Starting /dee2/code/volunteer_pipeline.sh ERR6133317 current disk space = 1548242874368 free memory = 1594987388 ERR6133317 SRAfilesize cd60fac6e9f8ee247b511e3661d6697c ERR6133317.sra ERR6133317.sra file validated ERR6133317 is single end ERR6133317 is conventional basespace ERR6133317 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133317_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 35.21325 37.0 33.0 37.0 33.0 37.0 2 36.457 37.0 37.0 37.0 37.0 37.0 3 36.14 37.0 37.0 37.0 33.0 37.0 4 35.66525 37.0 37.0 37.0 33.0 37.0 5 35.62475 37.0 37.0 37.0 33.0 37.0 6 35.8445 37.0 37.0 37.0 33.0 37.0 7 37.62075 40.0 37.0 40.0 33.0 40.0 8 37.62675 40.0 37.0 40.0 33.0 40.0 9 37.761 40.0 37.0 40.0 33.0 40.0 10-11 37.637375000000006 40.0 37.0 40.0 33.0 40.0 12-13 37.558125 40.0 37.0 40.0 33.0 40.0 14-15 37.574625 40.0 37.0 40.0 33.0 40.0 16-17 37.426875 40.0 37.0 40.0 33.0 40.0 18-19 37.412375 37.0 37.0 40.0 33.0 40.0 20-21 37.2035 37.0 37.0 40.0 33.0 40.0 22-23 37.2505 37.0 37.0 40.0 33.0 40.0 24-25 37.3845 37.0 37.0 40.0 33.0 40.0 26-27 37.193 37.0 37.0 40.0 33.0 40.0 28-29 37.135000000000005 37.0 37.0 40.0 33.0 40.0 30-31 37.10525 37.0 37.0 40.0 33.0 40.0 32-33 36.974875 37.0 37.0 40.0 33.0 40.0 34-35 36.876999999999995 37.0 37.0 40.0 33.0 40.0 36-37 36.793499999999995 37.0 37.0 40.0 33.0 40.0 38-39 36.53 37.0 37.0 40.0 33.0 40.0 40-41 36.40412499999999 37.0 37.0 40.0 33.0 40.0 42-43 36.24875 37.0 37.0 40.0 33.0 40.0 44-45 35.759 37.0 33.0 40.0 33.0 40.0 46-47 35.426375 37.0 33.0 38.5 30.0 40.0 48-49 35.388875 37.0 33.0 37.0 30.0 40.0 50-51 35.196625 37.0 33.0 37.0 27.0 40.0 52-53 34.992374999999996 37.0 33.0 37.0 27.0 40.0 54-55 34.90775 37.0 33.0 37.0 27.0 40.0 56-57 34.589875000000006 37.0 33.0 37.0 27.0 40.0 58-59 32.313874999999996 33.0 30.0 37.0 24.5 37.0 60-61 33.824375 37.0 33.0 37.0 27.0 37.0 62-63 34.036625 37.0 33.0 37.0 27.0 37.0 64-65 33.979375000000005 37.0 33.0 37.0 27.0 37.0 66-67 33.71662499999999 37.0 33.0 37.0 27.0 37.0 68-69 33.18575 35.0 33.0 37.0 27.0 37.0 70-71 33.19369267955801 35.0 33.0 37.0 27.0 37.0 72-73 33.57626207874136 37.0 33.0 37.0 27.0 37.0 74-75 33.489385739507675 37.0 33.0 37.0 27.0 37.0 76-77 33.56672279375691 37.0 33.0 37.0 27.0 37.0 78-79 33.59306423601301 37.0 33.0 37.0 27.0 37.0 80-81 33.615827661631194 37.0 33.0 37.0 27.0 37.0 82-83 33.30730534065469 35.0 33.0 37.0 27.0 37.0 84-85 33.037332641467614 33.0 33.0 37.0 27.0 37.0 86-87 33.071870794078066 35.0 33.0 37.0 27.0 37.0 88-89 33.23916554508749 37.0 33.0 37.0 27.0 37.0 90-91 32.930148048452224 33.0 33.0 37.0 27.0 37.0 92-93 32.84791386271871 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 13.0 21 16.0 22 13.0 23 30.0 24 26.0 25 37.0 26 38.0 27 43.0 28 59.0 29 78.0 30 92.0 31 115.0 32 149.0 33 195.0 34 299.0 35 429.0 36 812.0 37 893.0 38 645.0 39 18.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.2 3.55 4.125 8.125 2 66.35 18.925 9.375 5.35 3 33.300000000000004 39.550000000000004 16.35 10.8 4 30.125 28.000000000000004 21.925 19.950000000000003 5 22.900000000000002 29.675 31.3 16.125 6 18.15 37.75 27.175 16.925 7 33.2 29.475 22.475 14.85 8 27.325 29.025000000000002 27.400000000000002 16.25 9 21.85 27.700000000000003 31.75 18.7 10-11 22.35 28.125 31.3 18.224999999999998 12-13 24.875 27.275 29.3375 18.512500000000003 14-15 19.5625 30.5125 31.937500000000004 17.9875 16-17 21.637500000000003 31.75 25.75 20.8625 18-19 21.8 27.462500000000002 30.125 20.6125 20-21 24.4875 24.8625 29.612500000000004 21.0375 22-23 25.687500000000004 23.6125 29.375 21.325 24-25 25.0375 26.125 28.8875 19.950000000000003 26-27 22.975 25.3125 33.2625 18.45 28-29 24.712500000000002 28.287499999999998 28.4375 18.5625 30-31 24.95 27.500000000000004 28.812500000000004 18.7375 32-33 22.925 26.125 30.975 19.975 34-35 22.3 29.2375 27.3375 21.125 36-37 24.74059257407176 25.803225403175396 28.478559819977495 20.977622202775347 38-39 26.881720430107524 23.793448362090523 32.24556139034759 17.079269817454364 40-41 25.112499999999997 25.4375 26.8 22.650000000000002 42-43 22.840355044380548 30.05375671958995 28.87860982622828 18.227278409801226 44-45 21.54288572143036 27.106776694173547 31.745436359089773 19.604901225306325 46-47 22.7625 26.4625 30.2375 20.5375 48-49 24.3125 26.8125 30.599999999999998 18.275 50-51 23.646367387770415 26.985119419782418 30.23633862698512 19.132174565462048 52-53 23.470536719629674 29.1254847991993 27.261353684473917 20.14262479669711 54-55 23.3375 29.349999999999998 30.112499999999997 17.2 56-57 25.2875 27.400000000000002 28.325 18.987499999999997 58-59 23.075000000000003 25.6 30.1875 21.1375 60-61 24.5625 26.4625 29.1875 19.787499999999998 62-63 20.8125 29.275000000000002 32.425 17.4875 64-65 21.575 30.5125 29.262500000000003 18.65 66-67 23.1 28.3125 29.212500000000002 19.375 68-69 21.0625 27.9375 29.1625 21.837500000000002 70-71 22.51315459784515 28.48910047607116 29.153094462540718 19.84465046354297 72-73 24.204143506821627 25.240020212228398 30.015159171298635 20.54067710965134 74-75 22.843674353420816 27.927124474455344 29.991081666454328 19.238119505669513 76-77 22.708547888774458 25.553553038105047 29.209577754891864 22.52832131822863 78-79 23.08390610815718 26.287122292828425 31.254052652055503 19.374918946958893 80-81 21.239863981166625 31.362804080565 29.976458278838606 17.420873659429766 82-83 22.635761589403973 26.4635761589404 30.251655629139073 20.649006622516556 84-85 21.476510067114095 23.825503355704697 34.3489932885906 20.348993288590602 86-87 21.413189771197846 27.456258411843876 31.68236877523553 19.448183041722746 88-89 19.32705248990579 30.60565275908479 31.345895020188426 18.721399730820995 90-91 24.414535666218036 27.604306864064604 29.55585464333782 18.425302826379543 92-93 20.497981157469717 33.4185733512786 28.74831763122476 17.335127860026915 >>END_MODULE >>Per sequence GC content pass #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 1.0 16 1.5 17 12.5 18 15.5 19 7.0 20 4.5 21 2.0 22 6.0 23 9.0 24 9.5 25 12.5 26 15.5 27 19.5 28 32.5 29 44.0 30 54.5 31 57.0 32 66.5 33 89.0 34 104.5 35 121.0 36 149.5 37 195.5 38 235.0 39 217.0 40 195.5 41 200.5 42 217.5 43 244.5 44 209.5 45 181.0 46 196.5 47 170.5 48 141.0 49 142.5 50 149.0 51 130.5 52 112.5 53 116.5 54 109.0 55 82.5 56 56.5 57 51.5 58 43.5 59 26.5 60 19.0 61 20.0 62 17.0 63 17.0 64 14.0 65 10.5 66 9.5 67 10.0 68 8.0 69 4.0 70 4.5 71 5.0 72 4.0 73 2.0 74 2.0 75 2.0 76 1.0 77 0.5 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 0.0125 38-39 0.025 40-41 0.0 42-43 0.0125 44-45 0.025 46-47 0.0 48-49 0.0 50-51 0.0375 52-53 0.08750000000000001 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 18.0 71 13.0 72 22.0 73 10.0 74 25.0 75 21.0 76 14.0 77 13.0 78 17.0 79 15.0 80 18.0 81 23.0 82 32.0 83 24.0 84 20.0 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 3715.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.1 #Duplication Level Percentage of deduplicated Percentage of total 1 90.9500693481276 65.575 2 4.334257975034674 6.25 3 1.6296809986130374 3.5249999999999995 4 0.624133148404993 1.7999999999999998 5 0.6934812760055479 2.5 6 0.4160887656033287 1.7999999999999998 7 0.10402219140083217 0.525 8 0.06934812760055478 0.4 9 0.17337031900138697 1.125 >10 0.9361997226074895 13.200000000000001 >50 0.06934812760055478 3.3000000000000003 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 71 1.775 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 61 1.525 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 44 1.0999999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 37 0.9249999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 37 0.9249999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 29 0.7250000000000001 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 26 0.65 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 24 0.6 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 24 0.6 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 23 0.575 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 21 0.525 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 18 0.44999999999999996 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 18 0.44999999999999996 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 16 0.4 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 15 0.375 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 14 0.35000000000000003 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 14 0.35000000000000003 No Hit GGGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTT 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 12 0.3 No Hit GAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGC 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 9 0.22499999999999998 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 9 0.22499999999999998 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 8 0.2 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 8 0.2 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 7 0.17500000000000002 No Hit GGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAA 7 0.17500000000000002 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 6 0.15 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 6 0.15 No Hit GGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGA 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGA 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTTTTTA 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 6 0.15 No Hit GGGGGAGAAGTCTTATGTTATATATGGTAATCGCCTTGCCTATAGTGCCC 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGAAGAGTCCTCTTAATATTTATCTAATCTTATATAGGTTTCAGTATATT 5 0.125 No Hit GGTCGCGTTATTAATACTTTGGCTGATATCATCAACCGTGCTAATCTTGG 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAA 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 5 0.125 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 5 0.125 No Hit GGATCGCAACAAGATAATTTCTATCAGAAAACTACTAGAATTTTGGCTTT 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 5 0.125 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTTA 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235361 READS because READLEN < 1 Read 235361 spots for ERR6133317.sra Written 235361 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra Rejected 235358 READS because READLEN < 1 Read 235358 spots for ERR6133317.sra Written 235358 spots for ERR6133317.sra SRR ids: ['ERR6133317.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4g23gmwv ERR6133317.sra spots: 4707163 blocks: [[1, 235358], [235359, 470716], [470717, 706074], [706075, 941432], [941433, 1176790], [1176791, 1412148], [1412149, 1647506], [1647507, 1882864], [1882865, 2118222], [2118223, 2353580], [2353581, 2588938], [2588939, 2824296], [2824297, 3059654], [3059655, 3295012], [3295013, 3530370], [3530371, 3765728], [3765729, 4001086], [4001087, 4236444], [4236445, 4471802], [4471803, 4707163]] ERR6133317 file size 1035222 ERR6133317 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 ERR6133317 ERR6133317_1.fastq Input file: ERR6133317_1.fastq trimmed: ERR6133317-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 00:32:30 2024 >> started Sat Dec 7 00:32:32 2024 >> done (2.331s) 4707163 reads processed; of these: 304 ( 0.01%) short reads filtered out after trimming by size control 33 ( 0.00%) empty reads filtered out after trimming by size control 4706826 (99.99%) reads available; of these: 64688 ( 1.37%) trimmed reads available after processing 4642138 (98.63%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 118 0.00% 20 66 0.00% 21 76 0.00% 22 97 0.00% 23 23 0.00% 24 22 0.00% 25 18 0.00% 26 17 0.00% 27 25 0.00% 28 53 0.00% 29 66 0.00% 30 46 0.00% 31 69 0.00% 32 74 0.00% 33 44 0.00% 34 45 0.00% 35 603 0.01% 36 412 0.01% 37 49 0.00% 38 90 0.00% 39 395 0.01% 40 292 0.01% 41 153 0.00% 42 10 0.00% 43 27 0.00% 44 38 0.00% 45 17 0.00% 46 10 0.00% 47 6 0.00% 48 23 0.00% 49 17 0.00% 50 19 0.00% 51 122 0.00% 52 26 0.00% 53 12 0.00% 54 12 0.00% 55 18 0.00% 56 19 0.00% 57 48 0.00% 58 39 0.00% 59 17 0.00% 60 47 0.00% 61 23 0.00% 62 3 0.00% 63 4 0.00% 64 6 0.00% 65 10 0.00% 66 16 0.00% 67 26 0.00% 68 57 0.00% 69 191 0.00% 70 22583 0.48% 71 20032 0.43% 72 23730 0.50% 73 19690 0.42% 74 21029 0.45% 75 21714 0.46% 76 18357 0.39% 77 18899 0.40% 78 22143 0.47% 79 24543 0.52% 80 23162 0.49% 81 28907 0.61% 82 32205 0.68% 83 29272 0.62% 84 26875 0.57% 85 163 0.00% 86 312 0.01% 87 485 0.01% 88 959 0.02% 89 1707 0.04% 90 3616 0.08% 91 10880 0.23% 92 39605 0.84% 93 4292207 91.19% 4706826 reads passed initial QC criterion=sequence-density sequence-density=0.68 sequence-density-rank=1 fanout-score=5.01 fanout-score-rank=19 prefix-density=1.81 prefix-fanout=1.9 sequence=AGGCTAAATACTCCTGGGTGACCGATAGCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=97.07 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=6.1 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 00:32:47 Started mapping on | Dec 07 00:32:47 Finished on | Dec 07 00:32:55 Mapping speed, Million of reads per hour | 2118.07 Number of input reads | 4706826 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 2693376 Uniquely mapped reads % | 57.22% Average mapped length | 91.04 Number of splices: Total | 79683 Number of splices: Annotated (sjdb) | 61630 Number of splices: GT/AG | 74703 Number of splices: GC/AG | 2060 Number of splices: AT/AC | 96 Number of splices: Non-canonical | 2824 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 1.72 Insertion rate per base | 0.04% Insertion average length | 1.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1785296 % of reads mapped to multiple loci | 37.93% Number of reads mapped to too many loci | 153873 % of reads mapped to too many loci | 3.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.36% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 228154 228154 228154 N_multimapping 1785296 1785296 1785296 N_noFeature 290974 317950 2576548 N_ambiguous 103129 12844 853 UnstrandedReadsAssigned:2299273 PositiveStrandReadsAssigned:2362582 NegativeStrandReadsAssigned:115975 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133317 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: ERR6133317-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,706,826 reads, 3,617,233 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 985 rounds 52973 ERR6133317.ke.tsv 35125 ERR6133317.se.tsv 88098 total ==> ERR6133317.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 84 22.7878 PNS24243 293 194 0 0 KQK14069 1603 1504 23 5.6919 KQK14071 474 375 0 0 ==> ERR6133317.se.tsv <== BRADI_1g14170v3 23 BRADI_1g53295v3 22 BRADI_1g59795v3 31 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 27 BRADI_1g74790v3 22 BRADI_1g09890v3 0 BRADI_1g77505v3 95 BRADI_1g48960v3 0 ERR6133317 completed mapping pipeline successfully