Starting /dee2/code/volunteer_pipeline.sh ERR6133348 current disk space = 1548420739072 free memory = 1397932688 ERR6133348 SRAfilesize 72bf8b64ac89817401f6fa77a3b1d26a ERR6133348.sra ERR6133348.sra file validated ERR6133348 is single end ERR6133348 is conventional basespace ERR6133348 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133348_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 36.412 37.0 37.0 37.0 33.0 37.0 2 36.633 37.0 37.0 37.0 37.0 37.0 3 36.408 37.0 37.0 37.0 33.0 37.0 4 36.37375 37.0 37.0 37.0 37.0 37.0 5 36.357 37.0 37.0 37.0 37.0 37.0 6 36.40825 37.0 37.0 37.0 37.0 37.0 7 38.4065 40.0 37.0 40.0 37.0 40.0 8 38.542 40.0 37.0 40.0 37.0 40.0 9 38.62625 40.0 37.0 40.0 37.0 40.0 10-11 38.676625 40.0 37.0 40.0 37.0 40.0 12-13 38.60025 40.0 37.0 40.0 37.0 40.0 14-15 38.513625 40.0 37.0 40.0 37.0 40.0 16-17 38.4925 40.0 37.0 40.0 37.0 40.0 18-19 38.547124999999994 40.0 37.0 40.0 37.0 40.0 20-21 38.146125 40.0 37.0 40.0 37.0 40.0 22-23 38.373374999999996 40.0 37.0 40.0 37.0 40.0 24-25 38.33275 40.0 37.0 40.0 37.0 40.0 26-27 38.224625 40.0 37.0 40.0 37.0 40.0 28-29 38.240125 40.0 37.0 40.0 37.0 40.0 30-31 38.186 40.0 37.0 40.0 37.0 40.0 32-33 38.215875 40.0 37.0 40.0 37.0 40.0 34-35 38.183125000000004 40.0 37.0 40.0 37.0 40.0 36-37 37.957875 40.0 37.0 40.0 35.0 40.0 38-39 37.685500000000005 38.5 37.0 40.0 33.0 40.0 40-41 37.64625 37.0 37.0 40.0 33.0 40.0 42-43 37.724875 37.0 37.0 40.0 33.0 40.0 44-45 37.450375 37.0 37.0 40.0 33.0 40.0 46-47 37.21425 37.0 37.0 40.0 33.0 40.0 48-49 37.22 37.0 37.0 40.0 33.0 40.0 50-51 36.952875 37.0 37.0 40.0 33.0 40.0 52-53 36.760374999999996 37.0 37.0 40.0 33.0 40.0 54-55 36.554375 37.0 37.0 37.0 33.0 40.0 56-57 36.41674999999999 37.0 37.0 37.0 33.0 40.0 58-59 36.07925 37.0 37.0 37.0 33.0 40.0 60-61 35.966875 37.0 37.0 37.0 33.0 38.5 62-63 35.258 37.0 33.0 37.0 33.0 37.0 64-65 35.079875 37.0 33.0 37.0 33.0 37.0 66-67 34.912125 37.0 33.0 37.0 33.0 37.0 68-69 33.53037500000001 35.0 33.0 37.0 30.0 37.0 70-71 33.393056806743836 33.0 33.0 37.0 27.0 37.0 72-73 33.91160860871962 33.0 33.0 37.0 33.0 37.0 74-75 33.89134882570134 33.0 33.0 37.0 33.0 37.0 76-77 33.6359504655686 33.0 33.0 37.0 30.0 37.0 78-79 33.317831920197165 33.0 33.0 37.0 27.0 37.0 80-81 32.91199415620068 33.0 33.0 37.0 27.0 37.0 82-83 32.85546634406375 33.0 33.0 37.0 27.0 37.0 84-85 32.06953958232731 33.0 33.0 35.0 27.0 37.0 86-87 31.86166619757951 33.0 33.0 33.0 27.0 37.0 88-89 31.949760765550238 33.0 33.0 33.0 27.0 37.0 90-91 31.272445820433436 33.0 30.0 33.0 24.5 37.0 92-93 30.26822403602589 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 3.0 21 3.0 22 3.0 23 3.0 24 2.0 25 9.0 26 12.0 27 21.0 28 21.0 29 26.0 30 41.0 31 51.0 32 79.0 33 129.0 34 232.0 35 663.0 36 1046.0 37 1352.0 38 283.0 39 21.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 65.675 9.075 8.05 17.2 2 49.25 25.650000000000002 15.024999999999999 10.075000000000001 3 30.925000000000004 36.325 18.525 14.224999999999998 4 31.6 25.775 23.225 19.400000000000002 5 22.95 28.599999999999998 29.45 19.0 6 19.575 33.074999999999996 29.525000000000002 17.825 7 30.25 27.950000000000003 24.65 17.150000000000002 8 25.55 29.049999999999997 29.275000000000002 16.125 9 23.875 26.125 29.775000000000002 20.225 10-11 22.8125 28.037499999999998 29.4375 19.7125 12-13 24.3 27.725 29.799999999999997 18.175 14-15 21.3125 26.025 32.875 19.787499999999998 16-17 23.8625 30.1375 26.9625 19.037499999999998 18-19 22.875 25.662499999999998 30.2 21.2625 20-21 23.974999999999998 26.0 29.549999999999997 20.474999999999998 22-23 25.2875 25.2 28.975 20.5375 24-25 23.2625 26.5625 29.8375 20.3375 26-27 22.9375 25.4625 31.674999999999997 19.925 28-29 23.200000000000003 27.400000000000002 30.075000000000003 19.325 30-31 23.849999999999998 27.425 29.049999999999997 19.675 32-33 22.6375 27.237499999999997 30.725 19.400000000000002 34-35 22.725 26.700000000000003 29.6625 20.9125 36-37 22.8 28.525 27.187499999999996 21.4875 38-39 23.3 25.2375 30.4 21.0625 40-41 24.5125 25.5625 28.8875 21.0375 42-43 23.25 27.474999999999998 29.225 20.05 44-45 21.912499999999998 28.249999999999996 29.825000000000003 20.0125 46-47 23.1 27.425 29.212500000000002 20.2625 48-49 22.5875 26.387500000000003 30.475 20.549999999999997 50-51 22.2 27.6375 30.675 19.4875 52-53 23.0125 28.575 29.1125 19.3 54-55 23.325000000000003 28.799999999999997 29.7 18.175 56-57 23.3375 27.725 29.4375 19.5 58-59 23.125 27.800000000000004 29.612500000000004 19.4625 60-61 23.875 27.750000000000004 28.287499999999998 20.0875 62-63 21.525 28.199999999999996 31.45 18.825 64-65 22.0875 30.7 28.9375 18.275 66-67 23.799999999999997 28.025 29.2 18.975 68-69 21.1125 29.575000000000003 29.2875 20.025000000000002 70-71 24.166039628793577 27.928266867318786 28.680712315023825 19.224981188863808 72-73 23.749047498094995 27.597155194310393 29.197358394716787 19.45643891287783 74-75 22.265221878224974 28.637770897832816 29.927760577915375 19.16924664602683 76-77 22.427336999214454 27.939251112856766 28.60696517412935 21.026446713799423 78-79 22.92526974823498 28.22698814439856 29.572399094178763 19.27534301318769 80-81 21.754433464193852 29.80912413699743 29.308244212806283 19.128198186002436 82-83 20.72717256576229 28.09530367717945 29.81682963779094 21.36069411926732 84-85 24.08626242823134 25.808710264668814 29.88376978014284 20.22125752695701 86-87 22.38952997466929 28.947368421052634 29.01773149451168 19.645370109766393 88-89 19.92682240360259 31.269349845201237 29.313256403039684 19.49057134815649 90-91 22.178440754292147 31.480439065578388 27.4556712637208 18.885448916408667 92-93 19.828314100759922 33.91500140726147 27.694905713481567 18.561778778497047 >>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 0.5 19 1.5 20 2.0 21 3.0 22 6.0 23 8.5 24 8.5 25 11.0 26 16.0 27 23.0 28 29.0 29 31.5 30 42.0 31 61.0 32 75.0 33 90.5 34 104.0 35 105.5 36 148.0 37 195.0 38 212.5 39 218.0 40 232.0 41 253.5 42 270.5 43 286.0 44 232.0 45 194.5 46 188.0 47 164.5 48 161.0 49 150.0 50 124.5 51 112.0 52 113.0 53 125.5 54 111.5 55 70.5 56 65.5 57 74.5 58 55.0 59 30.0 60 17.0 61 9.5 62 8.0 63 4.5 64 4.0 65 4.0 66 3.5 67 2.5 68 2.5 69 5.5 70 4.5 71 1.0 72 1.0 73 0.5 74 0.0 75 1.0 76 1.0 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 0.012898232942086934 76-77 0.013090718680455556 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 26.0 71 23.0 72 28.0 73 31.0 74 31.0 75 28.0 76 27.0 77 37.0 78 31.0 79 33.0 80 23.0 81 36.0 82 31.0 83 27.0 84 35.0 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 3553.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.625 #Duplication Level Percentage of deduplicated Percentage of total 1 92.68445839874411 73.8 2 3.5164835164835164 5.6000000000000005 3 1.3186813186813187 3.15 4 0.5337519623233908 1.7000000000000002 5 0.43956043956043955 1.7500000000000002 6 0.18838304552590265 0.8999999999999999 7 0.21978021978021978 1.225 8 0.25117739403453687 1.6 9 0.12558869701726844 0.8999999999999999 >10 0.7221350078492936 9.375 >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 CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 31 0.775 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 31 0.775 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 29 0.7250000000000001 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 23 0.575 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 20 0.5 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 20 0.5 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 19 0.475 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 18 0.44999999999999996 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 17 0.42500000000000004 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 16 0.4 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 15 0.375 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 15 0.375 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 12 0.3 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 10 0.25 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 10 0.25 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 10 0.25 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 10 0.25 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 9 0.22499999999999998 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 9 0.22499999999999998 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 9 0.22499999999999998 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 8 0.2 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 8 0.2 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 8 0.2 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 7 0.17500000000000002 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 7 0.17500000000000002 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTTTAAACT 6 0.15 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 6 0.15 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 5 0.125 No Hit GGGGTTGTACTTGTGATGCGTAATTTGGTCGTCTTGTGACCAAAAGACAT 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTACCTGCTGT 5 0.125 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTACCTGCT 5 0.125 No Hit GATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAA 5 0.125 No Hit GGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAA 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.0875 0.0 0.0 0.0 0.0 24-25 0.1 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 0.1 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138260 READS because READLEN < 1 Read 138260 spots for ERR6133348.sra Written 138260 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra Rejected 138252 READS because READLEN < 1 Read 138252 spots for ERR6133348.sra Written 138252 spots for ERR6133348.sra SRR ids: ['ERR6133348.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_46wz_tth ERR6133348.sra spots: 2765048 blocks: [[1, 138252], [138253, 276504], [276505, 414756], [414757, 553008], [553009, 691260], [691261, 829512], [829513, 967764], [967765, 1106016], [1106017, 1244268], [1244269, 1382520], [1382521, 1520772], [1520773, 1659024], [1659025, 1797276], [1797277, 1935528], [1935529, 2073780], [2073781, 2212032], [2212033, 2350284], [2350285, 2488536], [2488537, 2626788], [2626789, 2765048]] ERR6133348 file size 602852 ERR6133348 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 ERR6133348 ERR6133348_1.fastq Input file: ERR6133348_1.fastq trimmed: ERR6133348-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 01:10:35 2024 >> started Sat Dec 7 01:10:37 2024 >> done (2.055s) 2765048 reads processed; of these: 525 ( 0.02%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 2764508 (99.98%) reads available; of these: 41628 ( 1.51%) trimmed reads available after processing 2722880 (98.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 33 0.00% 19 103 0.00% 20 60 0.00% 21 30 0.00% 22 37 0.00% 23 43 0.00% 24 21 0.00% 25 14 0.00% 26 14 0.00% 27 29 0.00% 28 40 0.00% 29 29 0.00% 30 25 0.00% 31 28 0.00% 32 83 0.00% 33 41 0.00% 34 29 0.00% 35 54 0.00% 36 28 0.00% 37 25 0.00% 38 45 0.00% 39 118 0.00% 40 148 0.01% 41 41 0.00% 42 25 0.00% 43 34 0.00% 44 42 0.00% 45 20 0.00% 46 25 0.00% 47 19 0.00% 48 17 0.00% 49 14 0.00% 50 31 0.00% 51 133 0.00% 52 33 0.00% 53 6 0.00% 54 17 0.00% 55 20 0.00% 56 25 0.00% 57 35 0.00% 58 20 0.00% 59 13 0.00% 60 23 0.00% 61 21 0.00% 62 2 0.00% 63 1 0.00% 64 2 0.00% 65 2 0.00% 66 3 0.00% 67 17 0.00% 68 25 0.00% 69 126 0.00% 70 22785 0.82% 71 21254 0.77% 72 23203 0.84% 73 21559 0.78% 74 20763 0.75% 75 20575 0.74% 76 20083 0.73% 77 21861 0.79% 78 21557 0.78% 79 22381 0.81% 80 21939 0.79% 81 27271 0.99% 82 28221 1.02% 83 24397 0.88% 84 29508 1.07% 85 49 0.00% 86 65 0.00% 87 105 0.00% 88 245 0.01% 89 611 0.02% 90 1370 0.05% 91 4802 0.17% 92 30059 1.09% 93 2377976 86.02% 2764508 reads passed initial QC criterion=sequence-density sequence-density=4.21 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=34 prefix-density=4.23 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=323.41 fanout-score-rank=1 prefix-density=1.64 prefix-fanout=1.0 sequence=GCAGCTTGCTGACAAGTACATGAGCGAGGCTGCTCTGGGAGATGCTAACTCAGATGCCATGAAGACTGGTTCCTTCTACGGTTAGAACACTCTTCATACACACACCATCTCTAGCTGCATAGGAGGAGGTAAAGGAGCACAACAAGGTAATTTGCCCGTCCCAGAAGGTTGCACTGACCGGAATGCCGAGAACTACGACCCAACAGCAAGGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAATTATTCTGATGTTTCACTCTTTGTACCTAAGTACCGCATTGCATCCAAGCAATTGCTGGGCATGAAAAGTTTTTGTTCATATATAAAGATATTGAGTATATTCATTTGGTGAACAGTAATATATATAACTACTTATCCTTGCAGTA 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 01:10:54 Started mapping on | Dec 07 01:10:54 Finished on | Dec 07 01:11:00 Mapping speed, Million of reads per hour | 1658.70 Number of input reads | 2764508 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 1623486 Uniquely mapped reads % | 58.73% Average mapped length | 89.93 Number of splices: Total | 52789 Number of splices: Annotated (sjdb) | 41322 Number of splices: GT/AG | 48843 Number of splices: GC/AG | 1317 Number of splices: AT/AC | 64 Number of splices: Non-canonical | 2565 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.06% Deletion average length | 1.73 Insertion rate per base | 0.02% Insertion average length | 1.65 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 962400 % of reads mapped to multiple loci | 34.81% Number of reads mapped to too many loci | 107117 % of reads mapped to too many loci | 3.87% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.40% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 178622 178622 178622 N_multimapping 962400 962400 962400 N_noFeature 145248 160955 1552426 N_ambiguous 66105 10706 341 UnstrandedReadsAssigned:1412133 PositiveStrandReadsAssigned:1451825 NegativeStrandReadsAssigned:70719 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133348 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: ERR6133348-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,764,508 reads, 2,014,202 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 948 rounds 52973 ERR6133348.ke.tsv 35125 ERR6133348.se.tsv 88098 total ==> ERR6133348.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 39 19.0735 PNS24243 293 194 0 0 KQK14069 1603 1504 38 16.9534 KQK14071 474 375 0 0 ==> ERR6133348.se.tsv <== BRADI_1g14170v3 38 BRADI_1g53295v3 24 BRADI_1g59795v3 22 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 11 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 22 BRADI_1g48960v3 0 ERR6133348 completed mapping pipeline successfully