Starting /dee2/code/volunteer_pipeline.sh ERR6133435 current disk space = 1546013421568 free memory = 1434985976 ERR6133435 SRAfilesize 26bfdc160ff04bb3f3c99481ae74272b ERR6133435.sra ERR6133435.sra file validated ERR6133435 is single end ERR6133435 is conventional basespace ERR6133435 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133435_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 35.21675 37.0 33.0 37.0 33.0 37.0 2 36.38425 37.0 37.0 37.0 37.0 37.0 3 35.7 37.0 37.0 37.0 33.0 37.0 4 35.3715 37.0 37.0 37.0 33.0 37.0 5 35.276 37.0 37.0 37.0 33.0 37.0 6 35.64225 37.0 37.0 37.0 33.0 37.0 7 37.30925 37.0 37.0 40.0 33.0 40.0 8 37.39575 37.0 37.0 40.0 33.0 40.0 9 37.38525 37.0 37.0 40.0 33.0 40.0 10-11 37.248 37.0 37.0 40.0 33.0 40.0 12-13 37.205875000000006 37.0 37.0 40.0 33.0 40.0 14-15 37.14675 37.0 37.0 40.0 33.0 40.0 16-17 37.028125 37.0 37.0 40.0 33.0 40.0 18-19 37.2405 37.0 37.0 40.0 33.0 40.0 20-21 37.37875 37.0 37.0 40.0 33.0 40.0 22-23 37.256375000000006 37.0 37.0 40.0 33.0 40.0 24-25 37.275375 37.0 37.0 40.0 33.0 40.0 26-27 36.92675 37.0 37.0 40.0 33.0 40.0 28-29 37.097750000000005 37.0 37.0 40.0 33.0 40.0 30-31 37.099000000000004 37.0 37.0 40.0 33.0 40.0 32-33 36.967749999999995 37.0 37.0 40.0 33.0 40.0 34-35 36.853125 37.0 37.0 40.0 33.0 40.0 36-37 36.83925 37.0 37.0 40.0 33.0 40.0 38-39 36.645624999999995 37.0 37.0 40.0 33.0 40.0 40-41 36.53475 37.0 37.0 40.0 33.0 40.0 42-43 36.352374999999995 37.0 37.0 40.0 33.0 40.0 44-45 36.2065 37.0 37.0 38.5 33.0 40.0 46-47 36.200125 37.0 37.0 37.0 33.0 40.0 48-49 35.9675 37.0 35.0 37.0 33.0 40.0 50-51 35.79025 37.0 33.0 37.0 33.0 40.0 52-53 35.675875 37.0 33.0 37.0 33.0 40.0 54-55 35.55175 37.0 33.0 37.0 33.0 40.0 56-57 35.3725 37.0 33.0 37.0 33.0 37.0 58-59 34.913875000000004 37.0 33.0 37.0 33.0 37.0 60-61 34.81462500000001 37.0 33.0 37.0 33.0 37.0 62-63 34.824375 37.0 33.0 37.0 33.0 37.0 64-65 34.436499999999995 37.0 33.0 37.0 30.0 37.0 66-67 34.40575 37.0 33.0 37.0 33.0 37.0 68-69 33.119875 35.0 33.0 35.0 30.0 37.0 70-71 33.386234629351364 33.0 33.0 37.0 27.0 37.0 72-73 34.15816425487019 37.0 33.0 37.0 30.0 37.0 74-75 34.41636503683837 37.0 33.0 37.0 33.0 37.0 76-77 34.37510364012699 37.0 33.0 37.0 33.0 37.0 78-79 34.331444587313584 37.0 33.0 37.0 33.0 37.0 80-81 34.234294002329335 37.0 33.0 37.0 33.0 37.0 82-83 33.942271124397365 37.0 33.0 37.0 27.0 37.0 84-85 34.05621931601533 37.0 33.0 37.0 30.0 37.0 86-87 33.92089590885551 37.0 33.0 37.0 27.0 37.0 88-89 33.890859658208186 37.0 33.0 37.0 27.0 37.0 90-91 33.72436561367167 35.0 33.0 37.0 27.0 37.0 92-93 33.47294148109788 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 7.0 22 7.0 23 15.0 24 12.0 25 24.0 26 26.0 27 40.0 28 43.0 29 63.0 30 64.0 31 104.0 32 137.0 33 180.0 34 220.0 35 505.0 36 1077.0 37 1037.0 38 428.0 39 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.125 2.5749999999999997 2.4 5.8999999999999995 2 73.86733416770964 15.969962453066334 5.88235294117647 4.280350438047559 3 39.5 37.15 13.5 9.85 4 34.825 28.749999999999996 18.0 18.425 5 25.4 33.275 22.075 19.25 6 20.25 38.775 25.2 15.775 7 36.425000000000004 28.825 18.05 16.7 8 31.374999999999996 30.049999999999997 23.125 15.45 9 26.05 27.825 27.650000000000002 18.475 10-11 26.2625 27.55 26.5625 19.625 12-13 30.1375 24.962500000000002 26.8375 18.0625 14-15 23.7875 29.625 28.462500000000002 18.125 16-17 24.4125 32.15 24.6125 18.825 18-19 24.6125 27.675 25.1 22.6125 20-21 25.4 27.237499999999997 26.200000000000003 21.1625 22-23 27.0875 23.3 27.0125 22.6 24-25 28.675 22.8625 27.0 21.462500000000002 26-27 25.974999999999998 25.525 28.8625 19.6375 28-29 27.175 26.437500000000004 25.35 21.0375 30-31 28.15 24.425 25.45 21.975 32-33 24.3625 28.775000000000002 25.912499999999998 20.95 34-35 26.025 23.724999999999998 27.975 22.275 36-37 24.25 24.7375 28.95 22.0625 38-39 26.1125 25.937500000000004 28.299999999999997 19.650000000000002 40-41 27.0625 26.625 25.025 21.2875 42-43 24.9375 28.4125 25.5375 21.1125 44-45 25.4875 25.4 27.0625 22.05 46-47 25.074999999999996 23.05 26.487500000000004 25.387500000000003 48-49 25.337500000000002 24.825 29.675 20.1625 50-51 26.737499999999997 26.3125 27.3875 19.5625 52-53 25.7625 28.1875 25.837500000000002 20.2125 54-55 23.1125 29.4125 26.5125 20.962500000000002 56-57 26.5875 24.5375 27.700000000000003 21.175 58-59 24.0625 25.6 27.037499999999998 23.3 60-61 24.85 24.0625 28.075 23.0125 62-63 24.075 27.187499999999996 29.875 18.862499999999997 64-65 24.7875 25.874999999999996 28.4 20.9375 66-67 26.075 27.2625 26.0375 20.625 68-69 24.637500000000003 27.125 27.0125 21.224999999999998 70-71 26.56074064806706 25.534842987614166 25.785061929188043 22.119354435130738 72-73 25.474425034560767 24.73293955008169 27.007666205856477 22.784969209501067 74-75 23.769250189346124 26.786165109820754 28.16208028275688 21.282504418076243 76-77 23.211567732115675 26.04008117706748 29.084221207508882 21.664129883307965 78-79 24.729402776009167 25.035018464281166 28.103909334012478 22.131669425697186 80-81 25.682779843569687 26.82395178869086 28.22156686754712 19.271701500192332 82-83 24.961399897066393 24.4981986618631 28.847143592382913 21.693257848687598 84-85 24.99353504008275 23.0411171450737 29.05352986811482 22.91181794672873 86-87 23.070947695494564 24.689280165717246 31.87467633350596 20.365095805282238 88-89 22.60486794407043 28.7674779906784 28.780424650440185 19.84722941481098 90-91 26.24287933713102 26.488865872604865 27.330398757120662 19.93785603314345 92-93 23.213360952874158 28.27550491973071 28.327291558777834 20.183842568617298 >>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 1.0 18 1.5 19 1.5 20 1.5 21 2.0 22 1.5 23 3.5 24 6.5 25 3.5 26 0.5 27 4.0 28 15.5 29 25.0 30 25.0 31 30.5 32 43.0 33 58.5 34 73.0 35 83.5 36 102.0 37 118.0 38 127.0 39 136.0 40 149.0 41 163.5 42 175.0 43 181.5 44 175.0 45 179.0 46 231.5 47 229.0 48 173.5 49 159.5 50 155.0 51 156.5 52 157.5 53 184.0 54 165.0 55 102.0 56 80.5 57 75.5 58 78.5 59 75.5 60 69.5 61 63.5 62 50.0 63 43.0 64 43.5 65 39.0 66 29.0 67 23.0 68 19.0 69 12.0 70 5.0 71 1.0 72 1.0 73 1.5 74 2.5 75 3.0 76 1.5 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 0.125 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 0.02585315408479835 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 7.0 71 11.0 72 7.0 73 8.0 74 12.0 75 9.0 76 8.0 77 6.0 78 11.0 79 16.0 80 11.0 81 5.0 82 6.0 83 9.0 84 12.0 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 3862.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.325 #Duplication Level Percentage of deduplicated Percentage of total 1 93.07622228970544 76.625 2 4.312177345885211 7.1 3 1.1539629517157608 2.85 4 0.3036744609778318 1.0 5 0.3644093531733981 1.5 6 0.12146978439113272 0.6 7 0.06073489219556636 0.35000000000000003 8 0.09110233829334953 0.6 9 0.09110233829334953 0.675 >10 0.3644093531733981 5.375 >50 0.06073489219556636 3.325 >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 69 1.725 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 64 1.6 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 32 0.8 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 30 0.75 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 24 0.6 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 23 0.575 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 23 0.575 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 16 0.4 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 13 0.325 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 12 0.3 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 10 0.25 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 10 0.25 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 9 0.22499999999999998 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 9 0.22499999999999998 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit GGACAATGTCAAGCGTGTGCAGCTTGCTGACAAGTACATGAGCGAGGCTG 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GGAGCAGGAGAACGTGAAGAGGGTGCAGCTTGCAGACAAGTACCTCAGTG 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GGAAATGGGTCGGGGAAATCGGCGTGGAGAACATTTCCAAGAGGCTGGTG 5 0.125 No Hit GGAGCACCGGCGCTGCGACCGCACGAACCTAACCAAGGAGCGAGCACACA 5 0.125 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 5 0.125 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 5 0.125 No Hit GGGAGATGCTAACTCAGATGCCATGAAGACTGGTTCCTTCTACGGTTAGA 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 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 0.0125 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 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 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 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 TGATTCT 25 6.950904E-7 85.950005 5 GGATGAT 30 1.8962965E-8 85.95 2 GATGATT 35 5.5269993E-8 73.67143 3 GGGATGA 35 5.5269993E-8 73.67143 1 TCTGTAT 30 2.0564803E-6 71.625 9 GATTCTG 30 2.0564803E-6 71.625 6 TTCTGTA 35 5.1380775E-6 61.392857 8 ATTCTGT 35 5.1380775E-6 61.392857 7 ATGATTC 45 3.1509262E-7 57.300003 4 TTACAAT 30 2.6184352E-6 42.975 14-15 GTATTAC 30 2.6184352E-6 42.975 12-13 ATTACAA 30 2.6184352E-6 42.975 14-15 TACAATT 30 2.6184352E-6 42.975 16-17 TTTGGTG 30 2.6184352E-6 42.975 20-21 TTGGTGG 30 2.6184352E-6 42.975 22-23 TATTACA 30 2.6184352E-6 42.975 12-13 TGGTGGA 30 2.6184352E-6 42.975 22-23 CAATTTG 35 7.5548105E-6 36.835716 18-19 AGGAACT 35 7.5548105E-6 36.835716 28-29 GGAGGAA 35 7.5548105E-6 36.835716 26-27 >>END_MODULE Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra Rejected 192856 READS because READLEN < 1 Read 192856 spots for ERR6133435.sra Written 192856 spots for ERR6133435.sra SRR ids: ['ERR6133435.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_07u24srs ERR6133435.sra spots: 3857120 blocks: [[1, 192856], [192857, 385712], [385713, 578568], [578569, 771424], [771425, 964280], [964281, 1157136], [1157137, 1349992], [1349993, 1542848], [1542849, 1735704], [1735705, 1928560], [1928561, 2121416], [2121417, 2314272], [2314273, 2507128], [2507129, 2699984], [2699985, 2892840], [2892841, 3085696], [3085697, 3278552], [3278553, 3471408], [3471409, 3664264], [3664265, 3857120]] ERR6133435 file size 852097 ERR6133435 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 ERR6133435 ERR6133435_1.fastq Input file: ERR6133435_1.fastq trimmed: ERR6133435-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 05:35:53 2024 >> started Sat Dec 7 05:35:57 2024 >> done (4.524s) 3857120 reads processed; of these: 1577 ( 0.04%) short reads filtered out after trimming by size control 34 ( 0.00%) empty reads filtered out after trimming by size control 3855509 (99.96%) reads available; of these: 58069 ( 1.51%) trimmed reads available after processing 3797440 (98.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 37 0.00% 19 49 0.00% 20 23 0.00% 21 18 0.00% 22 25 0.00% 23 14 0.00% 24 14 0.00% 25 10 0.00% 26 7 0.00% 27 11 0.00% 28 23 0.00% 29 42 0.00% 30 12 0.00% 31 6 0.00% 32 10 0.00% 33 5 0.00% 34 8 0.00% 35 3 0.00% 36 9 0.00% 37 11 0.00% 38 15 0.00% 39 41 0.00% 40 59 0.00% 41 23 0.00% 42 12 0.00% 43 43 0.00% 44 20 0.00% 45 22 0.00% 46 15 0.00% 47 23 0.00% 48 17 0.00% 49 19 0.00% 50 20 0.00% 51 40 0.00% 52 20 0.00% 53 22 0.00% 54 24 0.00% 55 25 0.00% 56 17 0.00% 57 17 0.00% 58 15 0.00% 59 16 0.00% 60 21 0.00% 61 18 0.00% 62 3 0.00% 63 2 0.00% 64 2 0.00% 65 5 0.00% 66 8 0.00% 67 15 0.00% 68 38 0.00% 69 117 0.00% 70 9661 0.25% 71 9010 0.23% 72 9992 0.26% 73 8697 0.23% 74 9388 0.24% 75 8989 0.23% 76 8135 0.21% 77 8438 0.22% 78 9871 0.26% 79 10952 0.28% 80 9886 0.26% 81 10250 0.27% 82 11461 0.30% 83 12782 0.33% 84 9541 0.25% 85 110 0.00% 86 233 0.01% 87 341 0.01% 88 661 0.02% 89 1393 0.04% 90 3278 0.09% 91 9858 0.26% 92 39331 1.02% 93 3652160 94.73% 3855509 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=2.73 fanout-score-rank=27 prefix-density=0.58 prefix-fanout=2.5 sequence=AAAAAATTCTTCCTGGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAAATTCGTTGACAAAATGTCTACGCTGGTTCAAATCCAGCTCGGCCCAAAAATCTGGGGCTTCGTGAATATGAACTAAATCTTTTTATTTTTC criterion=fanout-score sequence-density=0.16 sequence-density-rank=7 fanout-score=49.63 fanout-score-rank=1 prefix-density=0.70 prefix-fanout=11.2 sequence=GAAGAAGAAGAAACGCATGGTGCCCTGCTTCCGTCTGTCGGCTGCTTGCTTGGCAACGGCAGAGCAGAGCTTGGTGCAGTAAAACTACTGGTTATACTCTCTGTATGTAAAGTTAAAATTTTCACACACAGCTATGTGCTAAAGGA Started job on | Dec 07 05:36:16 Started mapping on | Dec 07 05:36:16 Finished on | Dec 07 05:36:42 Mapping speed, Million of reads per hour | 533.84 Number of input reads | 3855509 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2821403 Uniquely mapped reads % | 73.18% Average mapped length | 91.96 Number of splices: Total | 279289 Number of splices: Annotated (sjdb) | 244817 Number of splices: GT/AG | 271918 Number of splices: GC/AG | 4458 Number of splices: AT/AC | 57 Number of splices: Non-canonical | 2856 Mismatch rate per base, % | 0.46% Deletion rate per base | 0.04% Deletion average length | 1.87 Insertion rate per base | 0.02% Insertion average length | 2.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 933048 % of reads mapped to multiple loci | 24.20% Number of reads mapped to too many loci | 16547 % of reads mapped to too many loci | 0.43% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.16% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 101058 101058 101058 N_multimapping 933048 933048 933048 N_noFeature 153553 180029 2702015 N_ambiguous 104430 11665 411 UnstrandedReadsAssigned:2563420 PositiveStrandReadsAssigned:2629709 NegativeStrandReadsAssigned:118977 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133435 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: ERR6133435-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,855,509 reads, 3,343,420 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 999 rounds 52973 ERR6133435.ke.tsv 35125 ERR6133435.se.tsv 88098 total ==> ERR6133435.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 98 28.4562 PNS24243 293 194 0 0 KQK14069 1603 1504 106 28.0778 KQK14071 474 375 0 0 ==> ERR6133435.se.tsv <== BRADI_1g14170v3 105 BRADI_1g53295v3 32 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 39 BRADI_1g74790v3 28 BRADI_1g09890v3 0 BRADI_1g77505v3 52 BRADI_1g48960v3 0 ERR6133435 completed mapping pipeline successfully