Starting /dee2/code/volunteer_pipeline.sh ERR6133442 current disk space = 1545749639168 free memory = 1428952132 ERR6133442 SRAfilesize a2f3eb6984849d169905853ce630e083 ERR6133442.sra ERR6133442.sra file validated ERR6133442 is single end ERR6133442 is conventional basespace ERR6133442 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133442_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.18375 37.0 33.0 37.0 33.0 37.0 2 36.3325 37.0 37.0 37.0 33.0 37.0 3 35.66525 37.0 37.0 37.0 33.0 37.0 4 35.35225 37.0 37.0 37.0 33.0 37.0 5 35.3365 37.0 37.0 37.0 33.0 37.0 6 35.587 37.0 37.0 37.0 33.0 37.0 7 37.32675 37.0 37.0 40.0 33.0 40.0 8 37.303 37.0 37.0 40.0 33.0 40.0 9 37.26175 37.0 37.0 40.0 33.0 40.0 10-11 37.252625 37.0 37.0 40.0 33.0 40.0 12-13 37.2095 37.0 37.0 40.0 33.0 40.0 14-15 37.181250000000006 37.0 37.0 40.0 33.0 40.0 16-17 37.044375 37.0 37.0 40.0 33.0 40.0 18-19 37.09625 37.0 37.0 40.0 33.0 40.0 20-21 37.26625 37.0 37.0 40.0 33.0 40.0 22-23 37.161625 37.0 37.0 40.0 33.0 40.0 24-25 37.195375 37.0 37.0 40.0 33.0 40.0 26-27 36.979749999999996 37.0 37.0 40.0 33.0 40.0 28-29 37.030125 37.0 37.0 40.0 33.0 40.0 30-31 37.0235 37.0 37.0 40.0 33.0 40.0 32-33 36.86125 37.0 37.0 40.0 33.0 40.0 34-35 36.724999999999994 37.0 37.0 40.0 33.0 40.0 36-37 36.68 37.0 37.0 40.0 33.0 40.0 38-39 36.5045 37.0 37.0 40.0 33.0 40.0 40-41 36.39375 37.0 37.0 40.0 33.0 40.0 42-43 36.333875 37.0 37.0 40.0 33.0 40.0 44-45 36.17274999999999 37.0 37.0 40.0 33.0 40.0 46-47 35.997125 37.0 37.0 37.0 33.0 40.0 48-49 35.778625 37.0 35.0 37.0 33.0 40.0 50-51 35.6395 37.0 33.0 37.0 33.0 40.0 52-53 35.5085 37.0 33.0 37.0 33.0 40.0 54-55 35.334875 37.0 33.0 37.0 33.0 37.0 56-57 35.203 37.0 33.0 37.0 33.0 37.0 58-59 34.707499999999996 37.0 33.0 37.0 30.0 37.0 60-61 34.68725 37.0 33.0 37.0 33.0 37.0 62-63 34.7175 37.0 33.0 37.0 33.0 37.0 64-65 34.263625 37.0 33.0 37.0 30.0 37.0 66-67 34.159000000000006 37.0 33.0 37.0 27.0 37.0 68-69 32.704375 35.0 33.0 35.0 27.0 37.0 70-71 33.131944388777555 33.0 33.0 37.0 27.0 37.0 72-73 33.80527359322116 37.0 33.0 37.0 27.0 37.0 74-75 34.1736939055271 37.0 33.0 37.0 30.0 37.0 76-77 34.11785380724095 37.0 33.0 37.0 30.0 37.0 78-79 34.080178133842466 37.0 33.0 37.0 30.0 37.0 80-81 33.97176185039617 37.0 33.0 37.0 27.0 37.0 82-83 33.72623230393927 37.0 33.0 37.0 27.0 37.0 84-85 33.76629116869158 37.0 33.0 37.0 27.0 37.0 86-87 33.545118531735916 35.0 33.0 37.0 27.0 37.0 88-89 33.616492480244716 33.0 33.0 37.0 27.0 37.0 90-91 33.58590364516951 33.0 33.0 37.0 27.0 37.0 92-93 33.230690797858784 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 6.0 21 14.0 22 12.0 23 15.0 24 21.0 25 29.0 26 31.0 27 36.0 28 42.0 29 74.0 30 70.0 31 88.0 32 163.0 33 197.0 34 235.0 35 547.0 36 951.0 37 1086.0 38 380.0 39 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.55 2.75 2.5 6.2 2 73.07980985739304 16.262196647485613 6.830122591943957 3.8278709031773825 3 38.35 37.6 12.9 11.15 4 35.55 28.075 17.5 18.875 5 24.099999999999998 32.675 24.4 18.825 6 21.3 38.45 24.15 16.1 7 35.75 27.900000000000002 18.95 17.4 8 31.4 27.85 22.650000000000002 18.099999999999998 9 26.424999999999997 28.475 25.424999999999997 19.675 10-11 26.625 27.474999999999998 25.674999999999997 20.225 12-13 29.5875 24.7875 25.937500000000004 19.6875 14-15 23.962500000000002 28.6125 28.012500000000003 19.412499999999998 16-17 26.3125 30.049999999999997 25.074999999999996 18.5625 18-19 24.15 26.8125 25.224999999999998 23.8125 20-21 25.087500000000002 26.4625 26.8375 21.6125 22-23 26.5625 24.25 25.724999999999998 23.4625 24-25 27.762500000000003 22.6875 27.1625 22.3875 26-27 26.0375 26.087500000000002 28.375 19.5 28-29 26.700000000000003 25.5125 26.2875 21.5 30-31 27.625 25.75 23.825 22.8 32-33 24.85 28.462500000000002 25.5625 21.125 34-35 26.724999999999998 24.3 26.974999999999998 22.0 36-37 25.1875 23.1375 27.900000000000002 23.775 38-39 25.7625 25.662499999999998 29.275000000000002 19.3 40-41 27.775 25.4625 25.1 21.6625 42-43 24.8125 28.499999999999996 25.025 21.6625 44-45 23.925 24.4125 27.400000000000002 24.2625 46-47 23.9125 23.575 27.175 25.337500000000002 48-49 26.6125 23.6625 28.825 20.9 50-51 27.0125 25.1875 27.900000000000002 19.900000000000002 52-53 26.2625 27.474999999999998 24.675 21.587500000000002 54-55 23.8375 29.049999999999997 26.4625 20.65 56-57 26.474999999999998 25.374999999999996 27.575 20.575 58-59 24.8125 24.375 28.249999999999996 22.5625 60-61 24.462500000000002 23.724999999999998 27.9125 23.9 62-63 22.6125 28.175 29.45 19.7625 64-65 24.825 24.975 28.512500000000003 21.6875 66-67 25.525 26.6 26.6625 21.212500000000002 68-69 24.3875 27.224999999999998 26.737499999999997 21.65 70-71 25.88838838838839 23.86136136136136 27.32732732732733 22.922922922922922 72-73 27.368553143430795 23.465930480612375 26.339565817542983 22.825950558413854 74-75 23.466431540496284 27.87504723516816 28.164756266532308 20.49376495780325 76-77 22.226434167298457 26.3962597927723 29.18877937831691 22.188526661612332 78-79 24.588711718552265 24.120475828904077 29.486206023791446 21.804606428752216 80-81 24.651457541191384 26.172370088719898 29.074778200253487 20.101394169835235 82-83 25.108060005085175 23.963895245359776 28.998220188151535 21.929824561403507 84-85 24.891664542442008 22.26612286515422 30.13000254906959 22.71221004333418 86-87 22.72495539128218 26.013255161865917 32.347693092021416 18.914096354830487 88-89 22.342594952842212 28.396635228141726 29.492735151669642 19.768034667346416 90-91 26.306398164669897 25.98776446596992 28.447616619933726 19.25822074942646 92-93 23.476930920214123 28.269181748661737 29.00841192964568 19.24547540147846 >>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 0.5 17 4.0 18 5.0 19 2.0 20 4.0 21 3.5 22 4.0 23 6.0 24 4.0 25 6.0 26 6.5 27 7.0 28 13.5 29 16.5 30 20.0 31 22.0 32 30.5 33 48.5 34 55.0 35 67.5 36 83.5 37 105.0 38 127.0 39 138.5 40 154.0 41 176.5 42 182.5 43 173.5 44 175.0 45 165.5 46 220.0 47 226.5 48 175.5 49 169.5 50 168.5 51 169.0 52 156.0 53 163.5 54 154.5 55 106.0 56 84.5 57 94.0 58 88.0 59 82.0 60 67.0 61 52.5 62 46.5 63 47.5 64 46.0 65 38.5 66 39.0 67 33.5 68 23.5 69 13.5 70 8.0 71 8.0 72 7.0 73 4.0 74 2.5 75 2.5 76 1.0 77 0.0 78 0.5 79 0.5 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 0.075 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 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 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 0.025484199796126403 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 5.0 72 5.0 73 7.0 74 11.0 75 6.0 76 2.0 77 3.0 78 4.0 79 3.0 80 2.0 81 9.0 82 4.0 83 6.0 84 2.0 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 3923.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.55 #Duplication Level Percentage of deduplicated Percentage of total 1 93.35816263190566 75.2 2 4.003724394785848 6.45 3 0.8379888268156425 2.025 4 0.4345127250155183 1.4000000000000001 5 0.2482929857231533 1.0 6 0.3414028553693358 1.6500000000000001 7 0.12414649286157665 0.7000000000000001 8 0.06207324643078833 0.4 9 0.031036623215394164 0.22499999999999998 >10 0.4965859714463066 7.575 >50 0.06207324643078833 3.375 >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 GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 70 1.7500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 65 1.625 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 44 1.0999999999999999 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 36 0.8999999999999999 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 27 0.675 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 26 0.65 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 22 0.5499999999999999 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 22 0.5499999999999999 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 19 0.475 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 16 0.4 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 14 0.35000000000000003 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 13 0.325 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 12 0.3 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 11 0.27499999999999997 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 11 0.27499999999999997 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 10 0.25 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 9 0.22499999999999998 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAA 6 0.15 No Hit GAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAGTTTTTCTTA 6 0.15 No Hit GGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTAGATGCTGCCA 6 0.15 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 6 0.15 No Hit GGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCG 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAACACAGGG 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 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 0.025 0.0 0.0 0.0 0.0 10-11 0.037500000000000006 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 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 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154919 READS because READLEN < 1 Read 154919 spots for ERR6133442.sra Written 154919 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra Rejected 154907 READS because READLEN < 1 Read 154907 spots for ERR6133442.sra Written 154907 spots for ERR6133442.sra SRR ids: ['ERR6133442.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8zis74vg ERR6133442.sra spots: 3098152 blocks: [[1, 154907], [154908, 309814], [309815, 464721], [464722, 619628], [619629, 774535], [774536, 929442], [929443, 1084349], [1084350, 1239256], [1239257, 1394163], [1394164, 1549070], [1549071, 1703977], [1703978, 1858884], [1858885, 2013791], [2013792, 2168698], [2168699, 2323605], [2323606, 2478512], [2478513, 2633419], [2633420, 2788326], [2788327, 2943233], [2943234, 3098152]] ERR6133442 file size 685619 ERR6133442 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 ERR6133442 ERR6133442_1.fastq Input file: ERR6133442_1.fastq trimmed: ERR6133442-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 06:03:44 2024 >> started Sat Dec 7 06:03:46 2024 >> done (2.152s) 3098152 reads processed; of these: 1358 ( 0.04%) short reads filtered out after trimming by size control 29 ( 0.00%) empty reads filtered out after trimming by size control 3096765 (99.96%) reads available; of these: 46686 ( 1.51%) trimmed reads available after processing 3050079 (98.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 45 0.00% 19 31 0.00% 20 25 0.00% 21 14 0.00% 22 18 0.00% 23 15 0.00% 24 11 0.00% 25 6 0.00% 26 4 0.00% 27 16 0.00% 28 14 0.00% 29 60 0.00% 30 8 0.00% 31 8 0.00% 32 9 0.00% 33 8 0.00% 34 5 0.00% 35 7 0.00% 36 5 0.00% 37 5 0.00% 38 9 0.00% 39 29 0.00% 40 37 0.00% 41 27 0.00% 42 15 0.00% 43 25 0.00% 44 21 0.00% 45 11 0.00% 46 15 0.00% 47 18 0.00% 48 22 0.00% 49 20 0.00% 50 20 0.00% 51 35 0.00% 52 19 0.00% 53 19 0.00% 54 19 0.00% 55 23 0.00% 56 26 0.00% 57 22 0.00% 58 15 0.00% 59 15 0.00% 60 14 0.00% 61 9 0.00% 62 4 0.00% 63 5 0.00% 64 4 0.00% 65 2 0.00% 66 8 0.00% 67 8 0.00% 68 18 0.00% 69 59 0.00% 70 4799 0.15% 71 4123 0.13% 72 4375 0.14% 73 3886 0.13% 74 4218 0.14% 75 4059 0.13% 76 3529 0.11% 77 3808 0.12% 78 4192 0.14% 79 5031 0.16% 80 4068 0.13% 81 4309 0.14% 82 4882 0.16% 83 5422 0.18% 84 4150 0.13% 85 95 0.00% 86 197 0.01% 87 278 0.01% 88 610 0.02% 89 1143 0.04% 90 2714 0.09% 91 7870 0.25% 92 31922 1.03% 93 2986178 96.43% 3096765 reads passed initial QC criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=5.84 fanout-score-rank=17 prefix-density=1.08 prefix-fanout=2.5 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATCATCTTACTGTTTTAAATAAATCTGTTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=22 fanout-score=42.08 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=1.7 sequence=CAAGGAAGGCGTCGCCAACGGAACCCTCAAGCTCGTGGGCGGCCACTACGACTTCGTCTCCGGCAAGTTCGACACATGGGAGCTCTAAGTCCTCTCATCCGGTTAACTCCTATACATACAACGTATACTTATACATACAGATATGGAGATGACCCTACAGATCGATCCATTGATGTGGATGCGATGCCATGGAGTATATGTACTCGCTATTTTCCAGTACTGCATGCCGGATGGCTCGATGTGAATTTGTAATAAGCAATAGAAGTTTCTACCATTTTCTGACGTGGGGTTGTACTTGTGATGCGTAATTTGGTCATCTTGTGACCAAAAGACATCAACTATATAATTATAATACCATTTTCATCAAGACTCT Started job on | Dec 07 06:04:04 Started mapping on | Dec 07 06:04:04 Finished on | Dec 07 06:04:09 Mapping speed, Million of reads per hour | 2229.67 Number of input reads | 3096765 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2287981 Uniquely mapped reads % | 73.88% Average mapped length | 92.31 Number of splices: Total | 167630 Number of splices: Annotated (sjdb) | 141553 Number of splices: GT/AG | 162508 Number of splices: GC/AG | 3244 Number of splices: AT/AC | 54 Number of splices: Non-canonical | 1824 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 1.89 Insertion rate per base | 0.02% Insertion average length | 2.27 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 748144 % of reads mapped to multiple loci | 24.16% Number of reads mapped to too many loci | 10777 % of reads mapped to too many loci | 0.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.59% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 60640 60640 60640 N_multimapping 748144 748144 748144 N_noFeature 104506 125699 2191251 N_ambiguous 83084 7604 270 UnstrandedReadsAssigned:2100391 PositiveStrandReadsAssigned:2154678 NegativeStrandReadsAssigned:96460 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133442 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: ERR6133442-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,096,765 reads, 2,749,732 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,019 rounds 52973 ERR6133442.ke.tsv 35125 ERR6133442.se.tsv 88098 total ==> ERR6133442.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 61 21.1622 PNS24243 293 194 0 0 KQK14069 1603 1504 38 12.026 KQK14071 474 375 0 0 ==> ERR6133442.se.tsv <== BRADI_1g14170v3 38 BRADI_1g53295v3 34 BRADI_1g59795v3 26 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 29 BRADI_1g74790v3 28 BRADI_1g09890v3 0 BRADI_1g77505v3 42 BRADI_1g48960v3 0 ERR6133442 completed mapping pipeline successfully