Starting /dee2/code/volunteer_pipeline.sh ERR6133324 current disk space = 1548296851456 free memory = 1388464304 ERR6133324 SRAfilesize d0b116afc1fc009341d7a3ab72e62cea ERR6133324.sra ERR6133324.sra file validated ERR6133324 is single end ERR6133324 is conventional basespace ERR6133324 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133324_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 36.5205 37.0 37.0 37.0 37.0 37.0 2 36.59675 37.0 37.0 37.0 37.0 37.0 3 36.426 37.0 37.0 37.0 37.0 37.0 4 36.29725 37.0 37.0 37.0 37.0 37.0 5 36.398 37.0 37.0 37.0 37.0 37.0 6 36.49825 37.0 37.0 37.0 37.0 37.0 7 38.544 40.0 37.0 40.0 37.0 40.0 8 38.6895 40.0 37.0 40.0 37.0 40.0 9 38.69225 40.0 37.0 40.0 37.0 40.0 10-11 38.7185 40.0 37.0 40.0 37.0 40.0 12-13 38.670125 40.0 37.0 40.0 37.0 40.0 14-15 38.694625 40.0 37.0 40.0 37.0 40.0 16-17 38.670125 40.0 37.0 40.0 37.0 40.0 18-19 38.68375 40.0 37.0 40.0 37.0 40.0 20-21 38.455625 40.0 37.0 40.0 37.0 40.0 22-23 38.587 40.0 37.0 40.0 37.0 40.0 24-25 38.512 40.0 37.0 40.0 37.0 40.0 26-27 38.409 40.0 37.0 40.0 37.0 40.0 28-29 38.388 40.0 37.0 40.0 37.0 40.0 30-31 38.386125 40.0 37.0 40.0 37.0 40.0 32-33 38.328875 40.0 37.0 40.0 37.0 40.0 34-35 38.330875000000006 40.0 37.0 40.0 37.0 40.0 36-37 38.160125 40.0 37.0 40.0 37.0 40.0 38-39 37.951 40.0 37.0 40.0 37.0 40.0 40-41 37.862875 40.0 37.0 40.0 37.0 40.0 42-43 37.825125 38.5 37.0 40.0 37.0 40.0 44-45 37.6045 37.0 37.0 40.0 33.0 40.0 46-47 37.404875000000004 37.0 37.0 40.0 33.0 40.0 48-49 37.372249999999994 37.0 37.0 40.0 33.0 40.0 50-51 37.176500000000004 37.0 37.0 40.0 33.0 40.0 52-53 36.9785 37.0 37.0 40.0 33.0 40.0 54-55 36.79575 37.0 37.0 38.5 33.0 40.0 56-57 36.620625000000004 37.0 37.0 37.0 33.0 40.0 58-59 36.256875 37.0 37.0 37.0 33.0 40.0 60-61 36.10025 37.0 37.0 37.0 33.0 40.0 62-63 35.6505 37.0 33.0 37.0 33.0 37.0 64-65 35.267624999999995 37.0 33.0 37.0 33.0 37.0 66-67 35.134375000000006 37.0 33.0 37.0 33.0 37.0 68-69 33.683375 35.0 33.0 37.0 30.0 37.0 70-71 33.67366121819098 33.0 33.0 37.0 30.0 37.0 72-73 34.08490415436617 33.0 33.0 37.0 33.0 37.0 74-75 34.02295232087778 33.0 33.0 37.0 33.0 37.0 76-77 33.61163431840302 33.0 33.0 37.0 27.0 37.0 78-79 33.32911708918307 33.0 33.0 37.0 27.0 37.0 80-81 32.99215943337301 33.0 33.0 37.0 27.0 37.0 82-83 32.95583337697204 33.0 33.0 37.0 27.0 37.0 84-85 32.3883248289418 33.0 33.0 35.0 27.0 37.0 86-87 32.081381902283894 33.0 33.0 33.0 27.0 37.0 88-89 32.01199768719283 33.0 33.0 33.0 27.0 37.0 90-91 31.50925122867881 33.0 30.0 33.0 27.0 37.0 92-93 30.527898236484532 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 2.0 22 5.0 23 5.0 24 5.0 25 4.0 26 15.0 27 21.0 28 20.0 29 23.0 30 24.0 31 41.0 32 69.0 33 80.0 34 208.0 35 563.0 36 1040.0 37 1472.0 38 375.0 39 24.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 64.35 9.125 8.975 17.549999999999997 2 47.125 25.55 17.599999999999998 9.725 3 30.275000000000002 37.6 18.65 13.475000000000001 4 30.95 27.025 22.425 19.6 5 22.025 28.125 29.875 19.975 6 20.275000000000002 33.650000000000006 29.125 16.950000000000003 7 29.975 27.375 24.675 17.974999999999998 8 26.974999999999998 27.425 28.449999999999996 17.150000000000002 9 24.925 27.775 29.325000000000003 17.974999999999998 10-11 24.6 27.487499999999997 29.562500000000004 18.35 12-13 23.0875 29.1625 29.875 17.875 14-15 22.4875 27.037499999999998 30.7375 19.7375 16-17 22.175 29.1125 27.987499999999997 20.724999999999998 18-19 23.7375 25.387500000000003 30.5375 20.3375 20-21 23.3875 25.887500000000003 30.2875 20.4375 22-23 25.525 24.75 28.449999999999996 21.275 24-25 23.7125 26.85 29.2 20.2375 26-27 23.625 25.9875 30.162499999999998 20.225 28-29 23.9875 27.200000000000003 28.537499999999998 20.275000000000002 30-31 24.675 27.125 28.499999999999996 19.7 32-33 23.6125 25.7375 30.912499999999998 19.7375 34-35 23.0 27.900000000000002 28.849999999999998 20.25 36-37 23.125 28.599999999999998 27.762500000000003 20.5125 38-39 24.637500000000003 25.2625 29.612500000000004 20.4875 40-41 23.95 25.674999999999997 29.312500000000004 21.0625 42-43 24.637500000000003 27.1 28.4 19.8625 44-45 23.150000000000002 27.3625 29.2875 20.200000000000003 46-47 23.25 27.9375 28.475 20.3375 48-49 22.05 27.6125 29.6875 20.65 50-51 22.162499999999998 28.1625 30.337500000000002 19.3375 52-53 22.875 29.5 28.799999999999997 18.825 54-55 22.975 28.3875 30.675 17.962500000000002 56-57 22.525000000000002 27.8375 29.549999999999997 20.0875 58-59 24.25 27.400000000000002 28.449999999999996 19.900000000000002 60-61 24.9125 27.212500000000002 28.8625 19.0125 62-63 21.6125 29.312500000000004 30.0 19.075 64-65 22.375 29.6375 29.075 18.912499999999998 66-67 23.05 28.6375 28.7 19.6125 68-69 21.525 28.9375 29.6375 19.900000000000002 70-71 22.700464299159243 28.372443217467687 29.413979169280964 19.513113314092106 72-73 23.075942915392456 27.510193679918448 29.994903160040774 19.418960244648318 74-75 23.524080787156915 28.404971517348525 28.75453133091662 19.31641636457794 76-77 23.66341848828022 26.968659468001054 29.194100605741376 20.173821437977352 78-79 23.58857449376425 26.847257610299046 30.19981225693979 19.364355638996916 80-81 23.371490869446713 29.39493049877351 28.113927500681385 19.119651131098394 82-83 20.99023709902371 27.489539748953973 29.9302649930265 21.589958158995817 84-85 22.729876826124322 25.88083643655113 30.979661987969067 20.409624749355483 86-87 22.72333044232437 28.04278693263949 28.490893321769295 20.74298930326684 88-89 21.393466319745592 30.557964729690664 28.83781439722463 19.210754553339115 90-91 21.40792136455623 31.671003180109857 27.68141081237352 19.239664642960395 92-93 19.731136166522116 34.027175484244 27.580225498699047 18.66146285053484 >>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 0.5 17 1.0 18 0.5 19 0.5 20 0.5 21 1.0 22 3.0 23 7.5 24 10.0 25 9.0 26 15.5 27 22.5 28 28.0 29 35.5 30 44.5 31 50.5 32 55.5 33 81.0 34 107.5 35 131.0 36 159.5 37 208.5 38 238.0 39 212.5 40 213.5 41 229.5 42 240.0 43 250.0 44 224.5 45 218.5 46 206.0 47 156.0 48 133.0 49 131.5 50 128.0 51 126.0 52 127.5 53 124.5 54 115.0 55 94.0 56 80.0 57 78.5 58 53.0 59 29.5 60 24.0 61 19.5 62 15.0 63 6.5 64 4.0 65 3.0 66 1.5 67 0.5 68 3.0 69 5.5 70 2.5 71 0.0 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 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 26.0 72 38.0 73 27.0 74 32.0 75 30.0 76 38.0 77 34.0 78 31.0 79 27.0 80 34.0 81 45.0 82 44.0 83 40.0 84 64.0 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 3459.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.925 #Duplication Level Percentage of deduplicated Percentage of total 1 92.0494140006335 72.65 2 4.022806461830852 6.35 3 1.2987012987012987 3.075 4 0.6651884700665188 2.1 5 0.4434589800443459 1.7500000000000002 6 0.2850807728856509 1.35 7 0.15837820715869497 0.8750000000000001 8 0.15837820715869497 1.0 9 0.09502692429521697 0.675 >10 0.8235666772252138 10.174999999999999 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 26 0.65 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 23 0.575 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 22 0.5499999999999999 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 22 0.5499999999999999 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 21 0.525 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 20 0.5 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 19 0.475 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 16 0.4 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 16 0.4 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 15 0.375 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 15 0.375 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 15 0.375 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 13 0.325 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 12 0.3 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 11 0.27499999999999997 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 11 0.27499999999999997 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 11 0.27499999999999997 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 11 0.27499999999999997 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 10 0.25 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 9 0.22499999999999998 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 9 0.22499999999999998 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 8 0.2 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 8 0.2 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 8 0.2 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 7 0.17500000000000002 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 7 0.17500000000000002 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 7 0.17500000000000002 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit CGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTC 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 6 0.15 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 6 0.15 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 6 0.15 No Hit AGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAA 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit AGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGT 5 0.125 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 5 0.125 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 5 0.125 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 5 0.125 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 5 0.125 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 5 0.125 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 5 0.125 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.0625 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 35 0.007375323 27.49296 86-87 >>END_MODULE Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101191 READS because READLEN < 1 Read 101191 spots for ERR6133324.sra Written 101191 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra Rejected 101176 READS because READLEN < 1 Read 101176 spots for ERR6133324.sra Written 101176 spots for ERR6133324.sra SRR ids: ['ERR6133324.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qkcbpdal ERR6133324.sra spots: 2023535 blocks: [[1, 101176], [101177, 202352], [202353, 303528], [303529, 404704], [404705, 505880], [505881, 607056], [607057, 708232], [708233, 809408], [809409, 910584], [910585, 1011760], [1011761, 1112936], [1112937, 1214112], [1214113, 1315288], [1315289, 1416464], [1416465, 1517640], [1517641, 1618816], [1618817, 1719992], [1719993, 1821168], [1821169, 1922344], [1922345, 2023535]] ERR6133324 file size 440260 ERR6133324 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 ERR6133324 ERR6133324_1.fastq Input file: ERR6133324_1.fastq trimmed: ERR6133324-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 00:38:36 2024 >> started Sat Dec 7 00:38:37 2024 >> done (1.261s) 2023535 reads processed; of these: 416 ( 0.02%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 2023112 (99.98%) reads available; of these: 29187 ( 1.44%) trimmed reads available after processing 1993925 (98.56%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 32 0.00% 19 48 0.00% 20 38 0.00% 21 26 0.00% 22 26 0.00% 23 21 0.00% 24 14 0.00% 25 27 0.00% 26 18 0.00% 27 15 0.00% 28 31 0.00% 29 16 0.00% 30 22 0.00% 31 33 0.00% 32 41 0.00% 33 20 0.00% 34 29 0.00% 35 63 0.00% 36 10 0.00% 37 21 0.00% 38 25 0.00% 39 75 0.00% 40 95 0.00% 41 30 0.00% 42 13 0.00% 43 22 0.00% 44 20 0.00% 45 12 0.00% 46 11 0.00% 47 12 0.00% 48 12 0.00% 49 8 0.00% 50 10 0.00% 51 77 0.00% 52 21 0.00% 53 10 0.00% 54 4 0.00% 55 7 0.00% 56 9 0.00% 57 21 0.00% 58 15 0.00% 59 15 0.00% 60 9 0.00% 61 14 0.00% 62 2 0.00% 63 1 0.00% 64 0 0.00% 65 5 0.00% 66 4 0.00% 67 8 0.00% 68 18 0.00% 69 69 0.00% 70 16433 0.81% 71 15958 0.79% 72 16995 0.84% 73 16372 0.81% 74 15541 0.77% 75 15519 0.77% 76 14984 0.74% 77 16489 0.82% 78 16443 0.81% 79 17208 0.85% 80 17354 0.86% 81 22000 1.09% 82 22854 1.13% 83 19738 0.98% 84 24485 1.21% 85 24 0.00% 86 44 0.00% 87 87 0.00% 88 179 0.01% 89 399 0.02% 90 987 0.05% 91 3379 0.17% 92 20909 1.03% 93 1727526 85.39% 2023112 reads passed initial QC criterion=sequence-density sequence-density=5.54 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=31 prefix-density=5.59 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=140.45 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=9.4 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAGAAA 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 00:38:56 Started mapping on | Dec 07 00:38:56 Finished on | Dec 07 00:39:03 Mapping speed, Million of reads per hour | 1040.46 Number of input reads | 2023112 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 1138260 Uniquely mapped reads % | 56.26% Average mapped length | 89.80 Number of splices: Total | 39947 Number of splices: Annotated (sjdb) | 32942 Number of splices: GT/AG | 37098 Number of splices: GC/AG | 1158 Number of splices: AT/AC | 31 Number of splices: Non-canonical | 1660 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.06% Deletion average length | 1.77 Insertion rate per base | 0.03% Insertion average length | 1.73 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 721912 % of reads mapped to multiple loci | 35.68% Number of reads mapped to too many loci | 102273 % of reads mapped to too many loci | 5.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.66% % of reads unmapped: other | 0.33% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 162940 162940 162940 N_multimapping 721912 721912 721912 N_noFeature 100737 114560 1086826 N_ambiguous 44431 6805 200 UnstrandedReadsAssigned:993092 PositiveStrandReadsAssigned:1016895 NegativeStrandReadsAssigned:51234 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133324 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: ERR6133324-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,023,112 reads, 1,419,468 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 921 rounds 52973 ERR6133324.ke.tsv 35125 ERR6133324.se.tsv 88098 total ==> ERR6133324.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 32 22.3507 PNS24243 293 194 0 0 KQK14069 1603 1504 27 17.2033 KQK14071 474 375 0 0 ==> ERR6133324.se.tsv <== BRADI_1g14170v3 27 BRADI_1g53295v3 25 BRADI_1g59795v3 16 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 40 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 14 BRADI_1g48960v3 0 ERR6133324 completed mapping pipeline successfully