Starting /dee2/code/volunteer_pipeline.sh ERR6133320 current disk space = 1548301807616 free memory = 1601992516 ERR6133320 SRAfilesize 4c3d0b8aa892fc6affcaf9bef9500987 ERR6133320.sra ERR6133320.sra file validated ERR6133320 is single end ERR6133320 is conventional basespace ERR6133320 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133320_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 35.2725 37.0 33.0 37.0 33.0 37.0 2 36.4825 37.0 37.0 37.0 37.0 37.0 3 36.12925 37.0 37.0 37.0 33.0 37.0 4 35.5495 37.0 37.0 37.0 33.0 37.0 5 35.57025 37.0 37.0 37.0 33.0 37.0 6 35.925 37.0 37.0 37.0 33.0 37.0 7 37.59625 40.0 37.0 40.0 33.0 40.0 8 37.566 40.0 37.0 40.0 33.0 40.0 9 37.67825 40.0 37.0 40.0 33.0 40.0 10-11 37.608999999999995 38.5 37.0 40.0 33.0 40.0 12-13 37.575874999999996 38.5 37.0 40.0 33.0 40.0 14-15 37.598 38.5 37.0 40.0 33.0 40.0 16-17 37.50925 37.0 37.0 40.0 33.0 40.0 18-19 37.4765 37.0 37.0 40.0 33.0 40.0 20-21 37.31325 37.0 37.0 40.0 33.0 40.0 22-23 37.209625 37.0 37.0 40.0 33.0 40.0 24-25 37.343375 37.0 37.0 40.0 33.0 40.0 26-27 37.182125 37.0 37.0 40.0 33.0 40.0 28-29 37.09625 37.0 37.0 40.0 33.0 40.0 30-31 37.056875 37.0 37.0 40.0 33.0 40.0 32-33 36.993375 37.0 37.0 40.0 33.0 40.0 34-35 36.874375 37.0 37.0 40.0 33.0 40.0 36-37 36.755250000000004 37.0 37.0 40.0 33.0 40.0 38-39 36.470875 37.0 37.0 40.0 33.0 40.0 40-41 36.280874999999995 37.0 37.0 40.0 33.0 40.0 42-43 35.95 37.0 37.0 40.0 33.0 40.0 44-45 35.73975 37.0 33.0 40.0 33.0 40.0 46-47 35.347875 37.0 33.0 37.0 30.0 40.0 48-49 35.211124999999996 37.0 33.0 37.0 30.0 40.0 50-51 35.098 37.0 33.0 37.0 27.0 40.0 52-53 34.8605 37.0 33.0 37.0 27.0 40.0 54-55 34.6845 37.0 33.0 37.0 27.0 40.0 56-57 34.455375000000004 37.0 33.0 37.0 27.0 40.0 58-59 32.267875000000004 33.0 30.0 37.0 24.5 37.0 60-61 33.731625 37.0 33.0 37.0 27.0 37.0 62-63 33.949875000000006 37.0 33.0 37.0 27.0 37.0 64-65 33.844625 37.0 33.0 37.0 27.0 37.0 66-67 33.574375 37.0 33.0 37.0 27.0 37.0 68-69 32.894625000000005 35.0 33.0 37.0 27.0 37.0 70-71 32.96945030158331 35.0 33.0 37.0 27.0 37.0 72-73 33.257801277559 37.0 33.0 37.0 27.0 37.0 74-75 33.34861439670654 37.0 33.0 37.0 27.0 37.0 76-77 33.28680355254964 37.0 33.0 37.0 27.0 37.0 78-79 33.317454877456214 37.0 33.0 37.0 27.0 37.0 80-81 33.42013250382388 37.0 33.0 37.0 27.0 37.0 82-83 33.20684019698622 35.0 33.0 37.0 27.0 37.0 84-85 32.92630424636516 33.0 33.0 37.0 27.0 37.0 86-87 32.88126540673788 33.0 33.0 37.0 27.0 37.0 88-89 33.045056149000274 35.0 33.0 37.0 27.0 37.0 90-91 32.7282936181868 33.0 33.0 37.0 27.0 37.0 92-93 32.661325664201584 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 13.0 21 23.0 22 16.0 23 35.0 24 27.0 25 29.0 26 42.0 27 51.0 28 53.0 29 73.0 30 91.0 31 120.0 32 177.0 33 198.0 34 253.0 35 500.0 36 784.0 37 874.0 38 609.0 39 32.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.85000000000001 3.8249999999999997 3.325 8.0 2 67.525 19.175 8.924999999999999 4.375 3 33.875 39.675 15.15 11.3 4 30.275000000000002 27.950000000000003 20.65 21.125 5 23.150000000000002 31.624999999999996 28.975 16.25 6 19.525000000000002 37.05 26.375 17.05 7 34.599999999999994 28.9 22.15 14.35 8 27.750000000000004 28.95 26.400000000000002 16.900000000000002 9 25.874999999999996 27.500000000000004 29.45 17.175 10-11 24.25 27.400000000000002 30.025000000000002 18.325 12-13 25.2 27.6625 28.65 18.4875 14-15 19.725 30.2375 30.587500000000002 19.45 16-17 22.4875 31.4 25.5625 20.549999999999997 18-19 23.625 26.375 29.7875 20.2125 20-21 25.087500000000002 24.55 28.749999999999996 21.6125 22-23 26.625 23.8375 28.925 20.6125 24-25 25.15 26.25 28.3375 20.2625 26-27 23.9 24.975 32.2875 18.8375 28-29 25.55 28.375 27.0875 18.987499999999997 30-31 25.525 26.0625 28.575 19.8375 32-33 24.625 25.5 29.912499999999998 19.9625 34-35 23.2875 28.025 27.625 21.0625 36-37 25.365670708838607 25.728216027003377 27.728466058257283 21.177647205900737 38-39 26.19404851212803 25.006251562890725 30.945236309077266 17.854463615903978 40-41 25.337500000000002 24.725 27.575 22.3625 42-43 24.34054256782098 27.97849731216402 28.54106763345418 19.139892486560818 44-45 22.025 26.375 31.125000000000004 20.474999999999998 46-47 24.05 26.937499999999996 28.1875 20.825 48-49 24.175 26.5625 30.362499999999997 18.9 50-51 23.55588897224306 27.206801700425103 28.444611152788195 20.792698174543638 52-53 24.261761761761765 28.47847847847848 26.964464464464466 20.295295295295297 54-55 22.6375 28.6625 30.4875 18.212500000000002 56-57 25.474999999999998 27.462500000000002 27.650000000000002 19.412499999999998 58-59 24.15 25.662499999999998 30.0875 20.1 60-61 25.275 25.5375 30.85 18.337500000000002 62-63 21.125 29.775000000000002 31.5125 17.5875 64-65 22.925 29.5 29.049999999999997 18.525 66-67 24.425 28.6625 27.987499999999997 18.925 68-69 21.4 27.275 29.9625 21.3625 70-71 23.61198145130969 27.09612733425241 29.226720140368467 20.065171074069433 72-73 24.841007377257696 26.11294835919613 29.496311371152377 19.54973289239379 74-75 24.238529751959902 26.28196889859915 29.73910808379386 19.74039326564709 76-77 23.811374530379585 26.506024096385545 28.462236040937945 21.220365332296932 78-79 23.381389252948885 27.116644823066842 29.724770642201836 19.777195281782436 80-81 21.244692144373673 30.878450106157114 30.015923566878982 17.86093418259023 82-83 22.731549939507996 25.971232692566204 30.43419814491195 20.863019223013847 84-85 22.210095497953617 24.884038199181447 33.16507503410641 19.740791268758525 86-87 22.172007669131744 27.58148452478773 29.731580388934535 20.514927417145987 88-89 20.761435223226513 29.663105998356613 30.320460147904683 19.254998630512187 90-91 25.51355792933443 28.019720624486443 28.321007943029308 18.14571350314982 92-93 21.73377156943303 32.128184059161875 28.12927964941112 18.008764721993977 >>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 0.5 14 1.0 15 1.0 16 1.0 17 8.5 18 10.0 19 2.0 20 0.5 21 2.5 22 3.5 23 5.0 24 8.5 25 9.5 26 16.5 27 23.0 28 30.5 29 40.0 30 43.5 31 50.0 32 61.0 33 82.5 34 105.0 35 113.0 36 142.5 37 206.5 38 246.5 39 211.0 40 182.0 41 185.5 42 199.5 43 222.0 44 200.0 45 168.5 46 178.0 47 168.5 48 150.5 49 160.5 50 149.0 51 133.5 52 136.0 53 127.5 54 111.5 55 89.5 56 72.5 57 76.0 58 61.0 59 33.0 60 20.0 61 21.5 62 19.5 63 17.5 64 16.0 65 12.0 66 11.5 67 11.5 68 8.0 69 6.0 70 7.5 71 9.5 72 8.5 73 7.0 74 8.5 75 7.0 76 3.0 77 1.0 78 0.5 79 1.5 80 1.0 81 0.0 82 0.5 83 0.5 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 0.0 46-47 0.0 48-49 0.0 50-51 0.025 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 21.0 71 30.0 72 36.0 73 15.0 74 15.0 75 15.0 76 17.0 77 27.0 78 18.0 79 24.0 80 28.0 81 20.0 82 29.0 83 26.0 84 28.0 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 3651.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.35 #Duplication Level Percentage of deduplicated Percentage of total 1 92.5016160310278 71.55 2 4.169360051712992 6.45 3 1.0019392372333549 2.325 4 0.5171299288946347 1.6 5 0.2908855850032321 1.125 6 0.3232062055591467 1.5 7 0.12928248222365868 0.7000000000000001 8 0.12928248222365868 0.8 9 0.12928248222365868 0.8999999999999999 >10 0.7756948933419522 11.575000000000001 >50 0.03232062055591467 1.4749999999999999 >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 59 1.4749999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 50 1.25 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 49 1.225 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 38 0.95 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 28 0.7000000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 21 0.525 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 21 0.525 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 20 0.5 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 20 0.5 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 18 0.44999999999999996 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 17 0.42500000000000004 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 16 0.4 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 12 0.3 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 10 0.25 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 9 0.22499999999999998 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 9 0.22499999999999998 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 9 0.22499999999999998 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 9 0.22499999999999998 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 8 0.2 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 7 0.17500000000000002 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAA 6 0.15 No Hit GGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGAC 6 0.15 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 6 0.15 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit CAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 5 0.125 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGACATTATGGCAAAAAAAAGTTTGATTCAGAGGGAAAAGAAGCGGCAGA 5 0.125 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 5 0.125 No Hit GTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTA 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 0.025 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 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.1125 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.15 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.15 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.15 0.0 0.0 0.025 0.0 58-59 0.16249999999999998 0.0 0.0 0.025 0.0 60-61 0.175 0.0 0.0 0.025 0.0 62-63 0.175 0.0 0.0 0.025 0.0 64-65 0.175 0.0 0.0 0.025 0.0 66-67 0.175 0.0 0.0 0.025 0.0 68-69 0.175 0.0 0.0 0.025 0.0 70-71 0.1875 0.0 0.0 0.025 0.0 72-73 0.2 0.0 0.0 0.025 0.0 74-75 0.2 0.0 0.0 0.025 0.0 76-77 0.23750000000000002 0.0 0.0 0.025 0.0 78-79 0.275 0.0 0.0 0.025 0.0 80-81 0.2875 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCAAATT 20 6.0847076E-4 45.74 76-77 >>END_MODULE Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296917 READS because READLEN < 1 Read 296917 spots for ERR6133320.sra Written 296917 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra Rejected 296905 READS because READLEN < 1 Read 296905 spots for ERR6133320.sra Written 296905 spots for ERR6133320.sra SRR ids: ['ERR6133320.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_p92qe_de ERR6133320.sra spots: 5938112 blocks: [[1, 296905], [296906, 593810], [593811, 890715], [890716, 1187620], [1187621, 1484525], [1484526, 1781430], [1781431, 2078335], [2078336, 2375240], [2375241, 2672145], [2672146, 2969050], [2969051, 3265955], [3265956, 3562860], [3562861, 3859765], [3859766, 4156670], [4156671, 4453575], [4453576, 4750480], [4750481, 5047385], [5047386, 5344290], [5344291, 5641195], [5641196, 5938112]] ERR6133320 file size 1305210 ERR6133320 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 ERR6133320 ERR6133320_1.fastq Input file: ERR6133320_1.fastq trimmed: ERR6133320-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 00:35:34 2024 >> started Sat Dec 7 00:35:38 2024 >> done (3.494s) 5938112 reads processed; of these: 595 ( 0.01%) short reads filtered out after trimming by size control 42 ( 0.00%) empty reads filtered out after trimming by size control 5937475 (99.99%) reads available; of these: 90044 ( 1.52%) trimmed reads available after processing 5847431 (98.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 90 0.00% 19 273 0.00% 20 135 0.00% 21 171 0.00% 22 191 0.00% 23 37 0.00% 24 37 0.00% 25 42 0.00% 26 39 0.00% 27 66 0.00% 28 132 0.00% 29 141 0.00% 30 113 0.00% 31 163 0.00% 32 168 0.00% 33 69 0.00% 34 82 0.00% 35 544 0.01% 36 638 0.01% 37 135 0.00% 38 185 0.00% 39 820 0.01% 40 517 0.01% 41 250 0.00% 42 44 0.00% 43 53 0.00% 44 40 0.00% 45 37 0.00% 46 37 0.00% 47 28 0.00% 48 31 0.00% 49 41 0.00% 50 38 0.00% 51 209 0.00% 52 55 0.00% 53 17 0.00% 54 36 0.00% 55 31 0.00% 56 36 0.00% 57 62 0.00% 58 72 0.00% 59 24 0.00% 60 103 0.00% 61 39 0.00% 62 8 0.00% 63 7 0.00% 64 7 0.00% 65 13 0.00% 66 20 0.00% 67 16 0.00% 68 87 0.00% 69 265 0.00% 70 29890 0.50% 71 28931 0.49% 72 34721 0.58% 73 27714 0.47% 74 28572 0.48% 75 31099 0.52% 76 25755 0.43% 77 26584 0.45% 78 30341 0.51% 79 33729 0.57% 80 31450 0.53% 81 38521 0.65% 82 41954 0.71% 83 38702 0.65% 84 38035 0.64% 85 299 0.01% 86 473 0.01% 87 735 0.01% 88 1546 0.03% 89 2716 0.05% 90 5092 0.09% 91 15857 0.27% 92 52273 0.88% 93 5365992 90.37% 5937475 reads passed initial QC criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=5.40 fanout-score-rank=18 prefix-density=2.38 prefix-fanout=1.8 sequence=AGGCTAAATACTCCTGGGTGACCGATAGCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=204.41 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=7.8 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTTTAAAG Started job on | Dec 07 00:35:58 Started mapping on | Dec 07 00:35:59 Finished on | Dec 07 00:36:07 Mapping speed, Million of reads per hour | 2671.86 Number of input reads | 5937475 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 3677597 Uniquely mapped reads % | 61.94% Average mapped length | 91.08 Number of splices: Total | 110100 Number of splices: Annotated (sjdb) | 89977 Number of splices: GT/AG | 105002 Number of splices: GC/AG | 2901 Number of splices: AT/AC | 84 Number of splices: Non-canonical | 2113 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 1.75 Insertion rate per base | 0.02% Insertion average length | 1.75 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1893036 % of reads mapped to multiple loci | 31.88% Number of reads mapped to too many loci | 256665 % of reads mapped to too many loci | 4.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.59% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 366842 366842 366842 N_multimapping 1893036 1893036 1893036 N_noFeature 298666 335041 3512259 N_ambiguous 150397 20898 1046 UnstrandedReadsAssigned:3228534 PositiveStrandReadsAssigned:3321658 NegativeStrandReadsAssigned:164292 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133320 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: ERR6133320-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,937,475 reads, 4,573,246 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,091 rounds 52973 ERR6133320.ke.tsv 35125 ERR6133320.se.tsv 88098 total ==> ERR6133320.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 86 18.4971 PNS24243 293 194 0 0 KQK14069 1603 1504 19 3.7279 KQK14071 474 375 0 0 ==> ERR6133320.se.tsv <== BRADI_1g14170v3 19 BRADI_1g53295v3 108 BRADI_1g59795v3 46 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 63 BRADI_1g74790v3 43 BRADI_1g09890v3 0 BRADI_1g77505v3 147 BRADI_1g48960v3 0 ERR6133320 completed mapping pipeline successfully