.0 33.0 40.0 44-45 35.61125 37.0 33.0 37.0 33.0 40.0 46-47 35.2055 37.0 33.0 37.0 30.0 40.0 48-49 35.158875 37.0 33.0 37.0 30.0 40.0 50-51 35.144000000000005 37.0 33.0 37.0 33.0 40.0 52-53 34.810125 37.0 33.0 37.0 27.0 40.0 54-55 34.795500000000004 37.0 33.0 37.0 27.0 38.5 56-57 34.617625000000004 37.0 33.0 37.0 27.0 37.0 58-59 34.01575 37.0 33.0 37.0 27.0 37.0 60-61 34.286500000000004 37.0 33.0 37.0 27.0 37.0 62-63 34.191 37.0 33.0 37.0 27.0 37.0 64-65 34.211125 37.0 33.0 37.0 27.0 37.0 66-67 34.354875 37.0 33.0 37.0 30.0 37.0 68-69 33.43175 35.0 33.0 37.0 27.0 37.0 70-71 33.58939080100125 35.0 33.0 37.0 27.0 37.0 72-73 34.006677822963695 37.0 33.0 37.0 27.0 37.0 74-75 33.88358690531069 37.0 33.0 37.0 27.0 37.0 76-77 33.95011653975249 37.0 33.0 37.0 27.0 37.0 78-79 34.02002379413844 37.0 33.0 37.0 27.0 37.0 80-81 33.906005159779454 37.0 33.0 37.0 27.0 37.0 82-83 33.763036572993 37.0 33.0 37.0 27.0 37.0 84-85 33.687503279536934 37.0 33.0 37.0 27.0 37.0 86-87 33.5955185659411 37.0 33.0 37.0 27.0 37.0 88-89 33.557490396927015 37.0 33.0 37.0 27.0 37.0 90-91 33.21882202304738 37.0 33.0 37.0 27.0 37.0 92-93 33.16133162612036 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 21.0 21 19.0 22 12.0 23 19.0 24 26.0 25 40.0 26 40.0 27 36.0 28 65.0 29 84.0 30 90.0 31 110.0 32 149.0 33 192.0 34 243.0 35 402.0 36 965.0 37 913.0 38 567.0 39 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 90.675 1.725 2.475 5.125 2 75.97500000000001 14.325 5.8500000000000005 3.85 3 36.375 38.525 13.425 11.675 4 34.625 28.1 17.474999999999998 19.8 5 25.074999999999996 31.225 25.95 17.75 6 19.875 38.9 23.625 17.599999999999998 7 38.0 29.825000000000003 18.4 13.775 8 31.8 30.25 22.900000000000002 15.049999999999999 9 27.800000000000004 27.35 26.5 18.35 10-11 26.6 27.0625 27.450000000000003 18.8875 12-13 28.712500000000002 25.775 26.974999999999998 18.5375 14-15 22.3 31.112499999999997 27.200000000000003 19.3875 16-17 24.4375 32.3875 24.3125 18.862499999999997 18-19 23.4125 27.400000000000002 27.9375 21.25 20-21 25.640705088136016 25.84073009126141 27.69096137017127 20.827603450431305 22-23 27.650000000000002 23.0625 27.400000000000002 21.8875 24-25 26.150000000000002 24.8125 27.925 21.1125 26-27 26.1 24.5 30.912499999999998 18.4875 28-29 26.650000000000002 27.0875 26.825 19.4375 30-31 26.450000000000003 26.174999999999997 26.4625 20.9125 32-33 24.85 26.575 27.8625 20.7125 34-35 25.56597873671044 26.729205753596 26.40400250156348 21.30081300813008 36-37 25.4625 24.075 28.349999999999998 22.112499999999997 38-39 26.0375 25.137500000000003 29.349999999999998 19.475 40-41 27.913956978489246 24.23711855927964 26.575787893946973 21.273136568284144 42-43 25.359689728512446 27.699236832228202 26.2729888652571 20.66808457400225 44-45 23.839899937460913 26.19136960600375 29.255784865540964 20.712945590994373 46-47 25.162499999999998 24.5 27.8625 22.475 48-49 25.103137892236532 25.2281535191899 29.566195774471808 20.102512814101765 50-51 25.1 25.674999999999997 28.9875 20.2375 52-53 25.41609310474284 26.94281066199474 27.030409210361654 20.610687022900763 54-55 25.2875 27.125 27.987499999999997 19.6 56-57 27.1375 24.9 28.487499999999997 19.475 58-59 25.25 24.1625 28.375 22.2125 60-61 25.174999999999997 25.662499999999998 29.599999999999998 19.5625 62-63 22.75 27.35 31.6 18.3 64-65 23.3375 27.650000000000002 29.15 19.8625 66-67 24.9125 26.55 27.712500000000002 20.825 68-69 21.987499999999997 28.012500000000003 28.0875 21.912499999999998 70-71 25.115697310819264 26.178861788617887 28.180112570356474 20.52532833020638 72-73 26.505268439538384 24.473156046161566 28.173607626693425 20.84796788760662 74-75 23.762126748141615 26.281970517827897 30.175129141993196 19.780773592037292 76-77 23.44243649690383 25.944648047516743 29.293567547074435 21.319347908504994 78-79 23.461635857179033 24.271967586730817 31.40035452013168 20.866042035958472 80-81 23.96956246036779 28.9283449587825 27.85034876347495 19.251743817374763 82-83 22.425862288405245 26.829578719613085 29.858724704085525 20.885834287896145 84-85 24.824146310269857 22.854584985292238 31.090932344289552 21.230336360148357 86-87 23.213828425096033 25.92829705505762 30.84507042253521 20.01280409731114 88-89 21.895006402048654 28.706786171574905 29.308578745198467 20.089628681177977 90-91 26.325224071702948 25.58258642765685 28.297055057618437 19.795134443021766 92-93 23.649167733674776 30.499359795134446 27.464788732394368 18.386683738796414 >>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 0.0 17 7.0 18 10.5 19 4.5 20 2.0 21 2.0 22 2.5 23 5.0 24 5.0 25 4.0 26 5.0 27 5.0 28 14.0 29 23.0 30 24.0 31 25.5 32 39.0 33 55.0 34 63.0 35 77.0 36 91.5 37 114.0 38 168.0 39 183.5 40 177.0 41 210.5 42 232.5 43 234.5 44 213.0 45 200.5 46 215.0 47 187.0 48 161.0 49 165.0 50 164.0 51 156.0 52 148.0 53 158.5 54 132.0 55 90.5 56 72.5 57 62.5 58 57.0 59 52.5 60 42.5 61 30.5 62 30.0 63 30.5 64 35.0 65 34.5 66 27.0 67 21.5 68 18.0 69 16.5 70 12.5 71 10.0 72 7.0 73 3.5 74 3.5 75 4.0 76 2.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 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 0.0125 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 0.0625 36-37 0.0 38-39 0.0 40-41 0.05 42-43 0.08750000000000001 44-45 0.0625 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.11249999999999999 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 5.0 71 6.0 72 6.0 73 11.0 74 7.0 75 6.0 76 5.0 77 3.0 78 4.0 79 2.0 80 5.0 81 6.0 82 11.0 83 9.0 84 9.0 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 3905.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.425 #Duplication Level Percentage of deduplicated Percentage of total 1 91.77558176601849 71.975 2 4.781638508128785 7.5 3 1.5620019126554032 3.675 4 0.4781638508128785 1.5 5 0.22314313037934333 0.8750000000000001 6 0.19126554032515142 0.8999999999999999 7 0.1275103602167676 0.7000000000000001 8 0.1275103602167676 0.8 9 0.0318775900541919 0.22499999999999998 >10 0.66942939113803 10.325 >50 0.0318775900541919 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 49 1.225 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 44 1.0999999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 35 0.8750000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 29 0.7250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 27 0.675 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 22 0.5499999999999999 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 21 0.525 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 20 0.5 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 18 0.44999999999999996 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 15 0.375 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 15 0.375 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 12 0.3 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 10 0.25 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 7 0.17500000000000002 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 6 0.15 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCG 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GGGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAA 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 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 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATTTCA 20 0.0027298967 65.25 7 CAATTTC 20 0.0027298967 65.25 6 GGATTCA 20 0.0027298967 65.25 1 TTTCAAC 20 0.0027298967 65.25 9 TCAATTT 20 0.0027298967 65.25 5 ATTTCAA 20 0.0027298967 65.25 8 ATTCAAT 20 0.0027298967 65.25 3 TTCAATT 25 0.006606883 52.2 4 GATTCAA 25 0.006606883 52.2 2 >>END_MODULE Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96364 READS because READLEN < 1 Read 96364 spots for ERR6133547.sra Written 96364 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra Rejected 96355 READS because READLEN < 1 Read 96355 spots for ERR6133547.sra Written 96355 spots for ERR6133547.sra SRR ids: ['ERR6133547.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ixu85kds ERR6133547.sra spots: 1927109 blocks: [[1, 96355], [96356, 192710], [192711, 289065], [289066, 385420], [385421, 481775], [481776, 578130], [578131, 674485], [674486, 770840], [770841, 867195], [867196, 963550], [963551, 1059905], [1059906, 1156260], [1156261, 1252615], [1252616, 1348970], [1348971, 1445325], [1445326, 1541680], [1541681, 1638035], [1638036, 1734390], [1734391, 1830745], [1830746, 1927109]] ERR6133547 file size 425405 ERR6133547 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 ERR6133547 ERR6133547_1.fastq Input file: ERR6133547_1.fastq trimmed: ERR6133547-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 08:24:28 2024 >> started Sat Dec 7 08:24:29 2024 >> done (1.013s) 1927109 reads processed; of these: 63 ( 0.00%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 1927037 (100.00%) reads available; of these: 35449 ( 1.84%) trimmed reads available after processing 1891588 (98.16%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 30 0.00% 20 13 0.00% 21 8 0.00% 22 8 0.00% 23 0 0.00% 24 2 0.00% 25 1 0.00% 26 1 0.00% 27 4 0.00% 28 11 0.00% 29 141 0.01% 30 5 0.00% 31 6 0.00% 32 8 0.00% 33 1 0.00% 34 4 0.00% 35 21 0.00% 36 224 0.01% 37 4 0.00% 38 12 0.00% 39 19 0.00% 40 38 0.00% 41 8 0.00% 42 4 0.00% 43 5 0.00% 44 7 0.00% 45 3 0.00% 46 3 0.00% 47 3 0.00% 48 2 0.00% 49 1 0.00% 50 2 0.00% 51 29 0.00% 52 3 0.00% 53 6 0.00% 54 2 0.00% 55 3 0.00% 56 2 0.00% 57 5 0.00% 58 2 0.00% 59 3 0.00% 60 1 0.00% 61 2 0.00% 62 1 0.00% 63 3 0.00% 64 0 0.00% 65 2 0.00% 66 1 0.00% 67 7 0.00% 68 19 0.00% 69 41 0.00% 70 3030 0.16% 71 2831 0.15% 72 3049 0.16% 73 2885 0.15% 74 3063 0.16% 75 2933 0.15% 76 2645 0.14% 77 2795 0.15% 78 3231 0.17% 79 3545 0.18% 80 3402 0.18% 81 4039 0.21% 82 4488 0.23% 83 4188 0.22% 84 4094 0.21% 85 89 0.00% 86 146 0.01% 87 246 0.01% 88 485 0.03% 89 924 0.05% 90 1968 0.10% 91 5792 0.30% 92 24264 1.26% 93 1842168 95.60% 1927037 reads passed initial QC criterion=sequence-density sequence-density=0.61 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=30 prefix-density=0.62 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.06 sequence-density-rank=15 fanout-score=36.77 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=12.7 sequence=TTTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA Started job on | Dec 07 08:24:41 Started mapping on | Dec 07 08:24:41 Finished on | Dec 07 08:24:45 Mapping speed, Million of reads per hour | 1734.33 Number of input reads | 1927037 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1326772 Uniquely mapped reads % | 68.85% Average mapped length | 92.21 Number of splices: Total | 65318 Number of splices: Annotated (sjdb) | 54627 Number of splices: GT/AG | 62697 Number of splices: GC/AG | 1481 Number of splices: AT/AC | 45 Number of splices: Non-canonical | 1095 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 1.70 Insertion rate per base | 0.02% Insertion average length | 1.88 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 543297 % of reads mapped to multiple loci | 28.19% Number of reads mapped to too many loci | 30094 % of reads mapped to too many loci | 1.56% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.30% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 56968 56968 56968 N_multimapping 543297 543297 543297 N_noFeature 87733 100626 1268689 N_ambiguous 52362 7173 157 UnstrandedReadsAssigned:1186677 PositiveStrandReadsAssigned:1218973 NegativeStrandReadsAssigned:57926 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133547 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: ERR6133547-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,927,037 reads, 1,589,583 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,001 rounds 52973 ERR6133547.ke.tsv 35125 ERR6133547.se.tsv 88098 total ==> ERR6133547.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 45 26.7647 PNS24243 293 194 0 0 KQK14069 1603 1504 21 11.394 KQK14071 474 375 0 0 ==> ERR6133547.se.tsv <== BRADI_1g14170v3 21 BRADI_1g53295v3 26 BRADI_1g59795v3 15 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 30 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 40 BRADI_1g48960v3 0 ERR6133547 completed mapping pipeline successfully