Starting /dee2/code/volunteer_pipeline.sh ERR6133313 current disk space = 1548084211712 free memory = 1422296292 ERR6133313 SRAfilesize 263135c7f1d449f5c04ed2bc1bb3e423 ERR6133313.sra ERR6133313.sra file validated ERR6133313 is single end ERR6133313 is conventional basespace ERR6133313 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133313_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 35.131 37.0 33.0 37.0 33.0 37.0 2 36.379 37.0 37.0 37.0 33.0 37.0 3 35.87925 37.0 37.0 37.0 33.0 37.0 4 35.3875 37.0 37.0 37.0 33.0 37.0 5 35.369 37.0 37.0 37.0 33.0 37.0 6 35.623 37.0 37.0 37.0 33.0 37.0 7 37.283 37.0 37.0 40.0 33.0 40.0 8 37.33575 37.0 37.0 40.0 33.0 40.0 9 37.38725 37.0 37.0 40.0 33.0 40.0 10-11 37.225 37.0 37.0 40.0 33.0 40.0 12-13 37.18025 37.0 37.0 40.0 33.0 40.0 14-15 37.13975 37.0 37.0 40.0 33.0 40.0 16-17 37.023375 37.0 37.0 40.0 33.0 40.0 18-19 36.922625 37.0 37.0 40.0 33.0 40.0 20-21 36.761250000000004 37.0 37.0 40.0 33.0 40.0 22-23 36.654125 37.0 37.0 40.0 33.0 40.0 24-25 36.790625000000006 37.0 37.0 40.0 33.0 40.0 26-27 36.819874999999996 37.0 37.0 40.0 33.0 40.0 28-29 36.6975 37.0 37.0 40.0 33.0 40.0 30-31 36.631249999999994 37.0 37.0 40.0 33.0 40.0 32-33 36.52825 37.0 37.0 40.0 33.0 40.0 34-35 36.454625 37.0 37.0 40.0 33.0 40.0 36-37 36.328375 37.0 37.0 40.0 33.0 40.0 38-39 36.03425 37.0 35.0 40.0 33.0 40.0 40-41 35.867999999999995 37.0 33.0 40.0 33.0 40.0 42-43 35.576375 37.0 33.0 40.0 27.0 40.0 44-45 35.334875 37.0 33.0 40.0 27.0 40.0 46-47 34.85825 37.0 33.0 37.0 27.0 40.0 48-49 34.844375 37.0 33.0 37.0 27.0 40.0 50-51 34.729875 37.0 33.0 37.0 27.0 40.0 52-53 34.4205 37.0 33.0 37.0 27.0 40.0 54-55 34.396 37.0 33.0 37.0 27.0 40.0 56-57 34.17425 37.0 33.0 37.0 27.0 38.5 58-59 31.799 33.0 30.0 37.0 24.5 37.0 60-61 33.339625 35.0 33.0 37.0 27.0 37.0 62-63 33.515375 37.0 33.0 37.0 27.0 37.0 64-65 33.310875 37.0 33.0 37.0 27.0 37.0 66-67 33.12925 37.0 33.0 37.0 27.0 37.0 68-69 32.546625 35.0 33.0 37.0 24.5 37.0 70-71 32.607141305716446 33.0 33.0 37.0 27.0 37.0 72-73 32.96903799443842 35.0 33.0 37.0 27.0 37.0 74-75 32.86268140609883 37.0 33.0 37.0 27.0 37.0 76-77 32.93282007145924 37.0 33.0 37.0 27.0 37.0 78-79 33.04061160051571 35.0 33.0 37.0 27.0 37.0 80-81 33.03791574345251 33.0 33.0 37.0 27.0 37.0 82-83 32.847860880161065 33.0 33.0 37.0 27.0 37.0 84-85 32.518719722971085 33.0 33.0 37.0 27.0 37.0 86-87 32.49028716216216 33.0 33.0 37.0 24.5 37.0 88-89 32.501126126126124 33.0 33.0 37.0 24.5 37.0 90-91 32.23620495495496 33.0 33.0 37.0 22.0 37.0 92-93 32.265484234234236 33.0 33.0 37.0 24.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 18.0 21 26.0 22 35.0 23 35.0 24 40.0 25 41.0 26 55.0 27 62.0 28 71.0 29 74.0 30 119.0 31 149.0 32 166.0 33 202.0 34 287.0 35 445.0 36 750.0 37 874.0 38 535.0 39 16.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 85.02499999999999 3.4250000000000003 3.5249999999999995 8.025 2 67.27499999999999 18.3 9.675 4.75 3 33.5 39.825 15.7 10.975 4 29.599999999999998 27.6 21.65 21.15 5 22.025 31.7 30.425 15.85 6 18.8 36.05 28.000000000000004 17.150000000000002 7 35.05 29.525000000000002 21.05 14.374999999999998 8 24.875 31.275 27.775 16.075 9 25.35 26.5 30.875000000000004 17.275 10-11 23.9125 27.987499999999997 29.95 18.15 12-13 24.825 26.7125 29.812499999999996 18.65 14-15 19.8 29.5375 31.825 18.8375 16-17 22.6125 31.4 25.912499999999998 20.075000000000003 18-19 22.537499999999998 27.1625 30.4625 19.8375 20-21 24.190523815476936 25.440680085010626 28.91611451431429 21.45268158519815 22-23 26.55 23.7875 28.3875 21.275 24-25 25.8125 26.375 28.449999999999996 19.3625 26-27 23.674999999999997 24.887500000000003 31.324999999999996 20.1125 28-29 22.95 29.037499999999998 29.262500000000003 18.75 30-31 24.3625 25.7 29.525000000000002 20.4125 32-33 23.2125 26.275 31.2125 19.3 34-35 22.35 28.6625 28.025 20.962500000000002 36-37 25.128141017627204 26.828353544193025 27.17839729966246 20.865108138517314 38-39 25.32199574840565 25.97223958984619 30.486432412154556 18.2193322495936 40-41 25.275 25.4625 28.299999999999997 20.962500000000002 42-43 23.6625 28.4375 29.4875 18.4125 44-45 21.775 26.787499999999998 31.525 19.9125 46-47 23.3 27.3625 27.9375 21.4 48-49 23.425 26.3 31.4375 18.8375 50-51 22.611305652826413 26.3631815907954 30.927963981990995 20.097548774387196 52-53 23.276185708922537 29.833562758102865 27.218120385433615 19.672131147540984 54-55 22.125 29.099999999999998 31.75 17.025000000000002 56-57 24.1875 28.012500000000003 29.375 18.425 58-59 23.150000000000002 26.650000000000002 30.0375 20.1625 60-61 23.0625 27.750000000000004 30.225 18.9625 62-63 21.3625 29.799999999999997 31.374999999999996 17.4625 64-65 22.5625 29.812499999999996 29.6375 17.9875 66-67 22.8875 29.299999999999997 29.425 18.387500000000003 68-69 20.9 28.499999999999996 29.7875 20.8125 70-71 23.20913310751474 27.51223184042153 29.356417011667297 19.922218040396437 72-73 23.7029501525941 26.907426246185146 30.23906408952187 19.15055951169888 74-75 23.29984544049459 27.344152498712006 29.997424008243172 19.358578052550232 76-77 23.338566195709053 28.2312925170068 28.414442700156982 20.015698587127158 78-79 22.723652774090787 27.063976639235467 31.4839394743828 18.72843111229095 80-81 21.42664872139973 30.16150740242261 29.90578734858681 18.506056527590847 82-83 21.831955922865014 27.768595041322314 30.88154269972452 19.517906336088153 84-85 21.86229140373019 25.045575655588276 32.94068153134202 20.151451409339504 86-87 21.25563063063063 27.29448198198198 30.96846846846847 20.48141891891892 88-89 19.77759009009009 30.194256756756754 31.12331081081081 18.90484234234234 90-91 24.42286036036036 29.51858108108108 28.85698198198198 17.201576576576578 92-93 19.960585585585587 33.86824324324324 29.03997747747748 17.131193693693696 >>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 3.5 18 4.0 19 2.0 20 1.5 21 0.5 22 4.0 23 11.5 24 14.0 25 11.5 26 18.5 27 26.5 28 28.0 29 28.0 30 38.0 31 63.0 32 79.5 33 95.0 34 115.0 35 134.5 36 158.5 37 218.5 38 266.5 39 233.5 40 215.0 41 215.5 42 240.0 43 278.0 44 226.5 45 180.5 46 167.5 47 147.0 48 141.0 49 134.0 50 128.5 51 103.0 52 89.5 53 111.5 54 109.5 55 80.0 56 65.0 57 66.0 58 55.0 59 32.0 60 23.5 61 20.5 62 11.5 63 12.0 64 11.5 65 8.0 66 6.5 67 5.0 68 6.0 69 8.0 70 8.5 71 7.0 72 8.0 73 6.0 74 2.0 75 1.0 76 1.5 77 1.5 78 0.5 79 1.0 80 1.0 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 0.0125 38-39 0.0375 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.05 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 29.0 71 23.0 72 32.0 73 22.0 74 24.0 75 34.0 76 28.0 77 29.0 78 24.0 79 24.0 80 32.0 81 52.0 82 34.0 83 34.0 84 27.0 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 3552.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.14999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 91.48369926813041 68.75 2 4.624085163007319 6.950000000000001 3 1.0312707917498336 2.325 4 0.5988023952095809 1.7999999999999998 5 0.499001996007984 1.875 6 0.166333998669328 0.75 7 0.2328675981370592 1.225 8 0.29940119760479045 1.7999999999999998 9 0.2661343978709248 1.7999999999999998 >10 0.7318695941450433 9.925 >50 0.0665335994677312 2.8000000000000003 >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 60 1.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 52 1.3 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 37 0.9249999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 29 0.7250000000000001 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 27 0.675 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 25 0.625 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 22 0.5499999999999999 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 21 0.525 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 21 0.525 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 20 0.5 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 19 0.475 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 18 0.44999999999999996 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 17 0.42500000000000004 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 16 0.4 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 15 0.375 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 13 0.325 No Hit GAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGC 12 0.3 No Hit GGAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTG 12 0.3 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 10 0.25 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 10 0.25 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 9 0.22499999999999998 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 9 0.22499999999999998 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 9 0.22499999999999998 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 9 0.22499999999999998 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 8 0.2 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 8 0.2 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 8 0.2 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 7 0.17500000000000002 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 7 0.17500000000000002 No Hit GGATTCGATTACAGAAAGTCGAACTAGAAGCGGATGAGTATCGAATGAATGGATACTCTGAGATAGAACG 7 0.17500000000000002 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGAGGTGGAAGGCCTACGGGTCGTCAACTTCTTTTCTCGGAGAAGAAACA 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGT 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTT 5 0.125 No Hit GGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAAT 5 0.125 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GGATAATGACAGATCGAGAGGCTCGACTAAACAGAATTGGGGGAGAAGTC 5 0.125 No Hit CAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 5 0.125 No Hit GGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCAT 5 0.125 No Hit GGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAA 5 0.125 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 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 0.0125 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.0875 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.15 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.15 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.175 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.1875 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2375 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.30000000000000004 0.0 0.0 0.0 0.0 78-79 0.325 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCATTC 20 0.0029417912 64.03125 2 GGGCATT 20 0.0029417912 64.03125 1 TTCGTAT 20 0.0029417912 64.03125 6 GTATTTC 20 0.0029417912 64.03125 9 GGTTTTG 20 0.0029417912 64.03125 1 CATTCGT 20 0.0029417912 64.03125 4 ATTCGTA 20 0.0029417912 64.03125 5 TCGTATT 20 0.0029417912 64.03125 7 GCATTCG 20 0.0029417912 64.03125 3 CGTATTT 25 0.007118528 51.225 8 TTGAAAA 35 4.177686E-4 48.785713 5 ATTAATC 20 5.435999E-4 46.78082 86-87 AAAAAAA 20 5.435999E-4 46.78082 86-87 CCAAGGA 20 6.222068E-4 45.533333 72-73 TTTGCCA 20 6.222068E-4 45.533333 68-69 AGCATTT 20 8.322071E-4 42.955975 64-65 GAGGTGA 20 8.586341E-4 42.6875 22-23 ACTGCGA 20 8.586341E-4 42.6875 56-57 GGTGAAA 20 8.586341E-4 42.6875 24-25 TTCATAG 20 8.586341E-4 42.6875 12-13 >>END_MODULE Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180657 READS because READLEN < 1 Read 180657 spots for ERR6133313.sra Written 180657 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra Rejected 180654 READS because READLEN < 1 Read 180654 spots for ERR6133313.sra Written 180654 spots for ERR6133313.sra SRR ids: ['ERR6133313.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_tzpixunn ERR6133313.sra spots: 3613083 blocks: [[1, 180654], [180655, 361308], [361309, 541962], [541963, 722616], [722617, 903270], [903271, 1083924], [1083925, 1264578], [1264579, 1445232], [1445233, 1625886], [1625887, 1806540], [1806541, 1987194], [1987195, 2167848], [2167849, 2348502], [2348503, 2529156], [2529157, 2709810], [2709811, 2890464], [2890465, 3071118], [3071119, 3251772], [3251773, 3432426], [3432427, 3613083]] ERR6133313 file size 788731 ERR6133313 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 ERR6133313 ERR6133313_1.fastq Input file: ERR6133313_1.fastq trimmed: ERR6133313-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 00:26:43 2024 >> started Sat Dec 7 00:26:51 2024 >> done (8.577s) 3613083 reads processed; of these: 838 ( 0.02%) short reads filtered out after trimming by size control 60 ( 0.00%) empty reads filtered out after trimming by size control 3612185 (99.98%) reads available; of these: 63794 ( 1.77%) trimmed reads available after processing 3548391 (98.23%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 95 0.00% 19 491 0.01% 20 170 0.00% 21 224 0.01% 22 267 0.01% 23 53 0.00% 24 78 0.00% 25 52 0.00% 26 46 0.00% 27 55 0.00% 28 143 0.00% 29 97 0.00% 30 108 0.00% 31 167 0.00% 32 228 0.01% 33 68 0.00% 34 90 0.00% 35 430 0.01% 36 811 0.02% 37 155 0.00% 38 251 0.01% 39 712 0.02% 40 561 0.02% 41 254 0.01% 42 55 0.00% 43 56 0.00% 44 57 0.00% 45 50 0.00% 46 32 0.00% 47 17 0.00% 48 32 0.00% 49 42 0.00% 50 49 0.00% 51 221 0.01% 52 49 0.00% 53 41 0.00% 54 36 0.00% 55 31 0.00% 56 36 0.00% 57 82 0.00% 58 94 0.00% 59 47 0.00% 60 138 0.00% 61 57 0.00% 62 1 0.00% 63 4 0.00% 64 4 0.00% 65 11 0.00% 66 9 0.00% 67 30 0.00% 68 84 0.00% 69 350 0.01% 70 29794 0.82% 71 26921 0.75% 72 31808 0.88% 73 25864 0.72% 74 27379 0.76% 75 28288 0.78% 76 23511 0.65% 77 23842 0.66% 78 27834 0.77% 79 29920 0.83% 80 27197 0.75% 81 34704 0.96% 82 37428 1.04% 83 34354 0.95% 84 33711 0.93% 85 167 0.00% 86 307 0.01% 87 459 0.01% 88 874 0.02% 89 1606 0.04% 90 3210 0.09% 91 10141 0.28% 92 34761 0.96% 93 3110784 86.12% 3612185 reads passed initial QC criterion=sequence-density sequence-density=1.19 sequence-density-rank=1 fanout-score=5.07 fanout-score-rank=22 prefix-density=3.20 prefix-fanout=1.9 sequence=AGGCTAAATACTCCTGGGTGACCGATAGCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=25 fanout-score=41.46 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=5.2 sequence=CTTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATTTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACC Started job on | Dec 07 00:27:11 Started mapping on | Dec 07 00:27:11 Finished on | Dec 07 00:27:40 Mapping speed, Million of reads per hour | 448.41 Number of input reads | 3612185 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 2166491 Uniquely mapped reads % | 59.98% Average mapped length | 90.17 Number of splices: Total | 56737 Number of splices: Annotated (sjdb) | 45483 Number of splices: GT/AG | 53240 Number of splices: GC/AG | 1561 Number of splices: AT/AC | 18 Number of splices: Non-canonical | 1918 Mismatch rate per base, % | 0.55% Deletion rate per base | 0.06% Deletion average length | 1.78 Insertion rate per base | 0.03% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1182817 % of reads mapped to multiple loci | 32.75% Number of reads mapped to too many loci | 169990 % of reads mapped to too many loci | 4.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.27% % of reads unmapped: other | 0.30% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 262877 262877 262877 N_multimapping 1182817 1182817 1182817 N_noFeature 215835 239000 2066210 N_ambiguous 90920 13180 1004 UnstrandedReadsAssigned:1859736 PositiveStrandReadsAssigned:1914311 NegativeStrandReadsAssigned:99277 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133313 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: ERR6133313-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,612,185 reads, 2,681,377 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 980 rounds 52973 ERR6133313.ke.tsv 35125 ERR6133313.se.tsv 88098 total ==> ERR6133313.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 63 23.5764 PNS24243 293 194 0 0 KQK14069 1603 1504 16 5.46214 KQK14071 474 375 0 0 ==> ERR6133313.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 51 BRADI_1g59795v3 31 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 48 BRADI_1g74790v3 23 BRADI_1g09890v3 0 BRADI_1g77505v3 55 BRADI_1g48960v3 0 ERR6133313 completed mapping pipeline successfully