Starting /dee2/code/volunteer_pipeline.sh ERR6133333 current disk space = 1548176461824 free memory = 1436494276 ERR6133333 SRAfilesize 07c3461e98fb9adb8ffdb4f88d2ebe97 ERR6133333.sra ERR6133333.sra file validated ERR6133333 is single end ERR6133333 is conventional basespace ERR6133333 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133333_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.27375 37.0 37.0 37.0 33.0 37.0 2 36.67925 37.0 37.0 37.0 37.0 37.0 3 36.631 37.0 37.0 37.0 37.0 37.0 4 36.35675 37.0 37.0 37.0 37.0 37.0 5 36.36875 37.0 37.0 37.0 37.0 37.0 6 36.522 37.0 37.0 37.0 37.0 37.0 7 38.7285 40.0 37.0 40.0 37.0 40.0 8 38.78475 40.0 37.0 40.0 37.0 40.0 9 38.80925 40.0 37.0 40.0 37.0 40.0 10-11 38.755375 40.0 37.0 40.0 37.0 40.0 12-13 38.776125 40.0 37.0 40.0 37.0 40.0 14-15 38.772875 40.0 37.0 40.0 37.0 40.0 16-17 38.77125 40.0 37.0 40.0 37.0 40.0 18-19 38.649874999999994 40.0 37.0 40.0 37.0 40.0 20-21 38.59375 40.0 37.0 40.0 37.0 40.0 22-23 38.494625 40.0 37.0 40.0 37.0 40.0 24-25 38.462625 40.0 37.0 40.0 37.0 40.0 26-27 38.434 40.0 37.0 40.0 37.0 40.0 28-29 38.53475 40.0 37.0 40.0 37.0 40.0 30-31 38.449749999999995 40.0 37.0 40.0 37.0 40.0 32-33 38.289625 40.0 37.0 40.0 37.0 40.0 34-35 38.173874999999995 40.0 37.0 40.0 37.0 40.0 36-37 38.165125 40.0 37.0 40.0 37.0 40.0 38-39 38.1425 40.0 37.0 40.0 37.0 40.0 40-41 38.02775 40.0 37.0 40.0 37.0 40.0 42-43 37.925625 38.5 37.0 40.0 37.0 40.0 44-45 37.776375 37.0 37.0 40.0 37.0 40.0 46-47 37.70075 37.0 37.0 40.0 37.0 40.0 48-49 37.5135 37.0 37.0 40.0 37.0 40.0 50-51 37.313874999999996 37.0 37.0 40.0 35.0 40.0 52-53 37.189375 37.0 37.0 40.0 35.0 40.0 54-55 36.995000000000005 37.0 37.0 38.5 33.0 40.0 56-57 36.862875 37.0 37.0 37.0 33.0 40.0 58-59 36.64725 37.0 37.0 37.0 33.0 40.0 60-61 36.54475 37.0 37.0 37.0 33.0 40.0 62-63 36.372875 37.0 37.0 37.0 33.0 38.5 64-65 36.21575 37.0 37.0 37.0 33.0 37.0 66-67 35.973875 37.0 37.0 37.0 33.0 37.0 68-69 35.209 37.0 35.0 37.0 33.0 37.0 70-71 35.3543631778058 37.0 35.0 37.0 33.0 37.0 72-73 35.81206031793766 37.0 37.0 37.0 33.0 37.0 74-75 35.76109381609554 37.0 37.0 37.0 33.0 37.0 76-77 35.74541672885086 37.0 37.0 37.0 33.0 37.0 78-79 35.770214481535234 37.0 37.0 37.0 33.0 37.0 80-81 35.71906051304049 37.0 37.0 37.0 33.0 37.0 82-83 35.61104094777365 37.0 37.0 37.0 33.0 37.0 84-85 35.62225443106823 37.0 37.0 37.0 33.0 37.0 86-87 35.515989628349175 37.0 37.0 37.0 33.0 37.0 88-89 35.52175165658312 37.0 37.0 37.0 33.0 37.0 90-91 35.466004033419765 37.0 35.0 37.0 33.0 37.0 92-93 35.345145491212904 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 6.0 21 0.0 22 4.0 23 6.0 24 5.0 25 6.0 26 14.0 27 13.0 28 14.0 29 13.0 30 23.0 31 32.0 32 41.0 33 54.0 34 85.0 35 180.0 36 778.0 37 1056.0 38 1578.0 39 92.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.14203550887721 7.301825456364091 7.401850462615654 17.154288572143038 2 49.35 26.474999999999998 14.549999999999999 9.625 3 31.374999999999996 36.4 17.724999999999998 14.499999999999998 4 31.8 25.924999999999997 22.025 20.25 5 25.874999999999996 27.425 26.85 19.85 6 22.05 30.8 28.975 18.175 7 32.275 26.6 24.45 16.675 8 28.349999999999998 27.425 26.974999999999998 17.25 9 26.025 26.375 28.599999999999998 19.0 10-11 25.05 28.225 28.4375 18.2875 12-13 24.4125 28.9125 29.3375 17.3375 14-15 21.9625 26.275 32.0375 19.725 16-17 24.175 30.337500000000002 25.2375 20.25 18-19 24.725 25.95 28.625 20.7 20-21 25.0375 25.15 27.950000000000003 21.8625 22-23 26.6 25.7125 26.424999999999997 21.2625 24-25 23.925 27.1125 28.525 20.4375 26-27 24.4875 24.0125 29.65 21.85 28-29 25.1 27.200000000000003 27.1375 20.5625 30-31 24.587500000000002 26.9125 28.712500000000002 19.787499999999998 32-33 25.05 25.0375 29.362500000000004 20.549999999999997 34-35 23.3125 27.575 28.012500000000003 21.099999999999998 36-37 23.45 27.3875 26.937499999999996 22.225 38-39 25.04376094023506 26.156539134783696 28.019504876219052 20.78019504876219 40-41 25.424999999999997 25.95 27.1125 21.512500000000003 42-43 24.5 28.349999999999998 28.000000000000004 19.15 44-45 22.175 28.4375 28.95 20.4375 46-47 23.1125 28.425 26.974999999999998 21.4875 48-49 23.849999999999998 26.150000000000002 29.7 20.3 50-51 21.875 27.987499999999997 29.7 20.4375 52-53 23.5875 29.799999999999997 27.737499999999997 18.875 54-55 23.0375 30.275000000000002 28.037499999999998 18.65 56-57 23.1 27.787499999999998 28.3125 20.8 58-59 24.5125 27.650000000000002 27.675 20.1625 60-61 25.7125 27.5875 27.224999999999998 19.475 62-63 22.875 29.225 28.825 19.075 64-65 23.327079424640402 30.70669168230144 27.517198248905565 18.449030644152593 66-67 23.393348337084273 28.68217054263566 28.657164291072768 19.2673168292073 68-69 21.5625 30.275000000000002 27.1 21.0625 70-71 25.335844318895166 28.19836785938481 26.854990583804145 19.610797237915882 72-73 24.15378720143058 29.199131434410525 28.087878400817473 18.559202963341423 74-75 24.623767514270885 27.439024390243905 28.502854177477943 19.434353918007265 76-77 23.835291012273988 28.956051207601952 28.230170252078658 18.978487528045402 78-79 23.960289777300776 28.119130668097664 28.17279313120472 19.747786423396835 80-81 22.185837085550553 30.42707054168372 27.6981852913085 19.688907081457224 82-83 22.475978276006128 29.174209720094694 27.085364155410108 21.26444784848907 84-85 23.239537208970145 28.095986287673192 29.01014140837023 19.65433509498643 86-87 22.558340535868627 28.98300201670988 27.369634111207148 21.089023336214346 88-89 22.22702391241717 31.41745894554883 26.807836358398156 19.54768078363584 90-91 21.578795736099107 32.33938346297897 25.554595217516567 20.527225583405357 92-93 20.59925093632959 35.43647363872083 25.194468452895418 18.769806972054162 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 1.0 19 2.0 20 2.5 21 2.5 22 2.5 23 4.5 24 7.0 25 9.0 26 14.5 27 19.5 28 28.0 29 36.5 30 35.0 31 46.5 32 65.0 33 78.5 34 99.0 35 131.5 36 156.0 37 162.0 38 183.0 39 199.0 40 207.5 41 210.5 42 206.5 43 212.5 44 211.5 45 235.0 46 221.5 47 171.0 48 138.5 49 138.0 50 139.0 51 117.5 52 117.5 53 121.5 54 122.5 55 116.0 56 102.0 57 91.0 58 69.5 59 40.5 60 27.5 61 22.5 62 19.5 63 13.0 64 10.0 65 15.0 66 13.0 67 9.0 68 18.0 69 22.5 70 10.5 71 2.0 72 1.5 73 1.0 74 0.5 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 0.025 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 0.025 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 0.0625 66-67 0.025 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 0.0285591889190347 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 35.0 71 33.0 72 35.0 73 26.0 74 34.0 75 34.0 76 29.0 77 30.0 78 34.0 79 26.0 80 39.0 81 36.0 82 37.0 83 40.0 84 61.0 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 3471.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.17500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 91.15646258503402 70.35 2 4.826692581794623 7.449999999999999 3 1.1661807580174928 2.7 4 0.9070294784580499 2.8000000000000003 5 0.4859086491739553 1.875 6 0.32393909944930355 1.5 7 0.12957563977972142 0.7000000000000001 8 0.12957563977972142 0.8 9 0.12957563977972142 0.8999999999999999 >10 0.7450599287333981 10.925 >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 44 1.0999999999999999 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 42 1.05 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 34 0.8500000000000001 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 30 0.75 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 26 0.65 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 22 0.5499999999999999 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 21 0.525 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 19 0.475 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 17 0.42500000000000004 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 14 0.35000000000000003 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 14 0.35000000000000003 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 13 0.325 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 13 0.325 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 11 0.27499999999999997 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 11 0.27499999999999997 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 10 0.25 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 10 0.25 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 10 0.25 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 10 0.25 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 9 0.22499999999999998 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 9 0.22499999999999998 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 9 0.22499999999999998 No Hit GGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAA 9 0.22499999999999998 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 8 0.2 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 8 0.2 No Hit GGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTTGGGAA 7 0.17500000000000002 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 7 0.17500000000000002 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 7 0.17500000000000002 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 6 0.15 No Hit CAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGG 6 0.15 No Hit GCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGA 6 0.15 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 6 0.15 No Hit GAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACT 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 6 0.15 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 6 0.15 No Hit TGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAAT 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATC 5 0.125 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 5 0.125 No Hit GAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGC 5 0.125 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 5 0.125 No Hit CAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit ATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAATGC 5 0.125 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit CAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAG 5 0.125 No Hit GGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTT 5 0.125 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 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 0.0125 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 0.037500000000000006 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 pass >>END_MODULE Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68822 READS because READLEN < 1 Read 68822 spots for ERR6133333.sra Written 68822 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra Rejected 68805 READS because READLEN < 1 Read 68805 spots for ERR6133333.sra Written 68805 spots for ERR6133333.sra SRR ids: ['ERR6133333.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_oibmbq53 ERR6133333.sra spots: 1376117 blocks: [[1, 68805], [68806, 137610], [137611, 206415], [206416, 275220], [275221, 344025], [344026, 412830], [412831, 481635], [481636, 550440], [550441, 619245], [619246, 688050], [688051, 756855], [756856, 825660], [825661, 894465], [894466, 963270], [963271, 1032075], [1032076, 1100880], [1100881, 1169685], [1169686, 1238490], [1238491, 1307295], [1307296, 1376117]] ERR6133333 file size 298557 ERR6133333 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 ERR6133333 ERR6133333_1.fastq Input file: ERR6133333_1.fastq trimmed: ERR6133333-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 00:51:44 2024 >> started Sat Dec 7 00:51:48 2024 >> done (3.732s) 1376117 reads processed; of these: 89 ( 0.01%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 1376022 (99.99%) reads available; of these: 8406 ( 0.61%) trimmed reads available after processing 1367616 (99.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 18 0.00% 20 7 0.00% 21 2 0.00% 22 7 0.00% 23 6 0.00% 24 10 0.00% 25 4 0.00% 26 7 0.00% 27 10 0.00% 28 11 0.00% 29 222 0.02% 30 12 0.00% 31 12 0.00% 32 29 0.00% 33 268 0.02% 34 15 0.00% 35 25 0.00% 36 6 0.00% 37 12 0.00% 38 19 0.00% 39 36 0.00% 40 60 0.00% 41 17 0.00% 42 8 0.00% 43 9 0.00% 44 15 0.00% 45 9 0.00% 46 3 0.00% 47 4 0.00% 48 2 0.00% 49 6 0.00% 50 13 0.00% 51 49 0.00% 52 11 0.00% 53 3 0.00% 54 10 0.00% 55 9 0.00% 56 7 0.00% 57 15 0.00% 58 8 0.00% 59 5 0.00% 60 22 0.00% 61 9 0.00% 62 5 0.00% 63 7 0.00% 64 7 0.00% 65 11 0.00% 66 11 0.00% 67 23 0.00% 68 24 0.00% 69 69 0.01% 70 11704 0.85% 71 11200 0.81% 72 12660 0.92% 73 11382 0.83% 74 10980 0.80% 75 10599 0.77% 76 10388 0.75% 77 11132 0.81% 78 11629 0.85% 79 11637 0.85% 80 11712 0.85% 81 14943 1.09% 82 15932 1.16% 83 13596 0.99% 84 17846 1.30% 85 42 0.00% 86 72 0.01% 87 115 0.01% 88 140 0.01% 89 314 0.02% 90 446 0.03% 91 1138 0.08% 92 3731 0.27% 93 1181487 85.86% 1376022 reads passed initial QC criterion=sequence-density sequence-density=7.01 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=30 prefix-density=7.12 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=20 fanout-score=51.87 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=4.7 sequence=ATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCATGGCATTTTGCTTTGCGTTTTTCCTTTCCGGTTTGTTATTTCTCTTTGTCCCTATGGATATCGTGTGTGTACATTTGA 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 00:52:11 Started mapping on | Dec 07 00:52:11 Finished on | Dec 07 00:52:41 Mapping speed, Million of reads per hour | 165.12 Number of input reads | 1376022 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 732616 Uniquely mapped reads % | 53.24% Average mapped length | 89.69 Number of splices: Total | 17565 Number of splices: Annotated (sjdb) | 14014 Number of splices: GT/AG | 16130 Number of splices: GC/AG | 304 Number of splices: AT/AC | 11 Number of splices: Non-canonical | 1120 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.05% Deletion average length | 1.68 Insertion rate per base | 0.02% Insertion average length | 1.70 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 473244 % of reads mapped to multiple loci | 34.39% Number of reads mapped to too many loci | 124031 % of reads mapped to too many loci | 9.01% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.93% % of reads unmapped: other | 0.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 170162 170162 170162 N_multimapping 473244 473244 473244 N_noFeature 62668 69990 699103 N_ambiguous 30375 4170 128 UnstrandedReadsAssigned:639573 PositiveStrandReadsAssigned:658456 NegativeStrandReadsAssigned:33385 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133333 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: ERR6133333-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,376,022 reads, 895,018 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 977 rounds 52973 ERR6133333.ke.tsv 35125 ERR6133333.se.tsv 88098 total ==> ERR6133333.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 14 15.64 PNS24243 293 194 0 0 KQK14069 1603 1504 10 10.191 KQK14071 474 375 0 0 ==> ERR6133333.se.tsv <== BRADI_1g14170v3 10 BRADI_1g53295v3 14 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 11 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 15 BRADI_1g48960v3 0 ERR6133333 completed mapping pipeline successfully