Starting /dee2/code/volunteer_pipeline.sh ERR6133349 current disk space = 1548397010944 free memory = 1598256084 ERR6133349 SRAfilesize 0a41ad145cee624b27460d3de3d6a309 ERR6133349.sra ERR6133349.sra file validated ERR6133349 is single end ERR6133349 is conventional basespace ERR6133349 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133349_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.10425 37.0 37.0 37.0 33.0 37.0 2 36.5865 37.0 37.0 37.0 37.0 37.0 3 36.59625 37.0 37.0 37.0 37.0 37.0 4 36.2655 37.0 37.0 37.0 37.0 37.0 5 36.35725 37.0 37.0 37.0 37.0 37.0 6 36.54775 37.0 37.0 37.0 37.0 37.0 7 38.708 40.0 37.0 40.0 37.0 40.0 8 38.699 40.0 37.0 40.0 37.0 40.0 9 38.7685 40.0 37.0 40.0 37.0 40.0 10-11 38.729625 40.0 37.0 40.0 37.0 40.0 12-13 38.683125000000004 40.0 37.0 40.0 37.0 40.0 14-15 38.703125 40.0 37.0 40.0 37.0 40.0 16-17 38.68 40.0 37.0 40.0 37.0 40.0 18-19 38.560874999999996 40.0 37.0 40.0 37.0 40.0 20-21 38.508750000000006 40.0 37.0 40.0 37.0 40.0 22-23 38.42675 40.0 37.0 40.0 37.0 40.0 24-25 38.35675 40.0 37.0 40.0 37.0 40.0 26-27 38.433375 40.0 37.0 40.0 37.0 40.0 28-29 38.42775 40.0 37.0 40.0 37.0 40.0 30-31 38.368 40.0 37.0 40.0 37.0 40.0 32-33 38.24125 40.0 37.0 40.0 37.0 40.0 34-35 38.037375 40.0 37.0 40.0 37.0 40.0 36-37 37.983000000000004 40.0 37.0 40.0 37.0 40.0 38-39 38.003 40.0 37.0 40.0 37.0 40.0 40-41 37.873875 40.0 37.0 40.0 37.0 40.0 42-43 37.77375 37.0 37.0 40.0 37.0 40.0 44-45 37.5755 37.0 37.0 40.0 33.0 40.0 46-47 37.47075 37.0 37.0 40.0 35.0 40.0 48-49 37.343374999999995 37.0 37.0 40.0 33.0 40.0 50-51 37.202124999999995 37.0 37.0 40.0 33.0 40.0 52-53 37.1065 37.0 37.0 40.0 33.0 40.0 54-55 36.8945 37.0 37.0 37.0 33.0 40.0 56-57 36.75925 37.0 37.0 37.0 33.0 40.0 58-59 36.51925 37.0 37.0 37.0 33.0 40.0 60-61 36.39675 37.0 37.0 37.0 33.0 40.0 62-63 36.239125 37.0 37.0 37.0 33.0 37.0 64-65 36.123625000000004 37.0 37.0 37.0 33.0 37.0 66-67 35.945625 37.0 37.0 37.0 33.0 37.0 68-69 35.066 35.0 35.0 37.0 33.0 37.0 70-71 35.287744168356994 37.0 33.0 37.0 33.0 37.0 72-73 35.743129269252584 37.0 37.0 37.0 33.0 37.0 74-75 35.707781823687895 37.0 37.0 37.0 33.0 37.0 76-77 35.67248755924847 37.0 37.0 37.0 33.0 37.0 78-79 35.62562075605554 37.0 37.0 37.0 33.0 37.0 80-81 35.61863431186813 37.0 37.0 37.0 33.0 37.0 82-83 35.46318528005804 37.0 35.0 37.0 33.0 37.0 84-85 35.44149425776885 37.0 33.0 37.0 33.0 37.0 86-87 35.398090169067004 37.0 33.0 37.0 33.0 37.0 88-89 35.46102066374452 37.0 33.0 37.0 33.0 37.0 90-91 35.41734502191609 37.0 33.0 37.0 33.0 37.0 92-93 35.24890419536631 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 7.0 22 4.0 23 3.0 24 2.0 25 11.0 26 10.0 27 14.0 28 23.0 29 18.0 30 29.0 31 30.0 32 46.0 33 79.0 34 87.0 35 192.0 36 754.0 37 1156.0 38 1408.0 39 127.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 64.64999999999999 8.4 9.325 17.625 2 45.875 26.474999999999998 16.55 11.1 3 31.175000000000004 35.775 18.175 14.875 4 32.35 25.224999999999998 21.825 20.599999999999998 5 24.4 27.650000000000002 26.700000000000003 21.25 6 22.475 32.05 26.924999999999997 18.55 7 33.4 25.825 24.025 16.75 8 28.175 26.400000000000002 27.975 17.45 9 26.650000000000002 26.25 28.050000000000004 19.05 10-11 27.250000000000004 26.8375 25.874999999999996 20.0375 12-13 25.1875 27.950000000000003 28.287499999999998 18.575 14-15 22.5625 26.525 30.5375 20.375 16-17 24.9375 28.425 25.4375 21.2 18-19 24.725 25.874999999999996 28.4375 20.962500000000002 20-21 26.8375 24.8125 26.3625 21.987499999999997 22-23 27.125 25.55 26.1125 21.212500000000002 24-25 23.5625 27.787499999999998 27.800000000000004 20.849999999999998 26-27 25.0375 25.0625 28.287499999999998 21.6125 28-29 25.224999999999998 26.8125 26.025 21.9375 30-31 25.55 26.200000000000003 26.525 21.725 32-33 25.474999999999998 26.5875 27.487499999999997 20.45 34-35 23.9375 28.237499999999997 27.0125 20.8125 36-37 24.5 28.275 26.275 20.95 38-39 25.0125 27.125 26.35 21.512500000000003 40-41 24.9875 26.650000000000002 26.387500000000003 21.975 42-43 24.337500000000002 28.962500000000002 27.1375 19.5625 44-45 23.1875 28.625 27.175 21.0125 46-47 24.675 28.9125 26.400000000000002 20.0125 48-49 23.4875 27.8625 27.712500000000002 20.9375 50-51 21.925 29.4 28.0625 20.6125 52-53 23.525 30.65 26.650000000000002 19.175 54-55 24.175 30.375000000000004 27.500000000000004 17.95 56-57 23.400000000000002 29.0875 26.337500000000002 21.175 58-59 24.375 29.2 26.85 19.575 60-61 25.5625 27.8375 26.674999999999997 19.925 62-63 23.2125 30.3 27.4125 19.075 64-65 23.175 30.412499999999998 27.5875 18.825 66-67 23.875 29.75 26.3125 20.0625 68-69 22.1875 30.412499999999998 27.400000000000002 20.0 70-71 24.924471299093657 29.61983887210473 25.553877139979857 19.901812688821753 72-73 25.846034616378198 28.894342547145442 26.466029449754586 18.793593386721778 74-75 25.87783225122565 28.6206439644892 25.54657479793295 19.954948986352193 76-77 24.275411620628656 28.262348618859708 27.296230779697915 20.166008980813714 78-79 24.908835904628333 27.980364656381486 27.251051893408135 19.85974754558205 80-81 23.037100949094047 30.629853321829163 26.732815645671554 19.600230083405236 82-83 23.49791790600833 28.375966686496135 27.498512790005947 20.62760261748959 84-85 24.279962836791576 26.200061938680708 29.17311861257355 20.346856611954163 86-87 23.387601753287413 30.009392611145895 25.18785222291797 21.415153412648717 88-89 22.714464621164684 32.748904195366315 25.14088916718848 19.395742016280526 90-91 22.557921102066373 34.157795867251096 23.747651847213525 19.536631183469005 92-93 20.710707576706326 36.61552911709455 24.608641202254226 18.065122103944898 >>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 0.0 18 0.0 19 0.5 20 2.5 21 2.0 22 1.0 23 5.5 24 8.5 25 12.0 26 13.5 27 14.0 28 21.0 29 26.5 30 37.0 31 48.5 32 61.0 33 78.0 34 93.5 35 110.5 36 135.5 37 178.0 38 195.0 39 189.0 40 209.5 41 201.0 42 192.0 43 204.5 44 186.0 45 174.5 46 170.0 47 166.5 48 162.5 49 164.5 50 165.0 51 150.0 52 143.0 53 156.0 54 171.5 55 158.0 56 129.0 57 107.0 58 74.5 59 42.0 60 28.5 61 19.5 62 16.5 63 13.5 64 7.5 65 11.0 66 11.5 67 11.5 68 17.5 69 14.0 70 6.0 71 2.0 72 1.5 73 0.5 74 0.0 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 0.0 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 56.0 71 43.0 72 60.0 73 45.0 74 45.0 75 49.0 76 55.0 77 59.0 78 46.0 79 45.0 80 40.0 81 58.0 82 74.0 83 61.0 84 70.0 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 3194.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.05 #Duplication Level Percentage of deduplicated Percentage of total 1 89.67355096602265 67.30000000000001 2 5.02998001332445 7.55 3 1.698867421718854 3.8249999999999997 4 0.866089273817455 2.6 5 0.6995336442371752 2.625 6 0.36642238507661556 1.6500000000000001 7 0.4663557628247834 2.45 8 0.2664890073284477 1.6 9 0.1665556295802798 1.125 >10 0.7661558960692871 9.275 >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 fail #Sequence Count Percentage Possible Source GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 48 1.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 27 0.675 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 21 0.525 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 19 0.475 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 17 0.42500000000000004 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 16 0.4 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 16 0.4 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 15 0.375 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 14 0.35000000000000003 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 14 0.35000000000000003 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 13 0.325 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 12 0.3 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 12 0.3 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 12 0.3 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 11 0.27499999999999997 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 10 0.25 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 10 0.25 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 10 0.25 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 9 0.22499999999999998 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 9 0.22499999999999998 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 9 0.22499999999999998 No Hit GAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCC 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 9 0.22499999999999998 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 8 0.2 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 8 0.2 No Hit GGGCAAGTCCCCTCCTTTTGGCTCCAAGGCCCGGTCTGACCGGGCCGATC 8 0.2 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 8 0.2 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 8 0.2 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 8 0.2 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 7 0.17500000000000002 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 7 0.17500000000000002 No Hit CGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAA 7 0.17500000000000002 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 7 0.17500000000000002 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 7 0.17500000000000002 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 7 0.17500000000000002 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 7 0.17500000000000002 No Hit GGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAA 7 0.17500000000000002 No Hit CAAGTCGAACGGGAAGTGGTGTTTCCAGTGGCGAACGGGTGAGTAACGCG 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCC 7 0.17500000000000002 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit ATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAAT 6 0.15 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 6 0.15 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 6 0.15 No Hit GAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACT 5 0.125 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GGTAAAGCACTGTTTCGGTGCGGGCTGCGCGAGCGGTACCAAATCGAGGC 5 0.125 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 5 0.125 No Hit GCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGA 5 0.125 No Hit CGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTC 5 0.125 No Hit CGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATG 5 0.125 No Hit GGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCA 5 0.125 No Hit TATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAA 5 0.125 No Hit CAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 5 0.125 No Hit CGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACT 5 0.125 No Hit GAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAA 5 0.125 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 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 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.0625 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 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 0.15 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.15 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.21250000000000002 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0 0.0 0.0 66-67 0.25 0.0 0.0 0.0 0.0 68-69 0.25 0.0 0.0 0.0 0.0 70-71 0.2625 0.0 0.0 0.0 0.0 72-73 0.2875 0.0 0.0 0.0 0.0 74-75 0.325 0.0 0.0 0.0 0.0 76-77 0.35 0.0 0.0 0.0 0.0 78-79 0.35 0.0 0.0 0.0 0.0 80-81 0.3625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 35 1.4283869E-6 46.651054 86-87 >>END_MODULE Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32341 READS because READLEN < 1 Read 32341 spots for ERR6133349.sra Written 32341 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra Rejected 32334 READS because READLEN < 1 Read 32334 spots for ERR6133349.sra Written 32334 spots for ERR6133349.sra SRR ids: ['ERR6133349.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_x062172o ERR6133349.sra spots: 646687 blocks: [[1, 32334], [32335, 64668], [64669, 97002], [97003, 129336], [129337, 161670], [161671, 194004], [194005, 226338], [226339, 258672], [258673, 291006], [291007, 323340], [323341, 355674], [355675, 388008], [388009, 420342], [420343, 452676], [452677, 485010], [485011, 517344], [517345, 549678], [549679, 582012], [582013, 614346], [614347, 646687]] ERR6133349 file size 138443 ERR6133349 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 ERR6133349 ERR6133349_1.fastq Input file: ERR6133349_1.fastq trimmed: ERR6133349-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 01:11:42 2024 >> started Sat Dec 7 01:11:43 2024 >> done (0.604s) 646687 reads processed; of these: 208 ( 0.03%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 646468 (99.97%) reads available; of these: 5661 ( 0.88%) trimmed reads available after processing 640807 (99.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 18 0.00% 19 59 0.01% 20 28 0.00% 21 16 0.00% 22 22 0.00% 23 27 0.00% 24 26 0.00% 25 9 0.00% 26 17 0.00% 27 19 0.00% 28 56 0.01% 29 58 0.01% 30 13 0.00% 31 24 0.00% 32 49 0.01% 33 457 0.07% 34 23 0.00% 35 48 0.01% 36 26 0.00% 37 22 0.00% 38 42 0.01% 39 86 0.01% 40 107 0.02% 41 36 0.01% 42 17 0.00% 43 26 0.00% 44 28 0.00% 45 27 0.00% 46 11 0.00% 47 10 0.00% 48 10 0.00% 49 14 0.00% 50 16 0.00% 51 82 0.01% 52 26 0.00% 53 5 0.00% 54 14 0.00% 55 14 0.00% 56 9 0.00% 57 37 0.01% 58 28 0.00% 59 12 0.00% 60 24 0.00% 61 27 0.00% 62 4 0.00% 63 4 0.00% 64 4 0.00% 65 9 0.00% 66 15 0.00% 67 8 0.00% 68 18 0.00% 69 55 0.01% 70 9237 1.43% 71 8716 1.35% 72 9483 1.47% 73 8679 1.34% 74 8101 1.25% 75 7529 1.16% 76 7296 1.13% 77 7829 1.21% 78 7867 1.22% 79 8055 1.25% 80 7746 1.20% 81 9872 1.53% 82 10721 1.66% 83 9062 1.40% 84 11508 1.78% 85 24 0.00% 86 30 0.00% 87 60 0.01% 88 97 0.02% 89 163 0.03% 90 234 0.04% 91 527 0.08% 92 1829 0.28% 93 509961 78.88% 646468 reads passed initial QC criterion=sequence-density sequence-density=8.14 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=17 prefix-density=8.23 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=130.47 fanout-score-rank=1 prefix-density=1.73 prefix-fanout=1.4 sequence=TTAAAAGATTTATTAGATAATCGAAAACAGAGGATCTTGAGTACTATTCGAAATTCGGAAGAATTGCGTAGAGGGACCTTTGAGCAGCTCGAAAAAGCTCGGATTCGATTACAGAAAGTCGAACTAGAAGCGGATGAGTATCGAATGAATGGATACTCTGAGATAGAACGAG 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 01:11:58 Started mapping on | Dec 07 01:11:58 Finished on | Dec 07 01:12:03 Mapping speed, Million of reads per hour | 465.46 Number of input reads | 646468 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 322605 Uniquely mapped reads % | 49.90% Average mapped length | 88.11 Number of splices: Total | 7144 Number of splices: Annotated (sjdb) | 5606 Number of splices: GT/AG | 6631 Number of splices: GC/AG | 188 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 322 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.65 Insertion rate per base | 0.02% Insertion average length | 1.77 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 237436 % of reads mapped to multiple loci | 36.73% Number of reads mapped to too many loci | 56578 % of reads mapped to too many loci | 8.75% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.21% % of reads unmapped: other | 0.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 86427 86427 86427 N_multimapping 237436 237436 237436 N_noFeature 27977 31646 308172 N_ambiguous 12570 1786 82 UnstrandedReadsAssigned:282058 PositiveStrandReadsAssigned:289173 NegativeStrandReadsAssigned:14351 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133349 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: ERR6133349-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 646,468 reads, 395,466 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 874 rounds 52973 ERR6133349.ke.tsv 35125 ERR6133349.se.tsv 88098 total ==> ERR6133349.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 3 7.70981 PNS24243 293 194 0 0 KQK14069 1603 1504 3 7.03315 KQK14071 474 375 0 0 ==> ERR6133349.se.tsv <== BRADI_1g14170v3 3 BRADI_1g53295v3 0 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 5 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 3 BRADI_1g48960v3 0 ERR6133349 completed mapping pipeline successfully