Starting /dee2/code/volunteer_pipeline.sh ERR6133397 current disk space = 1547683381248 free memory = 1361477852 ERR6133397 SRAfilesize 818dea1f1c4d22e7e04f28c55427519c ERR6133397.sra ERR6133397.sra file validated ERR6133397 is single end ERR6133397 is conventional basespace ERR6133397 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133397_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.20925 33.0 27.0 33.0 15.0 37.0 2 33.28175 33.0 33.0 37.0 27.0 37.0 3 33.798 37.0 33.0 37.0 27.0 37.0 4 33.88 37.0 33.0 37.0 27.0 37.0 5 33.96325 37.0 33.0 37.0 27.0 37.0 6 34.1665 37.0 33.0 37.0 27.0 37.0 7 35.327 37.0 33.0 40.0 27.0 40.0 8 35.4545 37.0 33.0 40.0 27.0 40.0 9 35.3995 37.0 33.0 40.0 27.0 40.0 10-11 35.3835 37.0 33.0 40.0 30.0 40.0 12-13 35.27225 37.0 33.0 40.0 27.0 40.0 14-15 35.21225 37.0 33.0 38.5 27.0 40.0 16-17 34.867625000000004 37.0 33.0 37.0 27.0 40.0 18-19 34.76525 37.0 33.0 37.0 27.0 40.0 20-21 34.066375 37.0 33.0 37.0 24.5 40.0 22-23 33.823375 37.0 33.0 37.0 24.5 40.0 24-25 33.5325 37.0 33.0 37.0 24.5 40.0 26-27 33.35975 37.0 33.0 37.0 22.0 40.0 28-29 32.9655 37.0 33.0 37.0 22.0 40.0 30-31 32.769 37.0 33.0 37.0 22.0 40.0 32-33 32.220375000000004 33.0 33.0 37.0 22.0 40.0 34-35 31.5645 33.0 27.0 37.0 15.0 40.0 36-37 31.11825 33.0 27.0 37.0 15.0 38.5 38-39 31.558875 33.0 27.0 37.0 22.0 40.0 40-41 31.31625 33.0 27.0 37.0 18.5 40.0 42-43 31.052625 33.0 27.0 37.0 15.0 40.0 44-45 30.866500000000002 33.0 27.0 37.0 15.0 40.0 46-47 30.10125 33.0 27.0 37.0 15.0 37.0 48-49 29.9725 33.0 27.0 37.0 15.0 37.0 50-51 29.509375 33.0 27.0 37.0 15.0 37.0 52-53 29.389000000000003 33.0 27.0 37.0 15.0 37.0 54-55 29.37675 33.0 27.0 37.0 15.0 37.0 56-57 28.637500000000003 33.0 24.5 37.0 15.0 37.0 58-59 28.52825 33.0 27.0 35.0 15.0 37.0 60-61 28.11825 33.0 27.0 33.0 15.0 37.0 62-63 27.712375 33.0 22.0 33.0 15.0 37.0 64-65 27.250125 33.0 22.0 33.0 10.5 37.0 66-67 26.546 27.0 22.0 33.0 6.0 37.0 68-69 26.26375 27.0 22.0 33.0 10.5 35.0 70-71 28.31221459537572 33.0 27.0 33.0 15.0 37.0 72-73 28.641272180059925 33.0 27.0 33.0 15.0 37.0 74-75 28.55484798733541 33.0 27.0 33.0 15.0 37.0 76-77 28.163245657829748 33.0 27.0 33.0 15.0 37.0 78-79 27.443625164237922 33.0 27.0 33.0 6.0 37.0 80-81 26.778265724653313 33.0 24.5 33.0 6.0 37.0 82-83 25.97286125074502 33.0 22.0 33.0 2.0 37.0 84-85 25.470617980473683 33.0 22.0 33.0 2.0 37.0 86-87 24.284957914743416 30.0 15.0 33.0 2.0 37.0 88-89 23.484251968503937 30.0 10.5 33.0 2.0 35.0 90-91 22.290388270431713 27.0 2.0 33.0 2.0 33.0 92-93 21.149063263643768 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 91.0 21 103.0 22 143.0 23 142.0 24 210.0 25 213.0 26 218.0 27 244.0 28 238.0 29 260.0 30 246.0 31 260.0 32 297.0 33 283.0 34 253.0 35 296.0 36 292.0 37 182.0 38 29.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.9 9.049999999999999 8.0 16.05 2 48.6 24.4 16.650000000000002 10.35 3 32.1 34.925 18.825 14.149999999999999 4 25.5 30.075000000000003 22.175 22.25 5 26.55 24.125 28.599999999999998 20.724999999999998 6 16.725 39.550000000000004 24.8 18.925 7 33.4 28.275 22.2 16.125 8 24.125 27.0 26.424999999999997 22.45 9 22.15 32.175 26.700000000000003 18.975 10-11 21.575 28.249999999999996 32.3625 17.8125 12-13 21.2625 30.049999999999997 27.35 21.337500000000002 14-15 19.8375 33.3625 27.6 19.2 16-17 24.087500000000002 27.525 24.462500000000002 23.925 18-19 24.5 23.3 33.2 19.0 20-21 25.912499999999998 25.3125 29.575000000000003 19.2 22-23 27.900000000000002 22.2125 30.837500000000002 19.05 24-25 22.275 24.3125 30.562499999999996 22.85 26-27 24.05 24.3625 28.875 22.7125 28-29 22.8 28.1125 29.5375 19.55 30-31 30.0875 24.9375 25.15 19.825 32-33 27.0 23.75 27.775 21.475 34-35 21.15 33.1 26.625 19.125 36-37 26.0 26.200000000000003 24.9 22.900000000000002 38-39 30.25 22.8375 28.037499999999998 18.875 40-41 23.1 24.25 33.175 19.475 42-43 27.1125 29.2875 26.237500000000004 17.3625 44-45 25.4 25.4 29.562500000000004 19.6375 46-47 26.237500000000004 26.387500000000003 25.825 21.55 48-49 25.687500000000004 24.5 27.2625 22.55 50-51 21.1125 30.775000000000002 26.375 21.7375 52-53 21.6875 26.4625 26.387500000000003 25.4625 54-55 22.2 24.9875 31.525 21.2875 56-57 26.5625 28.6125 25.5 19.325 58-59 21.675 29.012500000000003 29.6625 19.650000000000002 60-61 28.3375 26.5625 26.2625 18.8375 62-63 20.525 26.775 30.562499999999996 22.1375 64-65 20.1875 34.55 26.887499999999996 18.375 66-67 25.2875 29.037499999999998 26.2625 19.412499999999998 68-69 19.5625 27.1 28.775000000000002 24.5625 70-71 22.54668504825166 28.98859506203785 26.419350795839076 22.04536909387141 72-73 25.123402100999876 25.591697253512212 31.185925832173144 18.09897481331477 74-75 26.385696040868456 29.42528735632184 27.100893997445723 17.088122605363985 76-77 21.08729338842975 24.31559917355372 27.530991735537192 27.066115702479337 78-79 25.345321866041175 29.098253844149074 26.817826426896012 18.738597862913732 80-81 21.22008940310281 35.65606100447016 25.861162240336576 17.262687352090456 82-83 23.92580731251668 25.980784627702164 25.48705631171604 24.60635174806512 84-85 20.578691184424013 27.149810708491078 31.544077879935102 20.72742022714981 86-87 21.544936193320662 30.491447189790932 24.55878360032582 23.404833016562584 88-89 19.399945696443115 26.635894651099644 30.93945153407548 23.024708118381753 90-91 25.156122726038554 31.88976377952756 24.911756720065164 18.04235677436872 92-93 18.436057561770298 31.50963888134673 28.305729025251154 21.748574531631824 >>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 1.0 18 4.0 19 4.5 20 2.5 21 3.0 22 5.5 23 5.5 24 6.5 25 10.0 26 14.0 27 15.5 28 17.0 29 21.0 30 32.5 31 46.5 32 51.5 33 51.5 34 56.5 35 83.0 36 127.0 37 194.0 38 246.0 39 237.5 40 217.5 41 218.5 42 226.0 43 232.5 44 212.5 45 186.5 46 166.5 47 136.0 48 121.5 49 111.0 50 97.5 51 106.0 52 108.0 53 128.5 54 226.0 55 217.0 56 107.5 57 73.5 58 62.5 59 46.0 60 29.0 61 16.5 62 15.0 63 16.0 64 15.5 65 9.0 66 4.5 67 4.5 68 5.0 69 10.5 70 11.5 71 8.0 72 4.0 73 1.0 74 1.5 75 1.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.5 81 0.5 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 21.0 71 19.0 72 19.0 73 17.0 74 18.0 75 21.0 76 26.0 77 17.0 78 10.0 79 16.0 80 26.0 81 32.0 82 22.0 83 23.0 84 30.0 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 3683.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.55 #Duplication Level Percentage of deduplicated Percentage of total 1 91.45416953824949 66.35 2 3.997243280496209 5.800000000000001 3 1.9297036526533424 4.2 4 0.5858028945554791 1.7000000000000002 5 0.5858028945554791 2.125 6 0.17229496898690558 0.75 7 0.10337698139214334 0.525 8 0.10337698139214334 0.6 9 0.20675396278428668 1.35 >10 0.8270158511371467 10.575 >50 0.0 0.0 >100 0.03445899379738111 6.0249999999999995 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 241 6.0249999999999995 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 42 1.05 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 33 0.8250000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 32 0.8 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 26 0.65 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 23 0.575 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 23 0.575 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 21 0.525 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 21 0.525 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 18 0.44999999999999996 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 17 0.42500000000000004 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 15 0.375 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 14 0.35000000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 14 0.35000000000000003 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 13 0.325 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 13 0.325 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 12 0.3 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 11 0.27499999999999997 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 11 0.27499999999999997 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 11 0.27499999999999997 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 11 0.27499999999999997 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 9 0.22499999999999998 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 9 0.22499999999999998 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 9 0.22499999999999998 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 8 0.2 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 7 0.17500000000000002 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit TGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit ATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAG 5 0.125 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 5 0.125 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 5 0.125 No Hit GGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAA 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGT 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 30 2.0265124E-6 71.80208 1 CAATACA 30 2.0265124E-6 71.80208 8 GAGCAAT 30 2.0265124E-6 71.80208 5 AGAGCAA 30 2.0265124E-6 71.80208 4 GAGAGCA 30 2.0265124E-6 71.80208 3 GGAGAGC 35 5.0633207E-6 61.544643 2 GCAATAC 35 5.0633207E-6 61.544643 7 AATACAA 35 5.0633207E-6 61.544643 9 AGCAATA 35 5.0633207E-6 61.544643 6 TGCTGCT 25 4.596562E-5 43.08125 22-23 GCGTTGT 25 4.596562E-5 43.08125 16-17 CGTTGTG 25 4.596562E-5 43.08125 16-17 TTGTGCT 25 4.596562E-5 43.08125 18-19 TGTGCTG 25 4.596562E-5 43.08125 20-21 GTTGTGC 25 4.596562E-5 43.08125 18-19 GTGCTGC 25 4.596562E-5 43.08125 20-21 AAGCATC 30 9.907194E-5 37.79057 80-81 AGCCGAA 30 1.0713638E-4 37.29978 74-75 GCCGAAA 30 1.0713638E-4 37.29978 74-75 CCGAAAG 30 1.0713638E-4 37.29978 76-77 >>END_MODULE Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54474 READS because READLEN < 1 Read 54474 spots for ERR6133397.sra Written 54474 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra Rejected 54466 READS because READLEN < 1 Read 54466 spots for ERR6133397.sra Written 54466 spots for ERR6133397.sra SRR ids: ['ERR6133397.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_p1pvmyir ERR6133397.sra spots: 1089328 blocks: [[1, 54466], [54467, 108932], [108933, 163398], [163399, 217864], [217865, 272330], [272331, 326796], [326797, 381262], [381263, 435728], [435729, 490194], [490195, 544660], [544661, 599126], [599127, 653592], [653593, 708058], [708059, 762524], [762525, 816990], [816991, 871456], [871457, 925922], [925923, 980388], [980389, 1034854], [1034855, 1089328]] ERR6133397 file size 237721 ERR6133397 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 ERR6133397 ERR6133397_1.fastq Input file: ERR6133397_1.fastq trimmed: ERR6133397-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 03:09:27 2024 >> started Sat Dec 7 03:09:28 2024 >> done (0.945s) 1089328 reads processed; of these: 18 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 1089307 (100.00%) reads available; of these: 278782 (25.59%) trimmed reads available after processing 810525 (74.41%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 4 0.00% 20 1 0.00% 21 2 0.00% 22 2 0.00% 23 2 0.00% 24 3 0.00% 25 4 0.00% 26 0 0.00% 27 3 0.00% 28 17 0.00% 29 12 0.00% 30 1 0.00% 31 4 0.00% 32 6 0.00% 33 7 0.00% 34 0 0.00% 35 8 0.00% 36 6 0.00% 37 2 0.00% 38 8 0.00% 39 3 0.00% 40 20 0.00% 41 9 0.00% 42 11 0.00% 43 21 0.00% 44 17 0.00% 45 17 0.00% 46 27 0.00% 47 66 0.01% 48 82 0.01% 49 85 0.01% 50 93 0.01% 51 182 0.02% 52 229 0.02% 53 327 0.03% 54 437 0.04% 55 596 0.05% 56 768 0.07% 57 1233 0.11% 58 867 0.08% 59 1031 0.09% 60 1308 0.12% 61 1498 0.14% 62 1594 0.15% 63 1764 0.16% 64 1833 0.17% 65 2041 0.19% 66 1999 0.18% 67 2049 0.19% 68 1905 0.17% 69 1875 0.17% 70 7590 0.70% 71 7772 0.71% 72 8903 0.82% 73 9167 0.84% 74 9581 0.88% 75 10304 0.95% 76 10858 1.00% 77 12026 1.10% 78 12146 1.12% 79 12908 1.18% 80 13699 1.26% 81 15990 1.47% 82 16943 1.56% 83 17099 1.57% 84 19469 1.79% 85 14036 1.29% 86 14427 1.32% 87 15853 1.46% 88 19319 1.77% 89 20609 1.89% 90 21378 1.96% 91 22742 2.09% 92 20296 1.86% 93 732104 67.21% 1089307 reads passed initial QC criterion=sequence-density sequence-density=3.48 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=25 prefix-density=3.57 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.11 sequence-density-rank=17 fanout-score=94.19 fanout-score-rank=1 prefix-density=10.54 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 03:09:45 Started mapping on | Dec 07 03:09:45 Finished on | Dec 07 03:09:51 Mapping speed, Million of reads per hour | 653.58 Number of input reads | 1089307 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 431557 Uniquely mapped reads % | 39.62% Average mapped length | 88.19 Number of splices: Total | 19268 Number of splices: Annotated (sjdb) | 15490 Number of splices: GT/AG | 18413 Number of splices: GC/AG | 310 Number of splices: AT/AC | 26 Number of splices: Non-canonical | 519 Mismatch rate per base, % | 0.82% Deletion rate per base | 0.04% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 1.79 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 562552 % of reads mapped to multiple loci | 51.64% Number of reads mapped to too many loci | 36590 % of reads mapped to too many loci | 3.36% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.81% % of reads unmapped: other | 0.57% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 95198 95198 95198 N_multimapping 562552 562552 562552 N_noFeature 41479 46006 413773 N_ambiguous 16557 3281 112 UnstrandedReadsAssigned:373521 PositiveStrandReadsAssigned:382270 NegativeStrandReadsAssigned:17672 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=85 echo kmer=81 ERR6133397 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: ERR6133397-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,089,307 reads, 698,929 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 814 rounds 52973 ERR6133397.ke.tsv 35125 ERR6133397.se.tsv 88098 total ==> ERR6133397.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 4.09454 PNS24243 293 194 0 0 KQK14069 1603 1504 18 22.4111 KQK14071 474 375 0 0 ==> ERR6133397.se.tsv <== BRADI_1g14170v3 18 BRADI_1g53295v3 4 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 12 BRADI_1g48960v3 0 ERR6133397 completed mapping pipeline successfully