Starting /dee2/code/volunteer_pipeline.sh ERR6133552 current disk space = 1544509337600 free memory = 1597663748 ERR6133552 SRAfilesize f1b39803a454145c4f649bc21644a4cb ERR6133552.sra ERR6133552.sra file validated ERR6133552 is single end ERR6133552 is conventional basespace ERR6133552 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133552_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.82925 37.0 33.0 37.0 27.0 37.0 2 36.02875 37.0 37.0 37.0 33.0 37.0 3 35.06525 37.0 33.0 37.0 33.0 37.0 4 35.24025 37.0 37.0 37.0 33.0 37.0 5 35.23225 37.0 37.0 37.0 33.0 37.0 6 35.52675 37.0 37.0 37.0 33.0 37.0 7 37.303 37.0 37.0 40.0 33.0 40.0 8 37.3325 37.0 37.0 40.0 33.0 40.0 9 37.389 37.0 37.0 40.0 33.0 40.0 10-11 37.414249999999996 37.0 37.0 40.0 33.0 40.0 12-13 37.283 37.0 37.0 40.0 33.0 40.0 14-15 37.309625 37.0 37.0 40.0 33.0 40.0 16-17 37.238125 37.0 37.0 40.0 33.0 40.0 18-19 37.223375000000004 37.0 37.0 40.0 33.0 40.0 20-21 37.041250000000005 37.0 37.0 40.0 33.0 40.0 22-23 37.023375 37.0 37.0 40.0 33.0 40.0 24-25 37.047625 37.0 37.0 40.0 33.0 40.0 26-27 37.170249999999996 37.0 37.0 40.0 33.0 40.0 28-29 37.0925 37.0 37.0 40.0 33.0 40.0 30-31 36.924 37.0 37.0 40.0 33.0 40.0 32-33 36.72125 37.0 37.0 40.0 33.0 40.0 34-35 36.5765 37.0 37.0 40.0 33.0 40.0 36-37 36.396125 37.0 37.0 40.0 33.0 40.0 38-39 36.333125 37.0 37.0 40.0 33.0 40.0 40-41 36.09825 37.0 37.0 40.0 33.0 40.0 42-43 36.090125 37.0 37.0 40.0 33.0 40.0 44-45 35.697374999999994 37.0 35.0 38.5 33.0 40.0 46-47 35.409875 37.0 33.0 37.0 30.0 40.0 48-49 35.542125 37.0 33.0 37.0 33.0 40.0 50-51 35.400625000000005 37.0 33.0 37.0 33.0 40.0 52-53 35.148125 37.0 33.0 37.0 30.0 40.0 54-55 35.091875 37.0 33.0 37.0 33.0 40.0 56-57 34.95975 37.0 33.0 37.0 33.0 37.0 58-59 34.249875 37.0 33.0 37.0 27.0 37.0 60-61 34.487875 37.0 33.0 37.0 27.0 37.0 62-63 34.480000000000004 37.0 33.0 37.0 27.0 37.0 64-65 34.474000000000004 37.0 33.0 37.0 27.0 37.0 66-67 34.471125 37.0 33.0 37.0 27.0 37.0 68-69 33.609625 35.0 33.0 37.0 27.0 37.0 70-71 33.81457133901705 35.0 33.0 37.0 27.0 37.0 72-73 34.15998396755633 37.0 33.0 37.0 27.0 37.0 74-75 34.13379105182411 37.0 33.0 37.0 27.0 37.0 76-77 34.113749837456425 37.0 33.0 37.0 27.0 37.0 78-79 34.11323067846746 37.0 33.0 37.0 27.0 37.0 80-81 34.10604616977446 37.0 33.0 37.0 27.0 37.0 82-83 33.92410359429615 37.0 33.0 37.0 27.0 37.0 84-85 33.94534740642156 37.0 33.0 37.0 27.0 37.0 86-87 33.92147685907436 37.0 33.0 37.0 27.0 37.0 88-89 34.02873114924597 37.0 33.0 37.0 27.0 37.0 90-91 33.6038741549662 37.0 33.0 37.0 27.0 37.0 92-93 33.61583463338533 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 11.0 21 11.0 22 22.0 23 22.0 24 27.0 25 38.0 26 38.0 27 55.0 28 51.0 29 60.0 30 87.0 31 87.0 32 133.0 33 187.0 34 228.0 35 424.0 36 992.0 37 880.0 38 631.0 39 16.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.64999999999999 2.5749999999999997 2.9250000000000003 5.8500000000000005 2 75.625 14.875 5.625 3.875 3 39.35 36.725 12.675 11.25 4 30.775000000000002 32.375 18.125 18.725 5 27.05 29.95 25.45 17.549999999999997 6 18.8 40.375 23.7 17.125 7 39.225 27.3 18.275 15.2 8 30.975 30.125 21.425 17.474999999999998 9 23.724999999999998 33.300000000000004 25.7 17.275 10-11 25.3125 29.175 28.037499999999998 17.474999999999998 12-13 27.05 28.012500000000003 25.7875 19.15 14-15 20.625 34.862500000000004 27.1 17.4125 16-17 23.974999999999998 31.362499999999997 23.8875 20.775 18-19 23.799999999999997 26.924999999999997 29.6875 19.5875 20-21 26.1625 25.087500000000002 29.512500000000003 19.2375 22-23 27.962500000000002 23.9875 27.925 20.125 24-25 24.7375 24.712500000000002 28.6875 21.8625 26-27 26.0625 24.2625 30.012499999999996 19.662499999999998 28-29 23.375 28.5875 28.625 19.412499999999998 30-31 29.512500000000003 25.137500000000003 25.1 20.25 32-33 24.887500000000003 25.837500000000002 26.6125 22.662499999999998 34-35 23.373373373373376 30.055055055055057 26.826826826826828 19.744744744744743 36-37 26.0125 23.7125 26.55 23.724999999999998 38-39 29.641205150643827 23.72796599574947 28.066008251031377 18.56482060257532 40-41 25.781836377282964 23.71778834125594 30.122591943957964 20.37778333750313 42-43 25.604106673344184 29.911105546513085 26.06735945912107 18.41742832102166 44-45 23.81131131131131 25.45045045045045 30.743243243243246 19.994994994994993 46-47 25.4625 24.0125 26.674999999999997 23.849999999999998 48-49 25.506376594148538 24.468617154288573 28.54463615903976 21.48037009252313 50-51 23.7125 27.9125 27.237499999999997 21.1375 52-53 24.2992992992993 27.164664664664667 24.71221221221221 23.823823823823822 54-55 22.5625 26.474999999999998 30.125 20.837500000000002 56-57 27.725 26.8375 26.125 19.3125 58-59 23.2625 26.7125 29.8375 20.1875 60-61 27.975 24.95 28.237499999999997 18.8375 62-63 21.05 26.937499999999996 32.7 19.3125 64-65 23.025000000000002 31.075000000000003 27.375 18.525 66-67 25.3125 28.175 27.625 18.8875 68-69 21.0625 26.387500000000003 29.1125 23.4375 70-71 22.383575363044567 26.69003505257887 28.367551326990487 22.55883825738608 72-73 27.794561933534744 23.187311178247736 29.94712990936556 19.070996978851966 74-75 24.12485782888917 28.964994313155568 28.383672437760648 18.526475420194615 76-77 22.106466776775505 24.32981832041672 28.484309490534876 25.079405412272898 78-79 24.760689215060623 26.44543714103382 29.253350350989148 19.5405232929164 80-81 22.013871050603647 32.91805805291549 27.780631903416385 17.287438993064473 82-83 23.67299496319256 26.501356063541266 26.888802789616427 22.93684618364975 84-85 22.158721911936617 24.301857384075852 32.7055461748279 20.833874529159633 86-87 20.722828913156526 29.290171606864273 28.77015080603224 21.21684867394696 88-89 19.40977639105564 27.249089963598543 31.70826833073323 21.632865314612584 90-91 26.417056682267294 28.159126365054604 27.83411336453458 17.589703588143525 92-93 20.95683827353094 28.71814872594904 29.771190847633903 20.553822152886113 >>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 9.0 18 10.0 19 1.0 20 1.0 21 1.0 22 1.5 23 6.5 24 7.5 25 8.0 26 10.5 27 13.5 28 18.5 29 19.0 30 30.5 31 42.0 32 45.5 33 64.0 34 75.5 35 78.5 36 97.5 37 126.5 38 167.5 39 185.0 40 204.0 41 203.5 42 214.0 43 250.5 44 212.0 45 173.5 46 199.0 47 190.0 48 163.5 49 163.0 50 154.0 51 137.5 52 125.5 53 128.5 54 186.0 55 165.0 56 74.5 57 64.0 58 56.5 59 46.0 60 34.5 61 30.5 62 32.5 63 26.5 64 20.5 65 21.5 66 19.5 67 15.5 68 13.5 69 8.5 70 8.5 71 11.0 72 6.5 73 3.5 74 2.5 75 1.0 76 1.5 77 0.5 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 0.1 36-37 0.0 38-39 0.0125 40-41 0.075 42-43 0.1625 44-45 0.1 46-47 0.0 48-49 0.025 50-51 0.0 52-53 0.1 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 12.0 71 11.0 72 10.0 73 6.0 74 9.0 75 14.0 76 5.0 77 9.0 78 13.0 79 12.0 80 12.0 81 9.0 82 13.0 83 12.0 84 7.0 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 3846.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.625 #Duplication Level Percentage of deduplicated Percentage of total 1 90.6368330464716 65.825 2 5.40447504302926 7.85 3 1.6867469879518073 3.675 4 0.5507745266781412 1.6 5 0.48192771084337355 1.7500000000000002 6 0.10327022375215145 0.44999999999999996 7 0.17211703958691912 0.8750000000000001 8 0.034423407917383825 0.2 9 0.06884681583476765 0.44999999999999996 >10 0.7917383820998278 11.15 >50 0.034423407917383825 1.275 >100 0.034423407917383825 4.9 >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 196 4.9 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 51 1.275 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 47 1.175 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 45 1.125 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 45 1.125 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 33 0.8250000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 26 0.65 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 24 0.6 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 19 0.475 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 15 0.375 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 13 0.325 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 13 0.325 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 10 0.25 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 9 0.22499999999999998 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 7 0.17500000000000002 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 6 0.15 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit GGGCGTGGCGTTCATGAACAAGTGAAACCTTATGGCTGGATGGGTCATCG 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 5 0.125 No Hit GGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAG 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 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 0.05 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAAAAG 15 9.0442906E-4 86.1875 1 GCAATAC 55 1.8189894E-12 70.517044 7 GGGAGAG 55 1.8189894E-12 70.517044 1 CAATACA 55 1.8189894E-12 70.517044 8 AGCAATA 55 1.8189894E-12 70.517044 6 GGAGAGC 60 5.456968E-12 64.640625 2 GAGCAAT 60 5.456968E-12 64.640625 5 GAGAGCA 60 5.456968E-12 64.640625 3 GAAAAGA 20 0.0028333697 64.64062 2 AGAGCAA 65 1.2732926E-11 59.66827 4 AATACAA 65 1.2732926E-11 59.66827 9 CATCACT 45 2.6557245E-10 45.361843 82-83 ATCACTA 45 2.6557245E-10 45.361843 84-85 CACTAGC 40 5.0422386E-9 45.361843 86-87 TCACTAG 45 2.6557245E-10 45.361843 84-85 GCATCAC 45 2.6557245E-10 45.361843 82-83 ACTAGCT 35 9.514588E-8 45.36184 86-87 GTTGAGT 45 3.947207E-10 43.639244 38-39 GGTTGAG 45 3.947207E-10 43.639244 38-39 GAGTGCC 45 3.947207E-10 43.639244 42-43 >>END_MODULE Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198557 READS because READLEN < 1 Read 198557 spots for ERR6133552.sra Written 198557 spots for ERR6133552.sra Rejected 198570 READS because READLEN < 1 Read 198570 spots for ERR6133552.sra Written 198570 spots for ERR6133552.sra SRR ids: ['ERR6133552.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ihaud6_5 ERR6133552.sra spots: 3971153 blocks: [[1, 198557], [198558, 397114], [397115, 595671], [595672, 794228], [794229, 992785], [992786, 1191342], [1191343, 1389899], [1389900, 1588456], [1588457, 1787013], [1787014, 1985570], [1985571, 2184127], [2184128, 2382684], [2382685, 2581241], [2581242, 2779798], [2779799, 2978355], [2978356, 3176912], [3176913, 3375469], [3375470, 3574026], [3574027, 3772583], [3772584, 3971153]] ERR6133552 file size 877363 ERR6133552 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 ERR6133552 ERR6133552_1.fastq Input file: ERR6133552_1.fastq trimmed: ERR6133552-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 08:30:18 2024 >> started Sat Dec 7 08:30:21 2024 >> done (3.323s) 3971153 reads processed; of these: 149 ( 0.00%) short reads filtered out after trimming by size control 16 ( 0.00%) empty reads filtered out after trimming by size control 3970988 (100.00%) reads available; of these: 66608 ( 1.68%) trimmed reads available after processing 3904380 (98.32%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 27 0.00% 19 44 0.00% 20 19 0.00% 21 11 0.00% 22 10 0.00% 23 4 0.00% 24 1 0.00% 25 9 0.00% 26 7 0.00% 27 11 0.00% 28 16 0.00% 29 60 0.00% 30 7 0.00% 31 12 0.00% 32 10 0.00% 33 14 0.00% 34 14 0.00% 35 67 0.00% 36 384 0.01% 37 17 0.00% 38 15 0.00% 39 61 0.00% 40 61 0.00% 41 23 0.00% 42 9 0.00% 43 6 0.00% 44 16 0.00% 45 7 0.00% 46 10 0.00% 47 5 0.00% 48 5 0.00% 49 8 0.00% 50 11 0.00% 51 29 0.00% 52 10 0.00% 53 3 0.00% 54 8 0.00% 55 6 0.00% 56 2 0.00% 57 8 0.00% 58 12 0.00% 59 4 0.00% 60 5 0.00% 61 16 0.00% 62 4 0.00% 63 4 0.00% 64 8 0.00% 65 11 0.00% 66 18 0.00% 67 21 0.00% 68 56 0.00% 69 141 0.00% 70 10826 0.27% 71 9057 0.23% 72 9285 0.23% 73 8382 0.21% 74 9148 0.23% 75 9326 0.23% 76 7899 0.20% 77 8533 0.21% 78 9978 0.25% 79 11454 0.29% 80 10455 0.26% 81 12036 0.30% 82 13265 0.33% 83 13165 0.33% 84 10836 0.27% 85 106 0.00% 86 306 0.01% 87 454 0.01% 88 813 0.02% 89 1554 0.04% 90 3589 0.09% 91 11112 0.28% 92 45413 1.14% 93 3752649 94.50% 3970988 reads passed initial QC criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=33 prefix-density=0.51 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=76.11 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=6.6 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 08:30:34 Started mapping on | Dec 07 08:30:34 Finished on | Dec 07 08:30:42 Mapping speed, Million of reads per hour | 1786.94 Number of input reads | 3970988 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2585350 Uniquely mapped reads % | 65.11% Average mapped length | 91.77 Number of splices: Total | 115666 Number of splices: Annotated (sjdb) | 95800 Number of splices: GT/AG | 109951 Number of splices: GC/AG | 3121 Number of splices: AT/AC | 92 Number of splices: Non-canonical | 2502 Mismatch rate per base, % | 0.57% Deletion rate per base | 0.05% Deletion average length | 1.83 Insertion rate per base | 0.05% Insertion average length | 2.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1292180 % of reads mapped to multiple loci | 32.54% Number of reads mapped to too many loci | 27963 % of reads mapped to too many loci | 0.70% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.61% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 93458 93458 93458 N_multimapping 1292180 1292180 1292180 N_noFeature 205383 230210 2465296 N_ambiguous 107984 12748 361 UnstrandedReadsAssigned:2271983 PositiveStrandReadsAssigned:2342392 NegativeStrandReadsAssigned:119693 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133552 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: ERR6133552-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,970,988 reads, 3,133,266 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,000 rounds 52973 ERR6133552.ke.tsv 35125 ERR6133552.se.tsv 88098 total ==> ERR6133552.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 55 16.9529 PNS24243 293 194 0 0 KQK14069 1603 1504 239 67.2024 KQK14071 474 375 0 0 ==> ERR6133552.se.tsv <== BRADI_1g14170v3 239 BRADI_1g53295v3 41 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 19 BRADI_1g74790v3 26 BRADI_1g09890v3 0 BRADI_1g77505v3 77 BRADI_1g48960v3 0 ERR6133552 completed mapping pipeline successfully