Starting /dee2/code/volunteer_pipeline.sh ERR6133510 current disk space = 1544411209728 free memory = 1604430112 ERR6133510 SRAfilesize 895fa4f90d792743ce420237f1db5fb4 ERR6133510.sra ERR6133510.sra file validated ERR6133510 is single end ERR6133510 is conventional basespace ERR6133510 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133510_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 36.61475 37.0 37.0 37.0 37.0 37.0 2 36.85175 37.0 37.0 37.0 37.0 37.0 3 36.501 37.0 37.0 37.0 37.0 37.0 4 35.79925 37.0 37.0 37.0 33.0 37.0 5 35.945 37.0 37.0 37.0 33.0 37.0 6 36.335 37.0 37.0 37.0 33.0 37.0 7 38.2755 40.0 37.0 40.0 37.0 40.0 8 38.28475 40.0 37.0 40.0 37.0 40.0 9 38.239 40.0 37.0 40.0 37.0 40.0 10-11 38.274125 40.0 37.0 40.0 37.0 40.0 12-13 38.210625 40.0 37.0 40.0 37.0 40.0 14-15 38.229875 40.0 37.0 40.0 37.0 40.0 16-17 38.112125 40.0 37.0 40.0 37.0 40.0 18-19 38.025875 40.0 37.0 40.0 37.0 40.0 20-21 38.00725 40.0 37.0 40.0 37.0 40.0 22-23 38.154875000000004 40.0 37.0 40.0 37.0 40.0 24-25 38.050125 40.0 37.0 40.0 37.0 40.0 26-27 38.033500000000004 40.0 37.0 40.0 37.0 40.0 28-29 37.99825 40.0 37.0 40.0 37.0 40.0 30-31 38.018 40.0 37.0 40.0 37.0 40.0 32-33 38.063 40.0 37.0 40.0 37.0 40.0 34-35 37.979875 38.5 37.0 40.0 37.0 40.0 36-37 37.940124999999995 37.0 37.0 40.0 37.0 40.0 38-39 37.801125 37.0 37.0 40.0 37.0 40.0 40-41 37.570375 37.0 37.0 40.0 37.0 40.0 42-43 37.534625 37.0 37.0 40.0 37.0 40.0 44-45 37.259625 37.0 37.0 40.0 35.0 40.0 46-47 37.174875 37.0 37.0 40.0 33.0 40.0 48-49 37.079125000000005 37.0 37.0 38.5 33.0 40.0 50-51 36.872375000000005 37.0 37.0 37.0 33.0 40.0 52-53 36.511250000000004 37.0 37.0 37.0 33.0 40.0 54-55 36.498875 37.0 37.0 37.0 33.0 40.0 56-57 36.3595 37.0 37.0 37.0 33.0 38.5 58-59 35.9885 37.0 37.0 37.0 33.0 37.0 60-61 36.033125 37.0 37.0 37.0 33.0 37.0 62-63 35.962 37.0 37.0 37.0 33.0 37.0 64-65 35.923625 37.0 37.0 37.0 33.0 37.0 66-67 35.8985 37.0 37.0 37.0 33.0 37.0 68-69 34.927625 35.0 35.0 37.0 33.0 37.0 70-71 35.112825400801604 37.0 33.0 37.0 33.0 37.0 72-73 35.63932018940373 37.0 33.0 37.0 33.0 37.0 74-75 35.62833377574671 37.0 33.0 37.0 33.0 37.0 76-77 35.53471095414231 37.0 33.0 37.0 33.0 37.0 78-79 35.528164480982895 37.0 33.0 37.0 33.0 37.0 80-81 35.417709509514665 37.0 33.0 37.0 33.0 37.0 82-83 35.343156541750616 37.0 33.0 37.0 33.0 37.0 84-85 35.122355646533215 37.0 33.0 37.0 33.0 37.0 86-87 35.06325845597728 37.0 33.0 37.0 33.0 37.0 88-89 35.02104311902917 37.0 33.0 37.0 33.0 37.0 90-91 35.07810482829848 37.0 33.0 37.0 33.0 37.0 92-93 34.97895688097083 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 4.0 22 7.0 23 4.0 24 3.0 25 4.0 26 8.0 27 7.0 28 8.0 29 15.0 30 24.0 31 32.0 32 52.0 33 78.0 34 107.0 35 334.0 36 1124.0 37 1416.0 38 762.0 39 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.275 2.5749999999999997 3.375 4.775 2 74.875 15.299999999999999 6.1 3.7249999999999996 3 36.875 38.5 12.75 11.875 4 34.375 28.249999999999996 18.099999999999998 19.275000000000002 5 25.275 30.95 26.025 17.75 6 21.224999999999998 38.224999999999994 24.675 15.875 7 37.175000000000004 28.975 18.7 15.15 8 31.775 30.425 22.15 15.65 9 25.974999999999998 29.225 26.950000000000003 17.849999999999998 10-11 26.224999999999998 28.237499999999997 28.1125 17.424999999999997 12-13 28.6625 25.85 27.0625 18.425 14-15 23.599999999999998 30.975 28.025 17.4 16-17 23.35 32.9625 26.025 17.6625 18-19 24.175 27.8875 27.325 20.6125 20-21 25.656414103525883 25.331332833208304 29.19479869967492 19.817454363590898 22-23 27.2625 23.5 27.200000000000003 22.037499999999998 24-25 26.387500000000003 25.662499999999998 27.725 20.225 26-27 25.7375 24.95 30.9375 18.375 28-29 25.0 26.825 27.925 20.25 30-31 26.950000000000003 25.362499999999997 28.4125 19.275000000000002 32-33 24.6125 27.275 27.1125 21.0 34-35 24.15 27.037499999999998 27.987499999999997 20.825 36-37 24.675 26.674999999999997 28.249999999999996 20.4 38-39 26.724999999999998 25.25 29.475 18.55 40-41 26.300650325162582 24.987493746873437 27.4512256128064 21.260630315157577 42-43 25.018754688672168 28.032008002000502 27.419354838709676 19.529882470617654 44-45 23.962500000000002 26.4125 28.8375 20.7875 46-47 24.3 24.212500000000002 28.8625 22.625 48-49 24.375 24.212500000000002 30.599999999999998 20.8125 50-51 24.253031628953618 26.153269158644832 29.97874734341793 19.614951868983624 52-53 24.5987963891675 27.695586760280843 27.80842527582748 19.89719157472417 54-55 24.753094136767096 28.82860357544693 28.116014501812725 18.30228778597325 56-57 25.575 25.8 28.3375 20.2875 58-59 24.25 25.3125 30.5 19.9375 60-61 24.337500000000002 26.325 29.125 20.2125 62-63 21.75 27.9375 31.9625 18.35 64-65 23.125 28.4 29.7375 18.7375 66-67 24.1875 27.1125 29.375 19.325 68-69 22.662499999999998 26.8625 27.975 22.5 70-71 24.987487487487485 26.514014014014016 28.015515515515517 20.482982982982982 72-73 25.46139359698682 24.821092278719398 29.328311362209668 20.389202762084118 74-75 23.766872713510786 28.232622681973 28.737227198183422 19.263277406332787 76-77 23.011651469098275 26.279128672745696 29.331306990881462 21.37791286727457 78-79 24.872838250254322 25.228891149542214 31.065615462868767 18.83265513733469 80-81 24.136172383016703 28.917506056355986 29.05775851077394 17.888563049853374 82-83 23.593489683455083 25.938741509675765 29.05292836088684 21.414840445982314 84-85 24.591008630684012 23.998454205848255 30.684013912147368 20.726523251320366 86-87 21.223857474825717 27.31732507100439 32.32636199328686 19.132455460883037 88-89 21.004389362251487 28.93106119287374 30.790085205267236 19.27446423960754 90-91 25.09682416731216 27.14949651432998 29.460366640846892 18.293312677510972 92-93 22.927962819519752 28.6857733023496 29.56364575264653 18.82261812548412 >>END_MODULE >>Per sequence GC content pass #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 1.0 19 0.5 20 1.5 21 3.5 22 3.0 23 3.0 24 4.5 25 6.0 26 8.5 27 9.0 28 16.0 29 23.5 30 27.5 31 29.5 32 34.0 33 50.0 34 66.5 35 78.0 36 111.0 37 138.5 38 164.5 39 172.5 40 195.0 41 230.0 42 223.5 43 224.0 44 222.0 45 214.0 46 227.5 47 226.0 48 192.0 49 164.0 50 174.5 51 169.5 52 145.5 53 174.5 54 159.5 55 97.0 56 70.0 57 67.0 58 56.0 59 31.5 60 20.0 61 17.0 62 12.5 63 13.0 64 13.0 65 13.0 66 9.0 67 4.5 68 5.5 69 7.0 70 4.0 71 1.0 72 1.5 73 1.5 74 1.0 75 0.5 76 0.5 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 0.025 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 0.05 42-43 0.025 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0125 52-53 0.3 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 0.0 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 8.0 71 7.0 72 5.0 73 10.0 74 13.0 75 4.0 76 10.0 77 7.0 78 8.0 79 4.0 80 5.0 81 14.0 82 7.0 83 8.0 84 17.0 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 3873.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.5 #Duplication Level Percentage of deduplicated Percentage of total 1 92.9192546583851 74.8 2 4.316770186335404 6.950000000000001 3 0.9937888198757764 2.4 4 0.4658385093167702 1.5 5 0.37267080745341613 1.5 6 0.18633540372670807 0.8999999999999999 7 0.062111801242236024 0.35000000000000003 8 0.062111801242236024 0.4 9 0.062111801242236024 0.44999999999999996 >10 0.5590062111801243 10.75 >50 0.0 0.0 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 42 1.05 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 41 1.0250000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 36 0.8999999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 35 0.8750000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 34 0.8500000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 31 0.775 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 30 0.75 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 29 0.7250000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 24 0.6 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 23 0.575 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 21 0.525 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 16 0.4 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit GGGTGTGAGCTGGAGAGACGATCGGGTCTCTCAGCCGGCGTCTTCATCAG 8 0.2 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTT 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 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 0.0 0.0 0.0 0.0 0.0 22-23 0.0125 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 0.0625 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 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 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.15 0.0125 0.0 0.0 0.0 66-67 0.15 0.025 0.0 0.0 0.0 68-69 0.15 0.025 0.0 0.0 0.0 70-71 0.15 0.025 0.0 0.0 0.0 72-73 0.15 0.025 0.0 0.0 0.0 74-75 0.15 0.025 0.0 0.0 0.0 76-77 0.15 0.025 0.0 0.0 0.0 78-79 0.15 0.025 0.0 0.0 0.0 80-81 0.15 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111115 READS because READLEN < 1 Read 111115 spots for ERR6133510.sra Written 111115 spots for ERR6133510.sra Rejected 111128 READS because READLEN < 1 Read 111128 spots for ERR6133510.sra Written 111128 spots for ERR6133510.sra SRR ids: ['ERR6133510.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_co03ibxi ERR6133510.sra spots: 2222313 blocks: [[1, 111115], [111116, 222230], [222231, 333345], [333346, 444460], [444461, 555575], [555576, 666690], [666691, 777805], [777806, 888920], [888921, 1000035], [1000036, 1111150], [1111151, 1222265], [1222266, 1333380], [1333381, 1444495], [1444496, 1555610], [1555611, 1666725], [1666726, 1777840], [1777841, 1888955], [1888956, 2000070], [2000071, 2111185], [2111186, 2222313]] ERR6133510 file size 490432 ERR6133510 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 ERR6133510 ERR6133510_1.fastq Input file: ERR6133510_1.fastq trimmed: ERR6133510-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 07:37:26 2024 >> started Sat Dec 7 07:37:28 2024 >> done (1.658s) 2222313 reads processed; of these: 859 ( 0.04%) short reads filtered out after trimming by size control 12 ( 0.00%) empty reads filtered out after trimming by size control 2221442 (99.96%) reads available; of these: 13664 ( 0.62%) trimmed reads available after processing 2207778 (99.38%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 40 0.00% 19 86 0.00% 20 111 0.00% 21 55 0.00% 22 34 0.00% 23 26 0.00% 24 44 0.00% 25 17 0.00% 26 15 0.00% 27 134 0.01% 28 157 0.01% 29 100 0.00% 30 103 0.00% 31 49 0.00% 32 33 0.00% 33 24 0.00% 34 25 0.00% 35 116 0.01% 36 376 0.02% 37 27 0.00% 38 49 0.00% 39 67 0.00% 40 102 0.00% 41 35 0.00% 42 131 0.01% 43 1204 0.05% 44 122 0.01% 45 929 0.04% 46 135 0.01% 47 22 0.00% 48 39 0.00% 49 12 0.00% 50 13 0.00% 51 26 0.00% 52 14 0.00% 53 13 0.00% 54 6 0.00% 55 17 0.00% 56 8 0.00% 57 10 0.00% 58 10 0.00% 59 8 0.00% 60 9 0.00% 61 14 0.00% 62 0 0.00% 63 0 0.00% 64 2 0.00% 65 2 0.00% 66 1 0.00% 67 3 0.00% 68 9 0.00% 69 40 0.00% 70 5183 0.23% 71 4493 0.20% 72 4677 0.21% 73 4426 0.20% 74 4655 0.21% 75 4272 0.19% 76 3942 0.18% 77 4038 0.18% 78 4334 0.20% 79 4663 0.21% 80 4434 0.20% 81 5323 0.24% 82 5776 0.26% 83 5234 0.24% 84 5188 0.23% 85 31 0.00% 86 46 0.00% 87 111 0.00% 88 136 0.01% 89 281 0.01% 90 580 0.03% 91 1501 0.07% 92 5985 0.27% 93 2137509 96.22% 2221442 reads passed initial QC criterion=sequence-density sequence-density=0.57 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=30 prefix-density=0.58 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=111.97 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=7.3 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTAT Started job on | Dec 07 07:37:44 Started mapping on | Dec 07 07:37:45 Finished on | Dec 07 07:37:49 Mapping speed, Million of reads per hour | 1999.30 Number of input reads | 2221442 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1580896 Uniquely mapped reads % | 71.17% Average mapped length | 92.05 Number of splices: Total | 88912 Number of splices: Annotated (sjdb) | 73910 Number of splices: GT/AG | 84685 Number of splices: GC/AG | 2450 Number of splices: AT/AC | 52 Number of splices: Non-canonical | 1725 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.05% Deletion average length | 1.82 Insertion rate per base | 0.02% Insertion average length | 1.75 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 562408 % of reads mapped to multiple loci | 25.32% Number of reads mapped to too many loci | 19420 % of reads mapped to too many loci | 0.87% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.60% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 78138 78138 78138 N_multimapping 562408 562408 562408 N_noFeature 110347 124408 1511642 N_ambiguous 62584 7361 231 UnstrandedReadsAssigned:1407965 PositiveStrandReadsAssigned:1449127 NegativeStrandReadsAssigned:69023 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133510 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: ERR6133510-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,221,442 reads, 1,837,547 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 982 rounds 52973 ERR6133510.ke.tsv 35125 ERR6133510.se.tsv 88098 total ==> ERR6133510.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 65 33.7106 PNS24243 293 194 0 0 KQK14069 1603 1504 48 22.7091 KQK14071 474 375 0 0 ==> ERR6133510.se.tsv <== BRADI_1g14170v3 48 BRADI_1g53295v3 23 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 50 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 45 BRADI_1g48960v3 0 ERR6133510 completed mapping pipeline successfully