Starting /dee2/code/volunteer_pipeline.sh ERR6133515 current disk space = 1544360341504 free memory = 1597881856 ERR6133515 SRAfilesize 20ddffe3f80deba41c365ddc2cb095ee ERR6133515.sra ERR6133515.sra file validated ERR6133515 is single end ERR6133515 is conventional basespace ERR6133515 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133515_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 36.60475 37.0 37.0 37.0 37.0 37.0 2 36.82875 37.0 37.0 37.0 37.0 37.0 3 36.52475 37.0 37.0 37.0 37.0 37.0 4 35.90125 37.0 37.0 37.0 33.0 37.0 5 36.024 37.0 37.0 37.0 33.0 37.0 6 36.28725 37.0 37.0 37.0 33.0 37.0 7 38.2465 40.0 37.0 40.0 37.0 40.0 8 38.269 40.0 37.0 40.0 37.0 40.0 9 38.32125 40.0 37.0 40.0 37.0 40.0 10-11 38.2595 40.0 37.0 40.0 37.0 40.0 12-13 38.17675 40.0 37.0 40.0 37.0 40.0 14-15 38.130250000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.067625 40.0 37.0 40.0 37.0 40.0 18-19 37.990624999999994 40.0 37.0 40.0 37.0 40.0 20-21 37.965 40.0 37.0 40.0 37.0 40.0 22-23 38.126000000000005 40.0 37.0 40.0 37.0 40.0 24-25 38.02375 40.0 37.0 40.0 37.0 40.0 26-27 37.956875 40.0 37.0 40.0 37.0 40.0 28-29 37.867000000000004 38.5 37.0 40.0 37.0 40.0 30-31 37.9945 38.5 37.0 40.0 37.0 40.0 32-33 38.032875000000004 40.0 37.0 40.0 37.0 40.0 34-35 37.937875 37.0 37.0 40.0 37.0 40.0 36-37 37.877750000000006 37.0 37.0 40.0 37.0 40.0 38-39 37.750875 37.0 37.0 40.0 37.0 40.0 40-41 37.541624999999996 37.0 37.0 40.0 35.0 40.0 42-43 37.4885 37.0 37.0 40.0 37.0 40.0 44-45 37.253125 37.0 37.0 40.0 35.0 40.0 46-47 37.209125 37.0 37.0 40.0 33.0 40.0 48-49 37.001125 37.0 37.0 37.0 33.0 40.0 50-51 36.785875000000004 37.0 37.0 37.0 33.0 40.0 52-53 36.446124999999995 37.0 37.0 37.0 33.0 40.0 54-55 36.446375 37.0 37.0 37.0 33.0 40.0 56-57 36.280874999999995 37.0 37.0 37.0 33.0 38.5 58-59 35.921625 37.0 37.0 37.0 33.0 37.0 60-61 36.062875 37.0 37.0 37.0 33.0 37.0 62-63 35.940625 37.0 37.0 37.0 33.0 37.0 64-65 35.810249999999996 37.0 37.0 37.0 33.0 37.0 66-67 35.850625 37.0 37.0 37.0 33.0 37.0 68-69 34.909875 35.0 35.0 37.0 33.0 37.0 70-71 35.11750939849624 37.0 33.0 37.0 33.0 37.0 72-73 35.600418490482184 37.0 33.0 37.0 33.0 37.0 74-75 35.526708499021396 37.0 33.0 37.0 33.0 37.0 76-77 35.54401164915592 37.0 33.0 37.0 33.0 37.0 78-79 35.57432506321994 37.0 33.0 37.0 33.0 37.0 80-81 35.34857663909979 37.0 33.0 37.0 33.0 37.0 82-83 35.163681078623256 37.0 33.0 37.0 33.0 37.0 84-85 35.012454207328695 37.0 33.0 37.0 33.0 37.0 86-87 34.98229974160206 37.0 33.0 37.0 33.0 37.0 88-89 34.95297157622739 37.0 33.0 37.0 33.0 37.0 90-91 34.89108527131783 37.0 33.0 37.0 33.0 37.0 92-93 34.889276485788116 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 7.0 23 8.0 24 5.0 25 5.0 26 7.0 27 15.0 28 14.0 29 14.0 30 32.0 31 37.0 32 40.0 33 68.0 34 101.0 35 310.0 36 1203.0 37 1431.0 38 686.0 39 14.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.4 2.4 2.55 5.65 2 75.8 14.249999999999998 6.275 3.675 3 39.025 37.675 12.675 10.625 4 33.575 29.9 17.599999999999998 18.925 5 26.85 30.575000000000003 26.075 16.5 6 20.775 39.900000000000006 24.05 15.275 7 37.025000000000006 30.475 18.8 13.700000000000001 8 28.875 29.849999999999998 24.525 16.75 9 25.25 29.2 28.000000000000004 17.549999999999997 10-11 23.8375 28.199999999999996 29.325000000000003 18.637500000000003 12-13 27.825 26.637499999999996 26.6625 18.875 14-15 21.925 32.975 28.175 16.925 16-17 24.762500000000003 31.937500000000004 24.2 19.1 18-19 23.3625 28.175 26.7625 21.7 20-21 24.803100387548444 26.778347293411674 29.866233279159893 18.552319039879986 22-23 27.762500000000003 21.9625 29.075 21.2 24-25 28.025 24.474999999999998 27.0 20.5 26-27 26.337500000000002 25.387500000000003 30.55 17.724999999999998 28-29 25.124999999999996 29.6875 26.687499999999996 18.5 30-31 29.9625 25.6125 25.087500000000002 19.3375 32-33 24.275 27.85 26.85 21.025 34-35 24.4 27.737499999999997 26.7625 21.099999999999998 36-37 24.462500000000002 24.5125 29.2375 21.7875 38-39 29.1125 24.725 28.675 17.4875 40-41 27.206801700425103 25.156289072268066 27.806951737934483 19.829957489372344 42-43 25.86573321665208 30.30378797349669 24.615576947118388 19.21490186273284 44-45 23.474999999999998 26.2875 29.212500000000002 21.025 46-47 24.8625 22.287499999999998 27.825 25.025 48-49 25.5375 24.725 30.612499999999997 19.125 50-51 25.6125 26.424999999999997 28.575 19.3875 52-53 25.059546195311523 27.980443775855584 25.059546195311523 21.900463833521375 54-55 23.0278784848106 31.003875484435557 27.11588948618577 18.85235654456807 56-57 27.900000000000002 26.387500000000003 26.3125 19.400000000000002 58-59 23.1875 26.2875 28.549999999999997 21.975 60-61 26.2625 25.174999999999997 28.000000000000004 20.5625 62-63 23.05 27.1 31.0125 18.8375 64-65 24.2875 30.0 26.8375 18.875 66-67 25.240655081885237 28.978622327790976 26.740842605325664 19.039879984998127 68-69 22.537499999999998 27.224999999999998 26.5 23.7375 70-71 24.918648310387987 27.697121401752188 25.056320400500624 22.327909887359198 72-73 26.49314724003521 23.21136677983151 28.794165723626303 21.50132025650698 74-75 24.53306410903584 29.36648157496214 27.80161534578496 18.298838970217062 76-77 22.0532319391635 26.00760456273764 28.162230671736378 23.776932826362483 78-79 24.987277353689567 25.687022900763356 28.524173027989825 20.801526717557252 80-81 23.384418901660283 31.085568326947637 28.199233716475096 17.330779054916988 82-83 25.930680359435172 24.35173299101412 27.90757381258023 21.810012836970476 84-85 24.122354155911204 24.432111512648426 30.17552916881776 21.270005162622613 86-87 22.10594315245478 26.5374677002584 30.994832041343667 20.361757105943152 88-89 20.775193798449614 29.857881136950905 30.297157622739018 19.069767441860467 90-91 28.204134366925064 27.76485788113695 26.27906976744186 17.751937984496124 92-93 23.074935400516797 30.594315245478036 27.10594315245478 19.224806201550386 >>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 1.0 18 2.0 19 1.5 20 1.0 21 1.0 22 1.0 23 7.5 24 11.0 25 9.5 26 9.0 27 9.5 28 18.5 29 24.0 30 24.5 31 28.5 32 36.5 33 49.0 34 58.0 35 69.0 36 91.5 37 131.5 38 176.5 39 168.5 40 163.5 41 185.0 42 181.5 43 176.0 44 161.0 45 186.0 46 281.5 47 256.0 48 173.5 49 168.0 50 177.5 51 189.0 52 166.0 53 180.5 54 209.5 55 140.0 56 64.0 57 52.0 58 49.0 59 35.0 60 24.5 61 26.5 62 18.5 63 10.0 64 12.5 65 14.0 66 12.5 67 11.0 68 7.0 69 6.0 70 5.0 71 2.0 72 2.0 73 1.5 74 1.0 75 1.0 76 1.0 77 0.5 78 0.0 79 0.0 80 0.0 81 0.5 82 0.5 83 0.5 84 0.5 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 0.0125 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 0.0 40-41 0.025 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2875 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 0.0125 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 0.012835322808368629 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 11.0 72 5.0 73 7.0 74 10.0 75 9.0 76 6.0 77 9.0 78 6.0 79 8.0 80 8.0 81 11.0 82 9.0 83 13.0 84 8.0 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 3870.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.875 #Duplication Level Percentage of deduplicated Percentage of total 1 91.93825042881647 67.0 2 4.734133790737564 6.9 3 1.234991423670669 2.7 4 0.5831903945111492 1.7000000000000002 5 0.30874785591766724 1.125 6 0.17152658662092624 0.75 7 0.10291595197255575 0.525 8 0.06861063464837049 0.4 9 0.03430531732418524 0.22499999999999998 >10 0.7204116638078902 11.875 >50 0.06861063464837049 4.0 >100 0.03430531732418524 2.8000000000000003 >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 112 2.8000000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 100 2.5 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 60 1.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 41 1.0250000000000001 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 40 1.0 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 39 0.975 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 34 0.8500000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 33 0.8250000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 32 0.8 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 32 0.8 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 29 0.7250000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 28 0.7000000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 23 0.575 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 21 0.525 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 11 0.27499999999999997 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 11 0.27499999999999997 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 10 0.25 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCA 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 5 0.125 No Hit GGGCGTGGCGTTCATGAACAAGTGAAACCTTATGGCTGGATGGGTCATCG 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 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 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.0625 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 25 7.3666786E-5 69.29 1 GAGCAAT 25 7.3666786E-5 69.29 5 AGCAATA 25 7.3666786E-5 69.29 6 GCAATAC 20 0.0027786458 64.959366 7 CAATACA 20 0.0027786458 64.959366 8 GGAGAGC 30 1.8166173E-4 57.741665 2 AGAGCAA 30 1.8166173E-4 57.741665 4 GAGAGCA 30 1.8166173E-4 57.741665 3 AATACAA 25 0.006724602 51.9675 9 CATCACT 20 6.610043E-4 44.993504 82-83 ATCACTA 20 6.610043E-4 44.993504 84-85 AGCATCA 20 6.610043E-4 44.993504 80-81 CACTAGC 20 6.610043E-4 44.993504 86-87 TCACTAG 20 6.610043E-4 44.993504 84-85 ACTAGCT 20 6.610043E-4 44.993504 86-87 AAGCATC 20 6.610043E-4 44.993504 80-81 AAAGCAT 20 6.8270986E-4 44.703224 78-79 GAAAGCA 20 6.8270986E-4 44.703224 78-79 CGAAAGC 20 7.512421E-4 43.854427 76-77 CCGAAAG 20 7.512421E-4 43.854427 76-77 >>END_MODULE Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74314 READS because READLEN < 1 Read 74314 spots for ERR6133515.sra Written 74314 spots for ERR6133515.sra Rejected 74325 READS because READLEN < 1 Read 74325 spots for ERR6133515.sra Written 74325 spots for ERR6133515.sra SRR ids: ['ERR6133515.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0xyrucu4 ERR6133515.sra spots: 1486291 blocks: [[1, 74314], [74315, 148628], [148629, 222942], [222943, 297256], [297257, 371570], [371571, 445884], [445885, 520198], [520199, 594512], [594513, 668826], [668827, 743140], [743141, 817454], [817455, 891768], [891769, 966082], [966083, 1040396], [1040397, 1114710], [1114711, 1189024], [1189025, 1263338], [1263339, 1337652], [1337653, 1411966], [1411967, 1486291]] ERR6133515 file size 327220 ERR6133515 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 ERR6133515 ERR6133515_1.fastq Input file: ERR6133515_1.fastq trimmed: ERR6133515-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 07:41:49 2024 >> started Sat Dec 7 07:41:50 2024 >> done (0.983s) 1486291 reads processed; of these: 221 ( 0.01%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 1486061 (99.98%) reads available; of these: 7483 ( 0.50%) trimmed reads available after processing 1478578 (99.50%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 29 0.00% 19 65 0.00% 20 31 0.00% 21 13 0.00% 22 23 0.00% 23 10 0.00% 24 5 0.00% 25 10 0.00% 26 14 0.00% 27 16 0.00% 28 14 0.00% 29 82 0.01% 30 16 0.00% 31 24 0.00% 32 30 0.00% 33 14 0.00% 34 15 0.00% 35 135 0.01% 36 291 0.02% 37 20 0.00% 38 28 0.00% 39 60 0.00% 40 86 0.01% 41 33 0.00% 42 9 0.00% 43 11 0.00% 44 11 0.00% 45 11 0.00% 46 5 0.00% 47 6 0.00% 48 3 0.00% 49 10 0.00% 50 11 0.00% 51 42 0.00% 52 7 0.00% 53 5 0.00% 54 4 0.00% 55 4 0.00% 56 5 0.00% 57 8 0.00% 58 13 0.00% 59 5 0.00% 60 8 0.00% 61 4 0.00% 62 0 0.00% 63 0 0.00% 64 2 0.00% 65 2 0.00% 66 1 0.00% 67 2 0.00% 68 2 0.00% 69 22 0.00% 70 3770 0.25% 71 3176 0.21% 72 3281 0.22% 73 2846 0.19% 74 3098 0.21% 75 2989 0.20% 76 2525 0.17% 77 2623 0.18% 78 3161 0.21% 79 3582 0.24% 80 3184 0.21% 81 4085 0.27% 82 4280 0.29% 83 4022 0.27% 84 3361 0.23% 85 16 0.00% 86 35 0.00% 87 69 0.00% 88 131 0.01% 89 215 0.01% 90 413 0.03% 91 1049 0.07% 92 4045 0.27% 93 1428828 96.15% 1486061 reads passed initial QC criterion=sequence-density sequence-density=0.64 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=30 prefix-density=0.64 prefix-fanout=1.9 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=23 fanout-score=40.23 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=1.7 sequence=TGCTGCAGCAGCTTAATTTGCATGCCAGGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCT Started job on | Dec 07 07:42:07 Started mapping on | Dec 07 07:42:09 Finished on | Dec 07 07:42:13 Mapping speed, Million of reads per hour | 1337.45 Number of input reads | 1486061 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 899550 Uniquely mapped reads % | 60.53% Average mapped length | 92.01 Number of splices: Total | 67110 Number of splices: Annotated (sjdb) | 57508 Number of splices: GT/AG | 65305 Number of splices: GC/AG | 1144 Number of splices: AT/AC | 34 Number of splices: Non-canonical | 627 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 544991 % of reads mapped to multiple loci | 36.67% Number of reads mapped to too many loci | 9178 % of reads mapped to too many loci | 0.62% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.15% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 41520 41520 41520 N_multimapping 544991 544991 544991 N_noFeature 59589 68486 861737 N_ambiguous 33728 4893 153 UnstrandedReadsAssigned:806233 PositiveStrandReadsAssigned:826171 NegativeStrandReadsAssigned:37660 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133515 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: ERR6133515-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,486,061 reads, 1,203,105 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 912 rounds 52973 ERR6133515.ke.tsv 35125 ERR6133515.se.tsv 88098 total ==> ERR6133515.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 47 38.0782 PNS24243 293 194 0 0 KQK14069 1603 1504 39 28.8237 KQK14071 474 375 0 0 ==> ERR6133515.se.tsv <== BRADI_1g14170v3 39 BRADI_1g53295v3 40 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 17 BRADI_1g48960v3 0 ERR6133515 completed mapping pipeline successfully