Starting /dee2/code/volunteer_pipeline.sh ERR6133551 current disk space = 1544525795328 free memory = 1465432460 ERR6133551 SRAfilesize 34ecd0b2d60875ad934b296f73a93193 ERR6133551.sra ERR6133551.sra file validated ERR6133551 is single end ERR6133551 is conventional basespace ERR6133551 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133551_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 34.05775 37.0 33.0 37.0 33.0 37.0 2 36.06475 37.0 37.0 37.0 33.0 37.0 3 35.1615 37.0 33.0 37.0 33.0 37.0 4 35.2675 37.0 37.0 37.0 33.0 37.0 5 35.18425 37.0 37.0 37.0 33.0 37.0 6 35.5875 37.0 37.0 37.0 33.0 37.0 7 37.36525 37.0 37.0 40.0 33.0 40.0 8 37.375 37.0 37.0 40.0 33.0 40.0 9 37.40225 37.0 37.0 40.0 33.0 40.0 10-11 37.423 37.0 37.0 40.0 33.0 40.0 12-13 37.351625 37.0 37.0 40.0 33.0 40.0 14-15 37.37975 37.0 37.0 40.0 33.0 40.0 16-17 37.281125 37.0 37.0 40.0 33.0 40.0 18-19 37.247125 37.0 37.0 40.0 33.0 40.0 20-21 37.128 37.0 37.0 40.0 33.0 40.0 22-23 37.00375 37.0 37.0 40.0 33.0 40.0 24-25 37.070625 37.0 37.0 40.0 33.0 40.0 26-27 37.083875000000006 37.0 37.0 40.0 33.0 40.0 28-29 37.039125 37.0 37.0 40.0 33.0 40.0 30-31 36.9495 37.0 37.0 40.0 33.0 40.0 32-33 36.81375 37.0 37.0 40.0 33.0 40.0 34-35 36.68375 37.0 37.0 40.0 33.0 40.0 36-37 36.511125 37.0 37.0 40.0 33.0 40.0 38-39 36.421875 37.0 37.0 40.0 33.0 40.0 40-41 36.209125 37.0 37.0 40.0 33.0 40.0 42-43 36.063500000000005 37.0 37.0 40.0 33.0 40.0 44-45 35.84525 37.0 35.0 40.0 33.0 40.0 46-47 35.554125 37.0 33.0 37.0 33.0 40.0 48-49 35.6025 37.0 33.0 37.0 33.0 40.0 50-51 35.5035 37.0 33.0 37.0 33.0 40.0 52-53 35.299625000000006 37.0 33.0 37.0 33.0 40.0 54-55 35.161 37.0 33.0 37.0 33.0 40.0 56-57 35.019499999999994 37.0 33.0 37.0 33.0 37.0 58-59 34.3955 37.0 33.0 37.0 27.0 37.0 60-61 34.5985 37.0 33.0 37.0 27.0 37.0 62-63 34.602625 37.0 33.0 37.0 27.0 37.0 64-65 34.581125 37.0 33.0 37.0 30.0 37.0 66-67 34.583875000000006 37.0 33.0 37.0 30.0 37.0 68-69 33.801 35.0 33.0 37.0 30.0 37.0 70-71 33.823510978670015 35.0 33.0 37.0 27.0 37.0 72-73 34.18323381576733 37.0 33.0 37.0 27.0 37.0 74-75 34.165205241248685 37.0 33.0 37.0 27.0 37.0 76-77 34.14493341712256 37.0 33.0 37.0 27.0 37.0 78-79 34.18762661554635 37.0 33.0 37.0 27.0 37.0 80-81 34.15074041001845 37.0 33.0 37.0 27.0 37.0 82-83 34.006195592740376 37.0 33.0 37.0 27.0 37.0 84-85 34.034011335429554 37.0 33.0 37.0 27.0 37.0 86-87 34.03141225337487 37.0 33.0 37.0 27.0 37.0 88-89 33.898364485981304 37.0 33.0 37.0 27.0 37.0 90-91 33.70080477673936 37.0 33.0 37.0 27.0 37.0 92-93 33.661993769470406 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 10.0 22 16.0 23 20.0 24 25.0 25 31.0 26 47.0 27 38.0 28 60.0 29 57.0 30 88.0 31 116.0 32 141.0 33 174.0 34 223.0 35 432.0 36 895.0 37 946.0 38 656.0 39 18.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.85 3.075 2.9000000000000004 6.175 2 73.425 15.525 6.375 4.675 3 37.2 37.775 13.850000000000001 11.175 4 32.475 29.4 18.95 19.175 5 26.400000000000002 30.675 25.1 17.825 6 21.05 38.95 23.875 16.125 7 36.975 29.299999999999997 19.075 14.649999999999999 8 30.0 29.325000000000003 23.625 17.05 9 25.124999999999996 29.25 29.4 16.225 10-11 25.0625 28.0625 28.9 17.974999999999998 12-13 27.85 26.5625 27.425 18.1625 14-15 21.512500000000003 31.175000000000004 28.225 19.0875 16-17 25.0 31.125000000000004 25.724999999999998 18.15 18-19 24.090511313914238 26.915864483060382 28.853606700837602 20.140017502187774 20-21 25.497061398024258 25.934725522070778 29.01087907965487 19.557334000250094 22-23 27.650000000000002 23.35 28.6625 20.3375 24-25 26.087500000000002 24.099999999999998 29.1875 20.625 26-27 26.737499999999997 24.15 29.9 19.2125 28-29 24.615576947118388 26.753344168021005 29.32866608326041 19.302412801600198 30-31 28.9 24.2 27.237499999999997 19.662499999999998 32-33 25.362499999999997 26.0125 27.237499999999997 21.3875 34-35 23.488925040670754 27.480916030534353 27.856338380678263 21.17382054811663 36-37 25.525 24.2 27.875 22.400000000000002 38-39 28.449999999999996 25.0 28.575 17.974999999999998 40-41 27.323908419867383 23.820843237833103 28.67509070436632 20.180157637933192 42-43 24.445835942391987 28.36568566061365 27.551659361302445 19.63681903569192 44-45 24.19617165019392 26.160390341548855 30.051294883022646 19.59214312523458 46-47 24.2375 24.55 28.1375 23.075000000000003 48-49 24.83431286732525 24.52169563586345 30.57396523696386 20.07002625984744 50-51 24.6875 26.724999999999998 28.675 19.9125 52-53 24.824737105658485 26.940410615923888 26.02653980971457 22.208312468703053 54-55 23.575 26.625 29.7125 20.0875 56-57 25.85 25.974999999999998 28.3125 19.8625 58-59 22.675 26.150000000000002 29.862499999999997 21.3125 60-61 26.437500000000004 24.212500000000002 29.799999999999997 19.55 62-63 23.674999999999997 25.7375 31.525 19.0625 64-65 23.974999999999998 29.012500000000003 28.65 18.3625 66-67 24.6 28.549999999999997 28.0875 18.7625 68-69 21.9375 25.337500000000002 29.862499999999997 22.8625 70-71 24.04508453350031 25.973700688791485 29.217282404508456 20.76393237319975 72-73 26.462080241479057 24.160482958118475 30.260344610740788 19.117092189661676 74-75 23.99241945672773 27.327858496525586 29.665192672141504 19.01452937460518 76-77 22.240569033405308 25.644608154451927 29.378889876794105 22.73593293534866 78-79 23.90611047327465 25.959943870391633 29.850746268656714 20.283199387677 80-81 23.382126348228045 30.49563430919363 28.338469440164353 17.783769902413972 82-83 24.31909126113334 24.977410610558927 29.288756938169612 21.414741190138116 84-85 22.84046692607004 25.23994811932555 31.66018158236057 20.25940337224384 86-87 20.898234683281412 27.15472481827622 31.295430944963655 20.65160955347871 88-89 20.482866043613708 26.804257528556597 32.126168224299064 20.586708203530634 90-91 26.298026998961575 27.232606438213914 29.140706126687437 17.32866043613707 92-93 22.936137071651093 28.180166147455864 29.906542056074763 18.977154724818277 >>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 3.5 18 4.0 19 3.0 20 3.0 21 1.0 22 1.0 23 3.0 24 4.0 25 4.0 26 7.5 27 9.0 28 14.5 29 21.0 30 22.0 31 27.0 32 48.5 33 77.0 34 82.0 35 93.5 36 120.0 37 145.5 38 170.0 39 185.0 40 198.0 41 191.5 42 205.0 43 228.5 44 209.0 45 189.0 46 228.0 47 215.5 48 170.0 49 166.0 50 155.0 51 150.0 52 127.0 53 127.0 54 160.5 55 129.0 56 70.0 57 59.5 58 50.5 59 44.0 60 38.0 61 29.0 62 27.0 63 25.5 64 24.0 65 19.0 66 13.5 67 11.0 68 8.5 69 7.5 70 7.5 71 7.0 72 6.0 73 3.5 74 1.0 75 1.0 76 1.0 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 0.0125 20-21 0.0375 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0125 30-31 0.0 32-33 0.0 34-35 0.11249999999999999 36-37 0.0 38-39 0.0 40-41 0.08750000000000001 42-43 0.1875 44-45 0.08750000000000001 46-47 0.0 48-49 0.0375 50-51 0.0 52-53 0.15 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 15.0 71 5.0 72 9.0 73 7.0 74 13.0 75 12.0 76 5.0 77 9.0 78 11.0 79 16.0 80 8.0 81 11.0 82 11.0 83 10.0 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 3852.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.10000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 93.53932584269663 74.925 2 3.526841448189763 5.65 3 1.0611735330836454 2.55 4 0.5617977528089888 1.7999999999999998 5 0.3433208489388265 1.375 6 0.12484394506866417 0.6 7 0.09363295880149813 0.525 8 0.09363295880149813 0.6 9 0.12484394506866417 0.8999999999999999 >10 0.4993757802746567 8.15 >50 0.0 0.0 >100 0.031210986267166042 2.9250000000000003 >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 117 2.9250000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 43 1.075 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 35 0.8750000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 30 0.75 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 27 0.675 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 26 0.65 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 24 0.6 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 21 0.525 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 17 0.42500000000000004 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 17 0.42500000000000004 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 15 0.375 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 14 0.35000000000000003 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 9 0.22499999999999998 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 9 0.22499999999999998 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGATCCGTTGAAGCGTGCGGCGTCTCTGTCTATGTATTACTGTTTTATGC 7 0.17500000000000002 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 6 0.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 6 0.15 No Hit GGTCTTGATCCCTCTGTGTTTCCCGTGTAACGGCTACTGATCCAGTGGTT 5 0.125 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 5 0.125 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 5 0.125 No Hit GGAGAGAGTGAGCATATATATTTATACGACGAATAAAAGGCTGCCACGTG 5 0.125 No Hit GGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAA 5 0.125 No Hit GGAGGAGATCGAGTTGTTACTTGAGAGTTTGTAACCCTTTATCATGCCAT 5 0.125 No Hit ACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATG 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGGTGTGAGCTGGAGAGACGATCGGGTCTCTCAGCCGGCGTCTTCATCAG 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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 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 GGAGAGC 20 0.0028301126 64.65938 2 GCAATAC 20 0.0028301126 64.65938 7 CAATACA 20 0.0028301126 64.65938 8 GAGCAAT 20 0.0028301126 64.65938 5 AGAGCAA 20 0.0028301126 64.65938 4 GAGAGCA 20 0.0028301126 64.65938 3 AATACAA 20 0.0028301126 64.65938 9 AGCAATA 20 0.0028301126 64.65938 6 GGGAGAG 30 1.8586869E-4 57.475 1 TTCAATT 25 0.006848882 51.727497 4 AATTTCA 25 0.006848882 51.727497 7 CAATTTC 25 0.006848882 51.727497 6 GGATTCA 25 0.006848882 51.727497 1 GATTCAA 25 0.006848882 51.727497 2 ATTTCAA 25 0.006848882 51.727497 8 ATTCAAT 25 0.006848882 51.727497 3 >>END_MODULE Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341398 READS because READLEN < 1 Read 341398 spots for ERR6133551.sra Written 341398 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra Rejected 341384 READS because READLEN < 1 Read 341384 spots for ERR6133551.sra Written 341384 spots for ERR6133551.sra SRR ids: ['ERR6133551.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xmhp5129 ERR6133551.sra spots: 6827694 blocks: [[1, 341384], [341385, 682768], [682769, 1024152], [1024153, 1365536], [1365537, 1706920], [1706921, 2048304], [2048305, 2389688], [2389689, 2731072], [2731073, 3072456], [3072457, 3413840], [3413841, 3755224], [3755225, 4096608], [4096609, 4437992], [4437993, 4779376], [4779377, 5120760], [5120761, 5462144], [5462145, 5803528], [5803529, 6144912], [6144913, 6486296], [6486297, 6827694]] ERR6133551 file size 1509916 ERR6133551 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 ERR6133551 ERR6133551_1.fastq Input file: ERR6133551_1.fastq trimmed: ERR6133551-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 08:28:23 2024 >> started Sat Dec 7 08:28:27 2024 >> done (3.632s) 6827694 reads processed; of these: 162 ( 0.00%) short reads filtered out after trimming by size control 20 ( 0.00%) empty reads filtered out after trimming by size control 6827512 (100.00%) reads available; of these: 119001 ( 1.74%) trimmed reads available after processing 6708511 (98.26%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 20 0.00% 19 40 0.00% 20 14 0.00% 21 5 0.00% 22 9 0.00% 23 5 0.00% 24 5 0.00% 25 2 0.00% 26 10 0.00% 27 4 0.00% 28 12 0.00% 29 8 0.00% 30 13 0.00% 31 17 0.00% 32 22 0.00% 33 20 0.00% 34 20 0.00% 35 83 0.00% 36 786 0.01% 37 17 0.00% 38 28 0.00% 39 60 0.00% 40 72 0.00% 41 29 0.00% 42 12 0.00% 43 10 0.00% 44 12 0.00% 45 14 0.00% 46 6 0.00% 47 9 0.00% 48 12 0.00% 49 9 0.00% 50 12 0.00% 51 44 0.00% 52 18 0.00% 53 7 0.00% 54 10 0.00% 55 7 0.00% 56 9 0.00% 57 7 0.00% 58 10 0.00% 59 7 0.00% 60 14 0.00% 61 9 0.00% 62 4 0.00% 63 5 0.00% 64 6 0.00% 65 8 0.00% 66 14 0.00% 67 16 0.00% 68 53 0.00% 69 187 0.00% 70 15669 0.23% 71 15635 0.23% 72 16573 0.24% 73 15382 0.23% 74 16260 0.24% 75 16633 0.24% 76 15205 0.22% 77 15531 0.23% 78 17796 0.26% 79 20357 0.30% 80 18237 0.27% 81 20521 0.30% 82 22439 0.33% 83 23669 0.35% 84 19762 0.29% 85 249 0.00% 86 463 0.01% 87 734 0.01% 88 1403 0.02% 89 2887 0.04% 90 6546 0.10% 91 19458 0.28% 92 81884 1.20% 93 6442387 94.36% 6827512 reads passed initial QC criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=5.12 fanout-score-rank=20 prefix-density=0.73 prefix-fanout=3.7 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=217.56 fanout-score-rank=1 prefix-density=0.52 prefix-fanout=7.5 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAA Started job on | Dec 07 08:28:45 Started mapping on | Dec 07 08:28:45 Finished on | Dec 07 08:28:53 Mapping speed, Million of reads per hour | 3072.38 Number of input reads | 6827512 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 4909271 Uniquely mapped reads % | 71.90% Average mapped length | 91.91 Number of splices: Total | 196545 Number of splices: Annotated (sjdb) | 160845 Number of splices: GT/AG | 187530 Number of splices: GC/AG | 4810 Number of splices: AT/AC | 80 Number of splices: Non-canonical | 4125 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.87 Insertion rate per base | 0.02% Insertion average length | 1.66 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1760163 % of reads mapped to multiple loci | 25.78% Number of reads mapped to too many loci | 59923 % of reads mapped to too many loci | 0.88% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.38% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 158078 158078 158078 N_multimapping 1760163 1760163 1760163 N_noFeature 307782 352109 4686756 N_ambiguous 199706 21509 584 UnstrandedReadsAssigned:4401783 PositiveStrandReadsAssigned:4535653 NegativeStrandReadsAssigned:221931 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133551 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: ERR6133551-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,827,512 reads, 5,601,571 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,115 rounds 52973 ERR6133551.ke.tsv 35125 ERR6133551.se.tsv 88098 total ==> ERR6133551.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 164 28.7487 PNS24243 293 194 0 0 KQK14069 1603 1504 83 13.2727 KQK14071 474 375 0 0 ==> ERR6133551.se.tsv <== BRADI_1g14170v3 83 BRADI_1g53295v3 62 BRADI_1g59795v3 41 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 92 BRADI_1g74790v3 51 BRADI_1g09890v3 0 BRADI_1g77505v3 143 BRADI_1g48960v3 0 ERR6133551 completed mapping pipeline successfully