Starting /dee2/code/volunteer_pipeline.sh ERR6133497 current disk space = 1544592064512 free memory = 1590562172 ERR6133497 SRAfilesize d1a0857bb4481016a725bd6709233f7a ERR6133497.sra ERR6133497.sra file validated ERR6133497 is single end ERR6133497 is conventional basespace ERR6133497 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133497_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.58525 37.0 33.0 37.0 33.0 37.0 2 36.55125 37.0 37.0 37.0 37.0 37.0 3 35.87975 37.0 37.0 37.0 33.0 37.0 4 35.119 37.0 37.0 37.0 33.0 37.0 5 35.258 37.0 37.0 37.0 33.0 37.0 6 35.57725 37.0 37.0 37.0 33.0 37.0 7 37.385 37.0 37.0 40.0 33.0 40.0 8 37.495 37.0 37.0 40.0 33.0 40.0 9 37.44175 37.0 37.0 40.0 33.0 40.0 10-11 37.356 37.0 37.0 40.0 33.0 40.0 12-13 37.385125 37.0 37.0 40.0 33.0 40.0 14-15 37.368624999999994 37.0 37.0 40.0 33.0 40.0 16-17 37.2535 37.0 37.0 40.0 33.0 40.0 18-19 37.0305 37.0 37.0 40.0 33.0 40.0 20-21 36.772999999999996 37.0 37.0 40.0 33.0 40.0 22-23 36.757875 37.0 37.0 40.0 33.0 40.0 24-25 36.70625 37.0 37.0 40.0 33.0 40.0 26-27 36.898624999999996 37.0 37.0 40.0 33.0 40.0 28-29 36.92875 37.0 37.0 40.0 33.0 40.0 30-31 36.836749999999995 37.0 37.0 40.0 33.0 40.0 32-33 36.799 37.0 37.0 40.0 33.0 40.0 34-35 36.622125 37.0 37.0 40.0 33.0 40.0 36-37 36.455875 37.0 37.0 40.0 33.0 40.0 38-39 36.463125000000005 37.0 37.0 40.0 33.0 40.0 40-41 36.06175 37.0 37.0 40.0 33.0 40.0 42-43 36.16775 37.0 37.0 40.0 33.0 40.0 44-45 36.217875 37.0 35.0 40.0 33.0 40.0 46-47 36.070375 37.0 37.0 37.0 33.0 40.0 48-49 36.035375 37.0 37.0 37.0 33.0 40.0 50-51 35.8875 37.0 37.0 37.0 33.0 40.0 52-53 35.652375 37.0 35.0 37.0 33.0 40.0 54-55 35.590125 37.0 33.0 37.0 33.0 40.0 56-57 35.42475 37.0 33.0 37.0 33.0 38.5 58-59 34.300375 37.0 33.0 37.0 27.0 37.0 60-61 34.90925 37.0 33.0 37.0 33.0 37.0 62-63 34.878875 37.0 33.0 37.0 33.0 37.0 64-65 34.793625 37.0 33.0 37.0 33.0 37.0 66-67 34.817625 37.0 33.0 37.0 33.0 37.0 68-69 33.92325 35.0 33.0 37.0 30.0 37.0 70-71 34.155306077694235 35.0 33.0 37.0 30.0 37.0 72-73 34.508943082474076 37.0 33.0 37.0 33.0 37.0 74-75 34.46828005185463 37.0 33.0 37.0 33.0 37.0 76-77 34.4631628011515 37.0 33.0 37.0 33.0 37.0 78-79 34.42473320944788 37.0 33.0 37.0 33.0 37.0 80-81 34.22551322300383 37.0 33.0 37.0 27.0 37.0 82-83 34.189443328765094 37.0 33.0 37.0 30.0 37.0 84-85 34.05967881305237 37.0 33.0 37.0 30.0 37.0 86-87 33.99987053340239 37.0 33.0 37.0 27.0 37.0 88-89 34.060460901087524 37.0 33.0 37.0 27.0 37.0 90-91 33.82949249093734 37.0 33.0 37.0 27.0 37.0 92-93 33.86794407042983 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 6.0 22 13.0 23 17.0 24 17.0 25 25.0 26 29.0 27 31.0 28 42.0 29 61.0 30 67.0 31 108.0 32 135.0 33 161.0 34 246.0 35 511.0 36 1031.0 37 952.0 38 534.0 39 9.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.725 2.825 2.7 6.75 2 73.1 15.325 7.124999999999999 4.45 3 41.275 36.199999999999996 13.225000000000001 9.3 4 31.35 34.4 17.5 16.75 5 30.525000000000002 28.425 23.125 17.925 6 19.625 42.875 24.05 13.450000000000001 7 40.0 26.700000000000003 17.974999999999998 15.325 8 27.325 29.125 21.375 22.175 9 24.7 33.525 25.0 16.775000000000002 10-11 23.525 29.212500000000002 29.675 17.5875 12-13 26.887499999999996 27.500000000000004 25.724999999999998 19.8875 14-15 21.2875 34.9625 26.387500000000003 17.3625 16-17 26.875 28.225 24.1125 20.7875 18-19 26.0375 24.4875 29.312500000000004 20.1625 20-21 27.325 24.45 29.3375 18.8875 22-23 27.975 22.75 29.362500000000004 19.9125 24-25 23.875 22.7625 29.45 23.9125 26-27 26.6125 24.075 27.700000000000003 21.6125 28-29 23.974999999999998 28.4 29.212500000000002 18.4125 30-31 32.175 24.525 24.65 18.65 32-33 27.025 25.137500000000003 25.15 22.6875 34-35 24.0125 31.387500000000003 25.924999999999997 18.675 36-37 27.1125 23.3 25.837500000000002 23.75 38-39 31.554553426030314 23.600150319428785 27.608668420393336 17.236627834147562 40-41 24.18325197146076 23.49480535736638 33.34585054449868 18.976092126674178 42-43 26.91682301438399 29.005628517823638 25.178236397748595 18.899312070043777 44-45 26.387500000000003 23.962500000000002 30.3875 19.2625 46-47 27.575 21.85 26.0375 24.5375 48-49 27.0125 23.4375 27.1125 22.4375 50-51 22.4375 27.800000000000004 26.4625 23.3 52-53 22.6634928589326 24.65547481834127 25.970934602856428 26.710097719869708 54-55 22.3 24.5125 30.5125 22.675 56-57 26.674999999999997 27.625 26.674999999999997 19.025 58-59 22.3625 26.6125 31.1875 19.8375 60-61 30.7375 23.1125 27.474999999999998 18.675 62-63 21.5375 24.325 32.8125 21.325 64-65 22.2125 32.625 26.85 18.3125 66-67 26.8125 29.7125 26.087500000000002 17.3875 68-69 21.6 24.825 30.2 23.375 70-71 23.479349186483102 27.15894868585732 26.33291614518148 23.028785982478098 72-73 27.253272910372605 22.885196374622357 31.243705941591138 18.617824773413897 74-75 25.797064777327932 28.125 27.416497975708502 18.661437246963565 76-77 20.95892153122218 24.16380516342363 28.43698333969223 26.44028996566196 78-79 26.119212074699412 27.23202865182911 28.204144282425176 18.444614991046304 80-81 22.173689619732787 33.32476875642343 28.00616649537513 16.495375128468652 82-83 25.161124001031194 24.323279195668988 28.190255220417633 22.325341582882185 84-85 22.716688227684347 24.61836998706339 32.82018111254851 19.84476067270375 86-87 20.973588814085968 28.46970481615743 29.091144484722943 21.46556188503366 88-89 20.779388917659244 26.10046607975142 32.34075608493009 20.779388917659244 90-91 27.019678922837908 27.36923873640601 27.770585189021237 17.84049715173485 92-93 20.274469186949766 27.602278612118074 30.890730191610565 21.232522009321595 >>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 8.5 18 9.5 19 1.5 20 0.5 21 2.0 22 3.0 23 3.5 24 4.5 25 4.0 26 9.0 27 12.5 28 14.5 29 19.0 30 24.5 31 32.5 32 42.5 33 51.0 34 68.0 35 82.5 36 96.5 37 124.0 38 147.5 39 167.0 40 177.0 41 184.0 42 204.0 43 218.0 44 209.0 45 189.0 46 182.0 47 172.5 48 155.5 49 159.0 50 165.5 51 151.5 52 134.5 53 154.0 54 263.5 55 226.0 56 75.0 57 48.0 58 49.0 59 38.5 60 32.0 61 37.5 62 38.5 63 35.5 64 23.5 65 15.5 66 13.0 67 10.0 68 10.0 69 10.0 70 8.5 71 7.0 72 4.0 73 1.0 74 1.0 75 0.5 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 0.0 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 0.21250000000000002 40-41 0.13749999999999998 42-43 0.0625 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.22499999999999998 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 10.0 71 15.0 72 6.0 73 12.0 74 10.0 75 11.0 76 9.0 77 12.0 78 12.0 79 8.0 80 6.0 81 8.0 82 4.0 83 9.0 84 6.0 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 3862.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.05 #Duplication Level Percentage of deduplicated Percentage of total 1 92.98526585522102 72.575 2 4.708520179372197 7.35 3 0.8007687379884689 1.875 4 0.25624599615631005 0.8 5 0.25624599615631005 1.0 6 0.12812299807815503 0.6 7 0.1601537475976938 0.8750000000000001 8 0.09609224855861628 0.6 9 0.09609224855861628 0.675 >10 0.4804612427930814 6.4750000000000005 >50 0.0 0.0 >100 0.032030749519538756 7.175 >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 287 7.175 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 36 0.8999999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 24 0.6 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 19 0.475 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 18 0.44999999999999996 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 18 0.44999999999999996 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 18 0.44999999999999996 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 17 0.42500000000000004 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 17 0.42500000000000004 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 15 0.375 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 14 0.35000000000000003 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 9 0.22499999999999998 No Hit GGGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTGGCGGG 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 8 0.2 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTCC 6 0.15 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 5 0.125 No Hit GGGCAGAGCGTGGAGAGCAAGTCCAGCGGCTTCTGGACCGCCGATGCCGA 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGATCGGTTGAAGCGTGCGGCGTCTCTGTCTATGTATTACTGTTTTATGC 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGAGGAGAGCGGCGGCGGTCTGTTCAAGATGGCTCAGGGCTTCATGAAGT 5 0.125 No Hit CTGAGCCGTGCTCTCTTCTGTGTACATCTTCATGTCATTTTAGCGATTCT 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 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 0.0125 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 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 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0125 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 20 2.4709738E-5 86.362495 7 GGGAGAG 20 2.4709738E-5 86.362495 1 CAATACA 20 2.4709738E-5 86.362495 8 AGCAATA 20 2.4709738E-5 86.362495 6 GGAGAGC 25 7.4729476E-5 69.09 2 GAGCAAT 25 7.4729476E-5 69.09 5 GAGAGCA 25 7.4729476E-5 69.09 3 AGAGCAA 30 1.842775E-4 57.575005 4 AATACAA 30 1.842775E-4 57.575005 9 TAGCCGA 20 6.7048805E-4 44.863636 72-73 CATCACT 20 6.7048805E-4 44.863636 82-83 ATCACTA 20 6.7048805E-4 44.863636 84-85 AGCATCA 20 6.7048805E-4 44.863636 80-81 CACTAGC 20 6.7048805E-4 44.863636 86-87 TCACTAG 20 6.7048805E-4 44.863636 84-85 AGCCGAA 20 6.7048805E-4 44.863636 74-75 GCATCAC 20 6.7048805E-4 44.863636 82-83 GCCGAAA 20 6.7048805E-4 44.863636 74-75 GTAGCCG 20 6.7048805E-4 44.863636 72-73 AAGCATC 20 6.7048805E-4 44.863636 80-81 >>END_MODULE Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297362 READS because READLEN < 1 Read 297362 spots for ERR6133497.sra Written 297362 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra Rejected 297344 READS because READLEN < 1 Read 297344 spots for ERR6133497.sra Written 297344 spots for ERR6133497.sra SRR ids: ['ERR6133497.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hnv2pi9s ERR6133497.sra spots: 5946898 blocks: [[1, 297344], [297345, 594688], [594689, 892032], [892033, 1189376], [1189377, 1486720], [1486721, 1784064], [1784065, 2081408], [2081409, 2378752], [2378753, 2676096], [2676097, 2973440], [2973441, 3270784], [3270785, 3568128], [3568129, 3865472], [3865473, 4162816], [4162817, 4460160], [4460161, 4757504], [4757505, 5054848], [5054849, 5352192], [5352193, 5649536], [5649537, 5946898]] ERR6133497 file size 1314862 ERR6133497 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 ERR6133497 ERR6133497_1.fastq Input file: ERR6133497_1.fastq trimmed: ERR6133497-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 07:21:13 2024 >> started Sat Dec 7 07:21:16 2024 >> done (3.022s) 5946898 reads processed; of these: 349 ( 0.01%) short reads filtered out after trimming by size control 42 ( 0.00%) empty reads filtered out after trimming by size control 5946507 (99.99%) reads available; of these: 84607 ( 1.42%) trimmed reads available after processing 5861900 (98.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 77 0.00% 19 97 0.00% 20 52 0.00% 21 50 0.00% 22 44 0.00% 23 26 0.00% 24 21 0.00% 25 14 0.00% 26 22 0.00% 27 27 0.00% 28 51 0.00% 29 22 0.00% 30 27 0.00% 31 41 0.00% 32 42 0.00% 33 26 0.00% 34 48 0.00% 35 515 0.01% 36 511 0.01% 37 43 0.00% 38 45 0.00% 39 159 0.00% 40 179 0.00% 41 74 0.00% 42 20 0.00% 43 25 0.00% 44 24 0.00% 45 14 0.00% 46 23 0.00% 47 11 0.00% 48 13 0.00% 49 12 0.00% 50 15 0.00% 51 67 0.00% 52 25 0.00% 53 11 0.00% 54 5 0.00% 55 10 0.00% 56 11 0.00% 57 13 0.00% 58 13 0.00% 59 10 0.00% 60 19 0.00% 61 11 0.00% 62 2 0.00% 63 6 0.00% 64 7 0.00% 65 14 0.00% 66 10 0.00% 67 21 0.00% 68 38 0.00% 69 93 0.00% 70 14790 0.25% 71 14226 0.24% 72 15446 0.26% 73 14076 0.24% 74 14099 0.24% 75 14053 0.24% 76 12927 0.22% 77 13970 0.23% 78 15092 0.25% 79 16392 0.28% 80 15370 0.26% 81 16893 0.28% 82 18856 0.32% 83 19209 0.32% 84 16080 0.27% 85 166 0.00% 86 297 0.00% 87 535 0.01% 88 995 0.02% 89 1745 0.03% 90 3625 0.06% 91 11167 0.19% 92 59846 1.01% 93 5633896 94.74% 5946507 reads passed initial QC criterion=sequence-density sequence-density=0.76 sequence-density-rank=1 fanout-score=4.16 fanout-score-rank=22 prefix-density=0.98 prefix-fanout=3.3 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=24 fanout-score=379.79 fanout-score-rank=1 prefix-density=0.67 prefix-fanout=7.3 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGC Started job on | Dec 07 07:21:27 Started mapping on | Dec 07 07:21:27 Finished on | Dec 07 07:21:35 Mapping speed, Million of reads per hour | 2675.93 Number of input reads | 5946507 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 4113840 Uniquely mapped reads % | 69.18% Average mapped length | 91.92 Number of splices: Total | 173730 Number of splices: Annotated (sjdb) | 141189 Number of splices: GT/AG | 167067 Number of splices: GC/AG | 4523 Number of splices: AT/AC | 100 Number of splices: Non-canonical | 2040 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.69 Insertion rate per base | 0.02% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1722126 % of reads mapped to multiple loci | 28.96% Number of reads mapped to too many loci | 38743 % of reads mapped to too many loci | 0.65% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.16% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 110541 110541 110541 N_multimapping 1722126 1722126 1722126 N_noFeature 242173 279073 3926185 N_ambiguous 167851 17148 456 UnstrandedReadsAssigned:3703816 PositiveStrandReadsAssigned:3817619 NegativeStrandReadsAssigned:187199 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133497 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: ERR6133497-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,946,507 reads, 4,672,178 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,121 rounds 52973 ERR6133497.ke.tsv 35125 ERR6133497.se.tsv 88098 total ==> ERR6133497.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 184 37.5713 PNS24243 293 194 0 0 KQK14069 1603 1504 128 23.8427 KQK14071 474 375 1 0.747071 ==> ERR6133497.se.tsv <== BRADI_1g14170v3 129 BRADI_1g53295v3 94 BRADI_1g59795v3 35 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 57 BRADI_1g74790v3 33 BRADI_1g09890v3 0 BRADI_1g77505v3 120 BRADI_1g48960v3 0 ERR6133497 completed mapping pipeline successfully