Starting /dee2/code/volunteer_pipeline.sh ERR6133400 current disk space = 1547647938560 free memory = 1602572048 ERR6133400 SRAfilesize 061eec5ece83399524a1f2178dd1a201 ERR6133400.sra ERR6133400.sra file validated ERR6133400 is single end ERR6133400 is conventional basespace ERR6133400 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133400_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 29.1875 33.0 27.0 33.0 15.0 37.0 2 33.57525 33.0 33.0 37.0 27.0 37.0 3 33.80825 37.0 33.0 37.0 27.0 37.0 4 34.141 37.0 33.0 37.0 27.0 37.0 5 34.19525 37.0 33.0 37.0 27.0 37.0 6 34.4205 37.0 33.0 37.0 27.0 37.0 7 35.42925 37.0 33.0 40.0 27.0 40.0 8 35.41975 37.0 33.0 40.0 27.0 40.0 9 35.6015 37.0 33.0 40.0 33.0 40.0 10-11 35.684875000000005 37.0 33.0 40.0 33.0 40.0 12-13 35.455875 37.0 33.0 40.0 30.0 40.0 14-15 35.2445 37.0 33.0 40.0 27.0 40.0 16-17 35.081125 37.0 33.0 38.5 27.0 40.0 18-19 35.016875 37.0 33.0 37.0 27.0 40.0 20-21 34.17975 37.0 33.0 37.0 27.0 40.0 22-23 34.074875000000006 37.0 33.0 37.0 24.5 40.0 24-25 33.6305 37.0 33.0 37.0 22.0 40.0 26-27 33.466875 37.0 33.0 37.0 22.0 40.0 28-29 33.056 37.0 33.0 37.0 22.0 40.0 30-31 32.77575 37.0 33.0 37.0 22.0 40.0 32-33 32.3815 35.0 33.0 37.0 22.0 40.0 34-35 31.675125 33.0 27.0 37.0 22.0 40.0 36-37 31.377499999999998 33.0 27.0 37.0 18.5 40.0 38-39 31.742874999999998 33.0 27.0 37.0 22.0 40.0 40-41 31.699875 33.0 27.0 37.0 22.0 40.0 42-43 31.443125000000002 33.0 27.0 37.0 22.0 40.0 44-45 31.37225 33.0 27.0 37.0 22.0 40.0 46-47 30.590125 33.0 27.0 37.0 15.0 37.0 48-49 30.500500000000002 33.0 27.0 37.0 15.0 37.0 50-51 29.850875000000002 33.0 27.0 37.0 15.0 37.0 52-53 29.558374999999998 33.0 27.0 37.0 15.0 37.0 54-55 29.554000000000002 33.0 27.0 37.0 15.0 37.0 56-57 28.82025 33.0 27.0 37.0 15.0 37.0 58-59 28.6755 33.0 27.0 35.0 15.0 37.0 60-61 28.38075 33.0 27.0 33.0 15.0 37.0 62-63 28.01425 33.0 22.0 33.0 15.0 37.0 64-65 27.308125 33.0 22.0 33.0 10.5 37.0 66-67 27.069499999999998 33.0 22.0 33.0 10.5 37.0 68-69 26.589624999999998 27.0 22.0 33.0 10.5 35.0 70-71 28.283065822625346 33.0 27.0 33.0 15.0 37.0 72-73 28.78794776016755 33.0 27.0 33.0 15.0 37.0 74-75 28.699619623358867 33.0 27.0 33.0 15.0 37.0 76-77 28.25252336900723 33.0 27.0 33.0 15.0 37.0 78-79 27.91294409430439 33.0 27.0 33.0 10.5 37.0 80-81 27.315444677062874 33.0 27.0 33.0 6.0 37.0 82-83 26.560800035079403 33.0 22.0 33.0 4.0 37.0 84-85 25.660907085508597 33.0 22.0 33.0 2.0 37.0 86-87 24.625412995594715 30.0 15.0 33.0 2.0 37.0 88-89 24.05781938325991 33.0 15.0 33.0 2.0 37.0 90-91 23.18158039647577 30.0 4.0 33.0 2.0 37.0 92-93 21.87045704845815 27.0 2.0 33.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 81.0 21 89.0 22 137.0 23 136.0 24 157.0 25 221.0 26 225.0 27 227.0 28 229.0 29 255.0 30 260.0 31 283.0 32 286.0 33 287.0 34 276.0 35 332.0 36 276.0 37 200.0 38 43.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.45 7.3 7.324999999999999 15.925 2 50.724999999999994 24.875 15.125 9.275 3 29.75 37.1 19.625 13.525 4 27.675 26.125 23.400000000000002 22.8 5 24.575 25.424999999999997 28.999999999999996 21.0 6 19.85 32.574999999999996 26.974999999999998 20.599999999999998 7 31.525 27.400000000000002 22.7 18.375 8 26.55 28.175 28.749999999999996 16.525000000000002 9 22.55 28.025 30.225 19.2 10-11 22.8875 27.287499999999998 31.0 18.825 12-13 21.8125 28.625 29.562500000000004 20.0 14-15 19.7125 29.2375 31.05 20.0 16-17 23.1375 30.2625 24.125 22.475 18-19 23.6625 24.762500000000003 31.0 20.575 20-21 25.25 25.2375 28.4125 21.099999999999998 22-23 27.787499999999998 23.225 27.9125 21.075 24-25 23.8375 26.4625 28.9 20.8 26-27 23.7875 25.0625 29.9875 21.1625 28-29 23.7375 27.6 27.962500000000002 20.7 30-31 25.2875 26.887499999999996 28.1625 19.662499999999998 32-33 24.975 24.0 29.975 21.05 34-35 22.3375 30.625000000000004 26.125 20.9125 36-37 23.875 26.2125 26.4125 23.5 38-39 25.174999999999997 25.624999999999996 28.675 20.525 40-41 25.374999999999996 25.2875 27.537499999999998 21.8 42-43 25.35 29.275000000000002 27.237499999999997 18.1375 44-45 21.65 27.650000000000002 30.599999999999998 20.1 46-47 24.5125 27.762500000000003 26.3125 21.4125 48-49 23.0875 25.387500000000003 30.612499999999997 20.9125 50-51 22.625 27.325 29.849999999999998 20.200000000000003 52-53 24.65 27.987499999999997 26.85 20.5125 54-55 23.3 28.775000000000002 29.762499999999996 18.1625 56-57 25.2 29.2 25.8625 19.7375 58-59 24.3625 28.050000000000004 27.85 19.7375 60-61 25.4875 29.012500000000003 26.687499999999996 18.8125 62-63 22.3875 28.1875 30.2 19.225 64-65 22.25 31.912499999999998 26.525 19.3125 66-67 24.25 28.9125 26.687499999999996 20.150000000000002 68-69 22.0125 29.225 27.325 21.4375 70-71 25.335675743506087 27.970887187852927 26.56544108420128 20.127995984439703 72-73 23.32236009116232 27.601924537857688 29.31121802988098 19.764497341099013 74-75 23.324362424708443 28.796616685890044 28.860694604639242 19.01832628476227 76-77 22.829331602855287 26.89162881245944 27.2809863724854 22.99805321219987 78-79 22.48133106249181 26.81776496790253 29.42486571466003 21.276038254945632 80-81 21.70747849106552 32.230311052283255 26.803441429516877 19.25876902713435 82-83 20.904563198277025 28.738726611926236 27.190738995827164 23.16597119396958 84-85 22.29674240350397 25.540651519299207 29.455242266630165 22.707363810566658 86-87 21.29680616740088 27.73953744493392 27.29900881057269 23.66464757709251 88-89 21.48953744493392 29.15748898678414 28.001101321585903 21.351872246696036 90-91 23.526982378854626 29.542951541850222 26.25275330396476 20.677312775330396 92-93 19.851321585903083 33.43887665198238 26.734581497797354 19.97522026431718 >>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 0.5 14 0.5 15 0.0 16 1.5 17 4.0 18 3.0 19 1.0 20 1.0 21 1.0 22 1.0 23 4.5 24 8.0 25 10.0 26 11.0 27 10.5 28 19.5 29 30.0 30 39.5 31 45.0 32 53.0 33 68.0 34 78.0 35 94.5 36 123.0 37 168.5 38 208.5 39 202.5 40 227.5 41 244.5 42 254.5 43 289.5 44 245.0 45 209.0 46 198.5 47 163.0 48 134.5 49 120.0 50 126.0 51 128.5 52 118.0 53 136.5 54 138.0 55 102.5 56 89.5 57 90.5 58 66.0 59 34.0 60 21.0 61 15.5 62 13.0 63 11.0 64 11.5 65 12.0 66 10.0 67 8.0 68 15.5 69 23.5 70 18.5 71 13.0 72 8.5 73 3.0 74 1.5 75 0.5 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 0.0 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 31.0 71 12.0 72 16.0 73 25.0 74 29.0 75 25.0 76 19.0 77 18.0 78 17.0 79 22.0 80 17.0 81 39.0 82 31.0 83 25.0 84 42.0 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 3632.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.475 #Duplication Level Percentage of deduplicated Percentage of total 1 91.83395712827492 67.475 2 3.844845185437223 5.65 3 1.1908812521265737 2.625 4 0.748553929908132 2.1999999999999997 5 0.4083021435862538 1.5 6 0.3062266076896904 1.35 7 0.1701258931609391 0.8750000000000001 8 0.27220142905750255 1.6 9 0.23817625042531473 1.575 >10 0.9527050017012589 13.175 >50 0.03402517863218782 1.975 >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 GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 79 1.975 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 47 1.175 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 44 1.0999999999999999 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 37 0.9249999999999999 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 30 0.75 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 26 0.65 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 24 0.6 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 23 0.575 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 23 0.575 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 23 0.575 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 22 0.5499999999999999 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 22 0.5499999999999999 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 17 0.42500000000000004 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 14 0.35000000000000003 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 14 0.35000000000000003 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 12 0.3 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 12 0.3 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 11 0.27499999999999997 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 11 0.27499999999999997 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 10 0.25 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 10 0.25 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 10 0.25 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 9 0.22499999999999998 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 9 0.22499999999999998 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 9 0.22499999999999998 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 7 0.17500000000000002 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 7 0.17500000000000002 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 6 0.15 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 6 0.15 No Hit TACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGC 6 0.15 No Hit GTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCG 6 0.15 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 6 0.15 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 5 0.125 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 5 0.125 No Hit GCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTA 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit AAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTT 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCAATA 20 2.5249283E-5 85.9875 6 GCAATAC 15 9.1281685E-4 85.987495 7 GGGAGAG 15 9.1281685E-4 85.987495 1 CAATACA 15 9.1281685E-4 85.987495 8 GAGCAAT 15 9.1281685E-4 85.987495 5 AGAGCAA 15 9.1281685E-4 85.987495 4 AATACAA 15 9.1281685E-4 85.987495 9 GGAGAGC 20 0.0028595875 64.49062 2 GAGAGCA 20 0.0028595875 64.49062 3 >>END_MODULE Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57459 READS because READLEN < 1 Read 57459 spots for ERR6133400.sra Written 57459 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra Rejected 57457 READS because READLEN < 1 Read 57457 spots for ERR6133400.sra Written 57457 spots for ERR6133400.sra SRR ids: ['ERR6133400.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_09gamdee ERR6133400.sra spots: 1149142 blocks: [[1, 57457], [57458, 114914], [114915, 172371], [172372, 229828], [229829, 287285], [287286, 344742], [344743, 402199], [402200, 459656], [459657, 517113], [517114, 574570], [574571, 632027], [632028, 689484], [689485, 746941], [746942, 804398], [804399, 861855], [861856, 919312], [919313, 976769], [976770, 1034226], [1034227, 1091683], [1091684, 1149142]] ERR6133400 file size 250865 ERR6133400 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 ERR6133400 ERR6133400_1.fastq Input file: ERR6133400_1.fastq trimmed: ERR6133400-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 03:13:18 2024 >> started Sat Dec 7 03:13:19 2024 >> done (0.747s) 1149142 reads processed; of these: 16 ( 0.00%) short reads filtered out after trimming by size control 5 ( 0.00%) empty reads filtered out after trimming by size control 1149121 (100.00%) reads available; of these: 287177 (24.99%) trimmed reads available after processing 861944 (75.01%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 1 0.00% 20 4 0.00% 21 3 0.00% 22 4 0.00% 23 2 0.00% 24 1 0.00% 25 1 0.00% 26 1 0.00% 27 1 0.00% 28 8 0.00% 29 32 0.00% 30 3 0.00% 31 5 0.00% 32 6 0.00% 33 3 0.00% 34 2 0.00% 35 4 0.00% 36 2 0.00% 37 3 0.00% 38 9 0.00% 39 21 0.00% 40 14 0.00% 41 6 0.00% 42 5 0.00% 43 14 0.00% 44 16 0.00% 45 25 0.00% 46 28 0.00% 47 47 0.00% 48 90 0.01% 49 106 0.01% 50 141 0.01% 51 168 0.01% 52 262 0.02% 53 376 0.03% 54 453 0.04% 55 677 0.06% 56 827 0.07% 57 1359 0.12% 58 883 0.08% 59 1046 0.09% 60 1268 0.11% 61 1452 0.13% 62 1579 0.14% 63 1746 0.15% 64 1951 0.17% 65 1944 0.17% 66 1863 0.16% 67 2033 0.18% 68 1968 0.17% 69 1951 0.17% 70 7474 0.65% 71 7608 0.66% 72 8950 0.78% 73 9531 0.83% 74 10043 0.87% 75 10400 0.91% 76 10792 0.94% 77 11944 1.04% 78 12417 1.08% 79 13655 1.19% 80 14495 1.26% 81 17263 1.50% 82 18628 1.62% 83 18577 1.62% 84 20953 1.82% 85 14623 1.27% 86 15102 1.31% 87 16798 1.46% 88 19207 1.67% 89 21127 1.84% 90 22688 1.97% 91 24825 2.16% 92 20875 1.82% 93 776728 67.59% 1149121 reads passed initial QC criterion=sequence-density sequence-density=4.42 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=25 prefix-density=4.54 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.11 sequence-density-rank=16 fanout-score=90.27 fanout-score-rank=1 prefix-density=9.54 prefix-fanout=1.0 sequence=GATAGTCAAGGGCGCGTTATTAA 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 03:13:31 Started mapping on | Dec 07 03:13:31 Finished on | Dec 07 03:13:38 Mapping speed, Million of reads per hour | 590.98 Number of input reads | 1149121 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 473899 Uniquely mapped reads % | 41.24% Average mapped length | 88.35 Number of splices: Total | 16364 Number of splices: Annotated (sjdb) | 12830 Number of splices: GT/AG | 15294 Number of splices: GC/AG | 343 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 698 Mismatch rate per base, % | 0.96% Deletion rate per base | 0.05% Deletion average length | 1.79 Insertion rate per base | 0.03% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 552369 % of reads mapped to multiple loci | 48.07% Number of reads mapped to too many loci | 63636 % of reads mapped to too many loci | 5.54% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.25% % of reads unmapped: other | 0.91% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 122853 122853 122853 N_multimapping 552369 552369 552369 N_noFeature 46103 51138 453145 N_ambiguous 18736 2973 113 UnstrandedReadsAssigned:409060 PositiveStrandReadsAssigned:419788 NegativeStrandReadsAssigned:20641 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=85 echo kmer=81 ERR6133400 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: ERR6133400-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,149,121 reads, 768,419 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,148 rounds 52973 ERR6133400.ke.tsv 35125 ERR6133400.se.tsv 88098 total ==> ERR6133400.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 5 6.24228 PNS24243 293 194 0 0 KQK14069 1603 1504 12 13.6666 KQK14071 474 375 0 0 ==> ERR6133400.se.tsv <== BRADI_1g14170v3 12 BRADI_1g53295v3 6 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 11 BRADI_1g48960v3 0 ERR6133400 completed mapping pipeline successfully