Starting /dee2/code/volunteer_pipeline.sh ERR6133494 current disk space = 1544545943552 free memory = 1604456816 ERR6133494 SRAfilesize cad171af721c762bd3db65b6c048e5f7 ERR6133494.sra ERR6133494.sra file validated ERR6133494 is single end ERR6133494 is conventional basespace ERR6133494 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133494_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.51675 37.0 33.0 37.0 33.0 37.0 2 36.44325 37.0 37.0 37.0 37.0 37.0 3 35.7685 37.0 37.0 37.0 33.0 37.0 4 35.0755 37.0 37.0 37.0 33.0 37.0 5 35.12675 37.0 37.0 37.0 33.0 37.0 6 35.49575 37.0 37.0 37.0 33.0 37.0 7 37.262 37.0 37.0 40.0 33.0 40.0 8 37.27425 37.0 37.0 40.0 33.0 40.0 9 37.2675 37.0 37.0 40.0 33.0 40.0 10-11 37.302125000000004 37.0 37.0 40.0 33.0 40.0 12-13 37.195 37.0 37.0 40.0 33.0 40.0 14-15 37.187875 37.0 37.0 40.0 33.0 40.0 16-17 37.115624999999994 37.0 37.0 40.0 33.0 40.0 18-19 36.976375000000004 37.0 37.0 40.0 33.0 40.0 20-21 36.7145 37.0 37.0 40.0 33.0 40.0 22-23 36.68875 37.0 37.0 40.0 33.0 40.0 24-25 36.505875 37.0 37.0 40.0 33.0 40.0 26-27 36.838125 37.0 37.0 40.0 33.0 40.0 28-29 36.767875000000004 37.0 37.0 40.0 33.0 40.0 30-31 36.8105 37.0 37.0 40.0 33.0 40.0 32-33 36.763999999999996 37.0 37.0 40.0 33.0 40.0 34-35 36.67725 37.0 37.0 40.0 33.0 40.0 36-37 36.4105 37.0 37.0 40.0 33.0 40.0 38-39 36.292874999999995 37.0 37.0 40.0 33.0 40.0 40-41 36.171375 37.0 37.0 40.0 33.0 40.0 42-43 36.152625 37.0 37.0 40.0 33.0 40.0 44-45 36.134625 37.0 37.0 40.0 33.0 40.0 46-47 35.961125 37.0 37.0 40.0 33.0 40.0 48-49 35.96 37.0 37.0 37.0 33.0 40.0 50-51 35.861375 37.0 35.0 37.0 33.0 40.0 52-53 35.609375 37.0 33.0 37.0 33.0 40.0 54-55 35.424375 37.0 33.0 37.0 33.0 40.0 56-57 35.308375 37.0 33.0 37.0 33.0 40.0 58-59 34.358375 37.0 33.0 37.0 27.0 37.0 60-61 34.812875 37.0 33.0 37.0 33.0 37.0 62-63 34.766375 37.0 33.0 37.0 33.0 37.0 64-65 34.740375 37.0 33.0 37.0 33.0 37.0 66-67 34.620999999999995 37.0 33.0 37.0 33.0 37.0 68-69 33.842749999999995 35.0 33.0 37.0 30.0 37.0 70-71 34.00083753784057 35.0 33.0 37.0 27.0 37.0 72-73 34.37149618689482 37.0 33.0 37.0 30.0 37.0 74-75 34.2761600874134 37.0 33.0 37.0 30.0 37.0 76-77 34.175879644523434 37.0 33.0 37.0 30.0 37.0 78-79 34.1334152665289 37.0 33.0 37.0 30.0 37.0 80-81 34.07678174534868 37.0 33.0 37.0 27.0 37.0 82-83 33.97097150708843 37.0 33.0 37.0 27.0 37.0 84-85 33.721762078342394 37.0 33.0 37.0 27.0 37.0 86-87 33.77136627906977 37.0 33.0 37.0 27.0 37.0 88-89 33.74825581395349 37.0 33.0 37.0 27.0 37.0 90-91 33.49563953488372 37.0 33.0 37.0 27.0 37.0 92-93 33.48953488372093 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 8.0 22 19.0 23 20.0 24 26.0 25 32.0 26 28.0 27 44.0 28 42.0 29 58.0 30 70.0 31 113.0 32 129.0 33 177.0 34 236.0 35 471.0 36 950.0 37 882.0 38 653.0 39 30.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.575 2.45 2.025 6.950000000000001 2 71.65 16.950000000000003 7.175 4.2250000000000005 3 36.475 39.574999999999996 14.224999999999998 9.725 4 32.2 27.675 21.725 18.4 5 25.4 29.95 26.950000000000003 17.7 6 21.45 36.95 26.700000000000003 14.899999999999999 7 34.725 28.975 20.9 15.4 8 29.849999999999998 31.85 23.799999999999997 14.499999999999998 9 27.375 28.825 28.15 15.65 10-11 27.037499999999998 28.6875 28.487499999999997 15.787499999999998 12-13 26.875 27.474999999999998 30.099999999999998 15.55 14-15 21.087500000000002 29.875 30.85 18.1875 16-17 22.7125 32.35 26.424999999999997 18.512500000000003 18-19 23.825 26.237500000000004 30.0 19.9375 20-21 24.30303787973497 26.040755094386796 30.116264533066634 19.5399424928116 22-23 25.8 25.424999999999997 28.8375 19.9375 24-25 23.962500000000002 26.1 29.675 20.2625 26-27 24.875 24.3 30.9375 19.8875 28-29 24.0625 27.1125 30.225 18.6 30-31 25.0375 24.9 29.599999999999998 20.4625 32-33 24.725 25.412499999999998 30.125 19.7375 34-35 22.4875 26.825 29.95 20.7375 36-37 24.25 27.1625 27.5875 21.0 38-39 24.401253918495296 25.19122257053292 31.09717868338558 19.310344827586206 40-41 25.178504321683576 25.153451083552547 28.773643993486157 20.894400601277717 42-43 23.942957217913435 27.820865649236925 29.02176632474356 19.21441080810608 44-45 22.0125 27.4125 30.9875 19.5875 46-47 23.275000000000002 26.525 29.225 20.974999999999998 48-49 22.5125 27.0625 30.8125 19.6125 50-51 23.0875 27.575 29.849999999999998 19.4875 52-53 22.547914317925592 29.036702993861958 28.999123136665418 19.41625955154704 54-55 21.925 29.025000000000002 30.5125 18.5375 56-57 23.599999999999998 27.425 29.8875 19.0875 58-59 23.275000000000002 28.262500000000003 29.799999999999997 18.6625 60-61 24.0125 27.212500000000002 29.9625 18.8125 62-63 22.2 28.775000000000002 30.9625 18.0625 64-65 23.275000000000002 28.9875 28.9 18.8375 66-67 22.4375 29.9 29.1875 18.475 68-69 20.9875 27.3625 30.825000000000003 20.825 70-71 22.388247112004017 27.78754394776494 30.19839276745354 19.625816172777498 72-73 24.348825331971398 26.762002042900917 30.656281920326865 18.232890704800816 74-75 23.2564202841872 27.102072741493938 29.99608916699257 19.645417807326293 76-77 22.922750199097425 27.435625165914523 30.355720732678527 19.28590390230953 78-79 22.994869025114774 27.31568998109641 30.529300567107747 19.160140426681068 80-81 22.132161011127902 29.674405824975956 29.674405824975956 18.519027338920182 82-83 22.251897666572955 27.01714928310374 30.011245431543436 20.71970761877987 84-85 22.787003610108304 27.10469314079422 31.00361010830325 19.104693140794225 86-87 20.218023255813954 29.127906976744182 30.58139534883721 20.072674418604652 88-89 21.25 30.63953488372093 30.23255813953488 17.87790697674419 90-91 23.415697674418603 30.82848837209302 27.601744186046513 18.15406976744186 92-93 20.61046511627907 32.00581395348837 29.273255813953487 18.11046511627907 >>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 0.5 16 0.5 17 3.0 18 5.0 19 3.5 20 2.0 21 1.5 22 1.5 23 3.0 24 5.5 25 9.0 26 12.5 27 18.0 28 34.0 29 45.0 30 46.0 31 57.5 32 89.0 33 117.0 34 120.5 35 140.0 36 166.0 37 197.5 38 231.0 39 237.5 40 237.0 41 228.5 42 216.0 43 210.5 44 203.0 45 204.0 46 197.0 47 164.0 48 150.5 49 134.5 50 102.5 51 95.5 52 93.0 53 93.5 54 100.5 55 79.5 56 67.5 57 73.0 58 52.0 59 33.5 60 30.0 61 21.5 62 17.5 63 17.5 64 14.5 65 14.5 66 12.5 67 10.0 68 10.0 69 9.5 70 9.5 71 8.0 72 9.0 73 8.0 74 3.0 75 0.0 76 0.0 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 0.0125 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 0.0 36-37 0.0 38-39 0.3125 40-41 0.21250000000000002 42-43 0.075 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.21250000000000002 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 36.0 71 27.0 72 42.0 73 43.0 74 33.0 75 34.0 76 36.0 77 31.0 78 30.0 79 33.0 80 31.0 81 43.0 82 48.0 83 48.0 84 45.0 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 3440.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.925 #Duplication Level Percentage of deduplicated Percentage of total 1 92.40158681721087 75.7 2 4.11962160512664 6.75 3 1.190112908147696 2.9250000000000003 4 0.7628928898382668 2.5 5 0.366188587122368 1.5 6 0.21361000915471468 1.05 7 0.15257857796765334 0.8750000000000001 8 0.12206286237412267 0.8 9 0.21361000915471468 1.575 >10 0.45773573390296 6.325 >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 warn #Sequence Count Percentage Possible Source GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 33 0.8250000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 31 0.775 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 26 0.65 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 18 0.44999999999999996 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 17 0.42500000000000004 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 16 0.4 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 16 0.4 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 13 0.325 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 13 0.325 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 13 0.325 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 11 0.27499999999999997 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 9 0.22499999999999998 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 9 0.22499999999999998 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 9 0.22499999999999998 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 7 0.17500000000000002 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 7 0.17500000000000002 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 7 0.17500000000000002 No Hit GGGTGTCAATATATGATGATGTGTTGTTATAATGTACGCGCCTGCAAACT 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGGGAGAAGTCTTATGTTATATATGGTAATCGCCTTGCCTATAGTGCCCG 5 0.125 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 5 0.125 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTACCTGCT 5 0.125 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 5 0.125 No Hit GGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAA 5 0.125 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 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 0.025 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 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260866 READS because READLEN < 1 Read 260866 spots for ERR6133494.sra Written 260866 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra Rejected 260847 READS because READLEN < 1 Read 260847 spots for ERR6133494.sra Written 260847 spots for ERR6133494.sra SRR ids: ['ERR6133494.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7qfz6j72 ERR6133494.sra spots: 5216959 blocks: [[1, 260847], [260848, 521694], [521695, 782541], [782542, 1043388], [1043389, 1304235], [1304236, 1565082], [1565083, 1825929], [1825930, 2086776], [2086777, 2347623], [2347624, 2608470], [2608471, 2869317], [2869318, 3130164], [3130165, 3391011], [3391012, 3651858], [3651859, 3912705], [3912706, 4173552], [4173553, 4434399], [4434400, 4695246], [4695247, 4956093], [4956094, 5216959]] ERR6133494 file size 1135552 ERR6133494 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 ERR6133494 ERR6133494_1.fastq Input file: ERR6133494_1.fastq trimmed: ERR6133494-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 07:14:53 2024 >> started Sat Dec 7 07:14:56 2024 >> done (2.799s) 5216959 reads processed; of these: 312 ( 0.01%) short reads filtered out after trimming by size control 32 ( 0.00%) empty reads filtered out after trimming by size control 5216615 (99.99%) reads available; of these: 81833 ( 1.57%) trimmed reads available after processing 5134782 (98.43%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 72 0.00% 19 193 0.00% 20 59 0.00% 21 39 0.00% 22 66 0.00% 23 17 0.00% 24 25 0.00% 25 26 0.00% 26 18 0.00% 27 21 0.00% 28 54 0.00% 29 108 0.00% 30 19 0.00% 31 38 0.00% 32 66 0.00% 33 47 0.00% 34 54 0.00% 35 305 0.01% 36 819 0.02% 37 78 0.00% 38 173 0.00% 39 274 0.01% 40 500 0.01% 41 85 0.00% 42 44 0.00% 43 48 0.00% 44 65 0.00% 45 35 0.00% 46 33 0.00% 47 15 0.00% 48 17 0.00% 49 26 0.00% 50 30 0.00% 51 201 0.00% 52 42 0.00% 53 22 0.00% 54 19 0.00% 55 15 0.00% 56 17 0.00% 57 44 0.00% 58 54 0.00% 59 18 0.00% 60 73 0.00% 61 34 0.00% 62 12 0.00% 63 2 0.00% 64 9 0.00% 65 20 0.00% 66 26 0.00% 67 47 0.00% 68 108 0.00% 69 430 0.01% 70 54961 1.05% 71 49574 0.95% 72 51413 0.99% 73 48077 0.92% 74 48314 0.93% 75 45830 0.88% 76 41850 0.80% 77 44984 0.86% 78 49065 0.94% 79 51090 0.98% 80 49411 0.95% 81 59412 1.14% 82 64879 1.24% 83 58536 1.12% 84 60136 1.15% 85 134 0.00% 86 235 0.00% 87 352 0.01% 88 686 0.01% 89 1528 0.03% 90 3068 0.06% 91 10077 0.19% 92 49618 0.95% 93 4368723 83.75% 5216615 reads passed initial QC criterion=sequence-density sequence-density=2.93 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=33 prefix-density=2.94 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.04 sequence-density-rank=15 fanout-score=104.93 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=15.3 sequence=TTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA 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 07:15:25 Started mapping on | Dec 07 07:15:25 Finished on | Dec 07 07:15:33 Mapping speed, Million of reads per hour | 2347.48 Number of input reads | 5216615 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 3620421 Uniquely mapped reads % | 69.40% Average mapped length | 89.87 Number of splices: Total | 89918 Number of splices: Annotated (sjdb) | 73189 Number of splices: GT/AG | 84743 Number of splices: GC/AG | 2312 Number of splices: AT/AC | 64 Number of splices: Non-canonical | 2799 Mismatch rate per base, % | 0.54% Deletion rate per base | 0.05% Deletion average length | 1.84 Insertion rate per base | 0.02% Insertion average length | 1.68 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1306641 % of reads mapped to multiple loci | 25.05% Number of reads mapped to too many loci | 174581 % of reads mapped to too many loci | 3.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.00% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 289553 289553 289553 N_multimapping 1306641 1306641 1306641 N_noFeature 312002 354712 3446160 N_ambiguous 154566 22859 1015 UnstrandedReadsAssigned:3153853 PositiveStrandReadsAssigned:3242850 NegativeStrandReadsAssigned:173246 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133494 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: ERR6133494-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,216,615 reads, 3,939,486 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,060 rounds 52973 ERR6133494.ke.tsv 35125 ERR6133494.se.tsv 88098 total ==> ERR6133494.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 96 25.2312 PNS24243 293 194 0 0 KQK14069 1603 1504 268 64.255 KQK14071 474 375 0 0 ==> ERR6133494.se.tsv <== BRADI_1g14170v3 268 BRADI_1g53295v3 50 BRADI_1g59795v3 67 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 35 BRADI_1g74790v3 50 BRADI_1g09890v3 1 BRADI_1g77505v3 94 BRADI_1g48960v3 0 ERR6133494 completed mapping pipeline successfully