Starting /dee2/code/volunteer_pipeline.sh ERR6133456 current disk space = 1545580007424 free memory = 1470118324 ERR6133456 SRAfilesize 6e6eb94e79f8068f61301dfbe21f2318 ERR6133456.sra ERR6133456.sra file validated ERR6133456 is single end ERR6133456 is conventional basespace ERR6133456 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133456_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 35.02975 37.0 33.0 37.0 33.0 37.0 2 36.304 37.0 37.0 37.0 33.0 37.0 3 35.44475 37.0 33.0 37.0 33.0 37.0 4 34.9995 37.0 37.0 37.0 33.0 37.0 5 34.8255 37.0 33.0 37.0 27.0 37.0 6 35.3135 37.0 37.0 37.0 33.0 37.0 7 36.87375 37.0 37.0 40.0 33.0 40.0 8 36.938 37.0 37.0 40.0 33.0 40.0 9 37.1975 37.0 37.0 40.0 33.0 40.0 10-11 37.168000000000006 37.0 37.0 40.0 33.0 40.0 12-13 37.014125 37.0 37.0 40.0 33.0 40.0 14-15 36.930875 37.0 37.0 40.0 33.0 40.0 16-17 36.76349999999999 37.0 37.0 40.0 33.0 40.0 18-19 36.4015 37.0 37.0 40.0 33.0 40.0 20-21 36.34075 37.0 37.0 40.0 33.0 40.0 22-23 36.080625 37.0 35.0 40.0 33.0 40.0 24-25 36.14675 37.0 35.0 40.0 33.0 40.0 26-27 36.3505 37.0 37.0 40.0 33.0 40.0 28-29 36.266999999999996 37.0 37.0 40.0 33.0 40.0 30-31 36.3095 37.0 37.0 40.0 33.0 40.0 32-33 36.233625 37.0 37.0 40.0 33.0 40.0 34-35 36.183875 37.0 37.0 40.0 33.0 40.0 36-37 36.161 37.0 37.0 40.0 33.0 40.0 38-39 36.022999999999996 37.0 35.0 40.0 33.0 40.0 40-41 35.899 37.0 33.0 40.0 33.0 40.0 42-43 35.806125 37.0 33.0 40.0 33.0 40.0 44-45 35.564499999999995 37.0 33.0 38.5 33.0 40.0 46-47 35.429625 37.0 33.0 37.0 30.0 40.0 48-49 35.513625000000005 37.0 33.0 37.0 33.0 40.0 50-51 35.307625 37.0 33.0 37.0 33.0 40.0 52-53 35.04375 37.0 33.0 37.0 33.0 40.0 54-55 35.061 37.0 33.0 37.0 33.0 38.5 56-57 34.895 37.0 33.0 37.0 33.0 37.0 58-59 34.281875 37.0 33.0 37.0 27.0 37.0 60-61 34.61575 37.0 33.0 37.0 30.0 37.0 62-63 34.480625 37.0 33.0 37.0 30.0 37.0 64-65 34.21725 37.0 33.0 37.0 27.0 37.0 66-67 34.147375 37.0 33.0 37.0 27.0 37.0 68-69 33.332499999999996 35.0 33.0 37.0 27.0 37.0 70-71 33.57593753126564 35.0 33.0 37.0 27.0 37.0 72-73 33.881916180330734 37.0 33.0 37.0 27.0 37.0 74-75 33.8822678109981 37.0 33.0 37.0 27.0 37.0 76-77 34.03066401188332 37.0 33.0 37.0 27.0 37.0 78-79 34.0672388122755 37.0 33.0 37.0 27.0 37.0 80-81 33.9386549241423 37.0 33.0 37.0 27.0 37.0 82-83 33.772721549596426 37.0 33.0 37.0 27.0 37.0 84-85 33.50680532413686 35.0 33.0 37.0 27.0 37.0 86-87 33.44249363867685 37.0 33.0 37.0 27.0 37.0 88-89 33.51119592875318 37.0 33.0 37.0 27.0 37.0 90-91 33.24376590330789 33.0 33.0 37.0 27.0 37.0 92-93 33.34325699745547 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 8.0 21 10.0 22 14.0 23 22.0 24 24.0 25 31.0 26 44.0 27 49.0 28 62.0 29 79.0 30 105.0 31 129.0 32 178.0 33 198.0 34 326.0 35 520.0 36 852.0 37 902.0 38 441.0 39 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.225 2.775 3.05 6.950000000000001 2 72.02499999999999 16.875 6.625 4.475 3 36.3 40.275 12.45 10.975 4 32.75 29.375 19.625 18.25 5 27.025 28.825 27.0 17.150000000000002 6 19.125 39.074999999999996 24.85 16.950000000000003 7 38.0 28.625 18.625 14.75 8 30.2 31.424999999999997 20.3 18.075 9 25.324999999999996 31.525 26.575 16.575 10-11 24.7875 27.375 30.025000000000002 17.8125 12-13 26.1 28.95 25.35 19.6 14-15 21.987499999999997 32.5125 26.2875 19.2125 16-17 24.337500000000002 31.65 24.3625 19.650000000000002 18-19 23.702962870358796 26.290786348293537 29.541192649081133 20.465058132266535 20-21 25.972726135368447 25.509821093456775 28.174652821218565 20.342799949956213 22-23 28.775000000000002 22.775000000000002 28.249999999999996 20.200000000000003 24-25 24.887500000000003 25.3 28.1875 21.625 26-27 26.474999999999998 23.25 31.0125 19.2625 28-29 25.8625 27.525 28.425 18.1875 30-31 27.85 25.4 27.175 19.575 32-33 26.2875 25.3125 27.575 20.825 34-35 23.3625 30.587500000000002 25.8 20.25 36-37 26.703337917239654 25.240655081885237 26.190773846730842 21.865233154144267 38-39 29.461047892959858 24.02150806552457 28.48568213079905 18.03176191071652 40-41 26.665833229153645 24.6530816352044 28.82860357544693 19.852481560195024 42-43 27.167919799498748 28.984962406015036 25.100250626566417 18.746867167919802 44-45 24.44027517198249 24.878048780487806 30.73170731707317 19.949968730456536 46-47 25.324999999999996 25.074999999999996 27.8375 21.762500000000003 48-49 24.95 25.05 29.562500000000004 20.4375 50-51 22.475 27.437499999999996 28.975 21.1125 52-53 24.288757989723024 26.080962526632412 26.394284998120064 23.235994485524504 54-55 22.777847230903863 26.015751968996128 30.52881610201275 20.677584698087262 56-57 27.474999999999998 25.324999999999996 27.762500000000003 19.4375 58-59 25.15 25.7375 28.849999999999998 20.2625 60-61 27.250000000000004 25.4625 29.5375 17.75 62-63 21.212500000000002 26.450000000000003 32.7125 19.625 64-65 22.575 31.0125 28.975 17.4375 66-67 24.099999999999998 29.125 28.0875 18.6875 68-69 20.5900737592199 26.003250406300786 30.078759844980624 23.32791598949869 70-71 23.818454613653415 27.806951737934483 27.981995498874717 20.392598149537385 72-73 26.869597895527995 24.61480646373544 28.610797945634474 19.90479769510209 74-75 25.54607080090384 27.102686417273414 28.65930203364298 18.691940748179764 76-77 22.966687617850408 25.355122564424892 27.881835323695785 23.79635449402891 78-79 25.273894975443902 26.596146581035136 28.850270746757335 19.27968769676363 80-81 21.234692589319533 32.6221436687287 28.08988764044944 18.053276101502334 82-83 23.097378751424593 24.4523236672154 29.707483854628343 22.74281372673167 84-85 23.46886912325286 24.218551461245237 32.64294790343075 19.669631512071156 86-87 21.62849872773537 28.231552162849873 30.114503816793892 20.025445292620866 88-89 20.89058524173028 27.83715012722646 31.43765903307888 19.834605597964376 90-91 26.501272264631044 26.017811704834603 28.676844783715012 18.804071246819337 92-93 21.959287531806616 27.7735368956743 29.60559796437659 20.661577608142494 >>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 0.5 16 0.5 17 10.0 18 12.0 19 4.5 20 5.0 21 2.5 22 2.5 23 4.0 24 2.5 25 1.5 26 5.0 27 8.5 28 14.0 29 20.0 30 27.0 31 36.0 32 46.0 33 62.0 34 64.0 35 69.5 36 107.5 37 153.5 38 205.0 39 202.5 40 192.5 41 195.0 42 191.0 43 209.5 44 194.5 45 174.5 46 186.0 47 198.5 48 183.5 49 166.0 50 158.5 51 154.0 52 133.0 53 124.5 54 165.0 55 142.0 56 74.5 57 61.0 58 55.5 59 46.0 60 37.5 61 29.5 62 22.0 63 22.5 64 28.5 65 24.5 66 14.5 67 9.5 68 8.5 69 9.0 70 11.0 71 12.0 72 9.5 73 5.0 74 2.0 75 1.0 76 1.0 77 1.0 78 0.5 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 0.0125 20-21 0.08750000000000001 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 0.0375 40-41 0.0125 42-43 0.25 44-45 0.0625 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2625 54-55 0.0125 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 0.0125 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 2.0 71 3.0 72 7.0 73 3.0 74 4.0 75 1.0 76 5.0 77 3.0 78 3.0 79 6.0 80 5.0 81 6.0 82 7.0 83 5.0 84 10.0 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 3930.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.10000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 93.19066147859922 71.85000000000001 2 3.631647211413749 5.6000000000000005 3 1.0700389105058365 2.475 4 0.2918287937743191 0.8999999999999999 5 0.4539559014267186 1.7500000000000002 6 0.25940337224383914 1.2 7 0.19455252918287938 1.05 8 0.12970168612191957 0.8 9 0.12970168612191957 0.8999999999999999 >10 0.5836575875486382 7.925 >50 0.03242542153047989 2.075 >100 0.03242542153047989 3.4750000000000005 >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 139 3.4750000000000005 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 83 2.075 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 40 1.0 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 30 0.75 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 27 0.675 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 25 0.625 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 21 0.525 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 18 0.44999999999999996 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 18 0.44999999999999996 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 18 0.44999999999999996 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 16 0.4 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 10 0.25 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 10 0.25 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 9 0.22499999999999998 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 7 0.17500000000000002 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 7 0.17500000000000002 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 7 0.17500000000000002 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 7 0.17500000000000002 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 7 0.17500000000000002 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 6 0.15 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 6 0.15 No Hit GAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAGTTTTTCTTA 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCG 5 0.125 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 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 0.025 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 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 25 6.577866E-7 86.75 2 GCAATAC 25 6.577866E-7 86.75 7 GGGAGAG 25 6.577866E-7 86.75 1 CAATACA 25 6.577866E-7 86.75 8 GAGCAAT 25 6.577866E-7 86.75 5 AGAGCAA 25 6.577866E-7 86.75 4 AATACAA 25 6.577866E-7 86.75 9 GAGAGCA 30 1.9462768E-6 72.291664 3 AGCAATA 35 4.86315E-6 61.964287 6 GGGGAAA 25 0.0066825324 52.05 1 CATCACT 25 3.7934726E-5 44.487183 82-83 ATCACTA 25 3.7934726E-5 44.487183 84-85 AGCATCA 25 3.7934726E-5 44.487183 80-81 CACTAGC 25 3.7934726E-5 44.487183 86-87 TCACTAG 25 3.7934726E-5 44.487183 84-85 ACTAGCT 25 3.7934726E-5 44.487183 86-87 GCATCAC 25 3.7934726E-5 44.487183 82-83 AAGCATC 25 3.7934726E-5 44.487183 80-81 GATGGCT 25 4.415777E-5 43.375 56-57 GGTTGAG 25 4.415777E-5 43.375 38-39 >>END_MODULE Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra Rejected 231588 READS because READLEN < 1 Read 231588 spots for ERR6133456.sra Written 231588 spots for ERR6133456.sra SRR ids: ['ERR6133456.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_7q8lvm2f ERR6133456.sra spots: 4631760 blocks: [[1, 231588], [231589, 463176], [463177, 694764], [694765, 926352], [926353, 1157940], [1157941, 1389528], [1389529, 1621116], [1621117, 1852704], [1852705, 2084292], [2084293, 2315880], [2315881, 2547468], [2547469, 2779056], [2779057, 3010644], [3010645, 3242232], [3242233, 3473820], [3473821, 3705408], [3705409, 3936996], [3936997, 4168584], [4168585, 4400172], [4400173, 4631760]] ERR6133456 file size 1026311 ERR6133456 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 ERR6133456 ERR6133456_1.fastq Input file: ERR6133456_1.fastq trimmed: ERR6133456-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 06:25:02 2024 >> started Sat Dec 7 06:25:15 2024 >> done (13.042s) 4631760 reads processed; of these: 217 ( 0.00%) short reads filtered out after trimming by size control 21 ( 0.00%) empty reads filtered out after trimming by size control 4631522 (99.99%) reads available; of these: 68332 ( 1.48%) trimmed reads available after processing 4563190 (98.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 32 0.00% 20 24 0.00% 21 19 0.00% 22 16 0.00% 23 13 0.00% 24 12 0.00% 25 11 0.00% 26 13 0.00% 27 28 0.00% 28 80 0.00% 29 48 0.00% 30 20 0.00% 31 15 0.00% 32 19 0.00% 33 20 0.00% 34 26 0.00% 35 84 0.00% 36 823 0.02% 37 20 0.00% 38 21 0.00% 39 44 0.00% 40 52 0.00% 41 33 0.00% 42 22 0.00% 43 27 0.00% 44 14 0.00% 45 38 0.00% 46 23 0.00% 47 17 0.00% 48 23 0.00% 49 7 0.00% 50 14 0.00% 51 17 0.00% 52 11 0.00% 53 13 0.00% 54 8 0.00% 55 7 0.00% 56 7 0.00% 57 12 0.00% 58 8 0.00% 59 8 0.00% 60 7 0.00% 61 7 0.00% 62 2 0.00% 63 7 0.00% 64 2 0.00% 65 6 0.00% 66 9 0.00% 67 18 0.00% 68 27 0.00% 69 71 0.00% 70 6183 0.13% 71 5808 0.13% 72 6187 0.13% 73 5707 0.12% 74 5805 0.13% 75 5553 0.12% 76 5094 0.11% 77 5153 0.11% 78 5802 0.13% 79 6076 0.13% 80 5779 0.12% 81 6943 0.15% 82 7733 0.17% 83 6753 0.15% 84 6955 0.15% 85 172 0.00% 86 287 0.01% 87 514 0.01% 88 944 0.02% 89 1816 0.04% 90 3702 0.08% 91 12011 0.26% 92 45493 0.98% 93 4473134 96.58% 4631522 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=29 prefix-density=0.52 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=40.24 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=6.2 sequence=AGCAGAAGAAAGTGCCGTTCATCAGTGACGACCTGGAGATCGAGTGCGAGGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGATGCGTGTGTATGTGGCATGCCAGCGTTTGTACCTAGAAGATGTGAAAAACTGCAGAAATGTTTTGGATGTTAACTTGTCGTCCGTCCGCCT Started job on | Dec 07 06:26:42 Started mapping on | Dec 07 06:26:42 Finished on | Dec 07 06:27:38 Mapping speed, Million of reads per hour | 297.74 Number of input reads | 4631522 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2967216 Uniquely mapped reads % | 64.07% Average mapped length | 92.34 Number of splices: Total | 125904 Number of splices: Annotated (sjdb) | 103890 Number of splices: GT/AG | 120440 Number of splices: GC/AG | 3456 Number of splices: AT/AC | 92 Number of splices: Non-canonical | 1916 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.04% Deletion average length | 1.81 Insertion rate per base | 0.02% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1524551 % of reads mapped to multiple loci | 32.92% Number of reads mapped to too many loci | 53845 % of reads mapped to too many loci | 1.16% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.75% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 139755 139755 139755 N_multimapping 1524551 1524551 1524551 N_noFeature 223366 250884 2837977 N_ambiguous 116555 14682 397 UnstrandedReadsAssigned:2627295 PositiveStrandReadsAssigned:2701650 NegativeStrandReadsAssigned:128842 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133456 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: ERR6133456-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,631,522 reads, 3,649,095 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52973 ERR6133456.ke.tsv 35125 ERR6133456.se.tsv 88098 total ==> ERR6133456.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 108 28.1627 PNS24243 293 194 0 0 KQK14069 1603 1504 28 6.66061 KQK14071 474 375 0 0 ==> ERR6133456.se.tsv <== BRADI_1g14170v3 28 BRADI_1g53295v3 22 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 50 BRADI_1g74790v3 47 BRADI_1g09890v3 0 BRADI_1g77505v3 80 BRADI_1g48960v3 0 ERR6133456 completed mapping pipeline successfully