Starting /dee2/code/volunteer_pipeline.sh ERR6133541 current disk space = 1544462528512 free memory = 1419294268 ERR6133541 SRAfilesize 9b9950936b184aafe58c2566f0ac76c8 ERR6133541.sra ERR6133541.sra file validated ERR6133541 is single end ERR6133541 is conventional basespace ERR6133541 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133541_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 33.931 37.0 33.0 37.0 27.0 37.0 2 36.0285 37.0 37.0 37.0 33.0 37.0 3 35.213 37.0 33.0 37.0 33.0 37.0 4 35.2035 37.0 37.0 37.0 33.0 37.0 5 35.15875 37.0 37.0 37.0 33.0 37.0 6 35.55125 37.0 37.0 37.0 33.0 37.0 7 37.29725 37.0 37.0 40.0 33.0 40.0 8 37.416 37.0 37.0 40.0 33.0 40.0 9 37.38475 37.0 37.0 40.0 33.0 40.0 10-11 37.47475 37.0 37.0 40.0 33.0 40.0 12-13 37.324124999999995 37.0 37.0 40.0 33.0 40.0 14-15 37.360875 37.0 37.0 40.0 33.0 40.0 16-17 37.363125 37.0 37.0 40.0 33.0 40.0 18-19 37.232625 37.0 37.0 40.0 33.0 40.0 20-21 37.120000000000005 37.0 37.0 40.0 33.0 40.0 22-23 37.121375 37.0 37.0 40.0 33.0 40.0 24-25 37.167 37.0 37.0 40.0 33.0 40.0 26-27 37.140125 37.0 37.0 40.0 33.0 40.0 28-29 37.084500000000006 37.0 37.0 40.0 33.0 40.0 30-31 37.008375 37.0 37.0 40.0 33.0 40.0 32-33 36.80525 37.0 37.0 40.0 33.0 40.0 34-35 36.75725 37.0 37.0 40.0 33.0 40.0 36-37 36.59325 37.0 37.0 40.0 33.0 40.0 38-39 36.5105 37.0 37.0 40.0 33.0 40.0 40-41 36.2485 37.0 37.0 40.0 33.0 40.0 42-43 36.164874999999995 37.0 37.0 40.0 33.0 40.0 44-45 35.897625 37.0 35.0 40.0 33.0 40.0 46-47 35.6455 37.0 33.0 37.0 33.0 40.0 48-49 35.6225 37.0 33.0 37.0 33.0 40.0 50-51 35.470375000000004 37.0 33.0 37.0 33.0 40.0 52-53 35.162875 37.0 33.0 37.0 30.0 40.0 54-55 35.132125 37.0 33.0 37.0 33.0 40.0 56-57 35.032875000000004 37.0 33.0 37.0 33.0 37.0 58-59 34.335625 37.0 33.0 37.0 27.0 37.0 60-61 34.573125000000005 37.0 33.0 37.0 27.0 37.0 62-63 34.47775 37.0 33.0 37.0 27.0 37.0 64-65 34.435874999999996 37.0 33.0 37.0 27.0 37.0 66-67 34.445375 37.0 33.0 37.0 27.0 37.0 68-69 33.705125 35.0 33.0 37.0 27.0 37.0 70-71 33.76061967418546 35.0 33.0 37.0 27.0 37.0 72-73 34.08006224185899 37.0 33.0 37.0 27.0 37.0 74-75 34.110182214766105 37.0 33.0 37.0 27.0 37.0 76-77 34.12657587819409 37.0 33.0 37.0 27.0 37.0 78-79 34.115276632896936 37.0 33.0 37.0 27.0 37.0 80-81 33.9696602774094 37.0 33.0 37.0 27.0 37.0 82-83 33.85129318595081 37.0 33.0 37.0 27.0 37.0 84-85 33.792301420996246 37.0 33.0 37.0 27.0 37.0 86-87 33.79570871261379 37.0 33.0 37.0 27.0 37.0 88-89 33.88361508452536 37.0 33.0 37.0 27.0 37.0 90-91 33.58829648894668 37.0 33.0 37.0 27.0 37.0 92-93 33.4888166449935 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 15.0 22 16.0 23 14.0 24 23.0 25 32.0 26 43.0 27 45.0 28 55.0 29 66.0 30 85.0 31 106.0 32 137.0 33 172.0 34 228.0 35 445.0 36 902.0 37 911.0 38 683.0 39 10.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.7 2.5749999999999997 2.9000000000000004 5.825 2 74.75 14.374999999999998 6.65 4.2250000000000005 3 37.9 38.25 13.175 10.674999999999999 4 32.074999999999996 29.425 18.15 20.349999999999998 5 25.85 30.75 24.9 18.5 6 21.475 37.3 25.874999999999996 15.35 7 37.925 29.675 19.025 13.375 8 30.575000000000003 31.474999999999998 21.925 16.025 9 25.75 29.4 28.199999999999996 16.650000000000002 10-11 27.987499999999997 26.637499999999996 27.9375 17.4375 12-13 28.287499999999998 26.8625 28.812500000000004 16.037499999999998 14-15 21.7 29.7125 30.1875 18.4 16-17 24.2625 32.0125 25.424999999999997 18.3 18-19 23.849999999999998 27.187499999999996 28.237499999999997 20.724999999999998 20-21 25.18129532383096 26.831707926981746 28.207051762940733 19.779944986246562 22-23 26.650000000000002 24.3125 28.299999999999997 20.7375 24-25 26.825 24.95 28.225 20.0 26-27 26.025 24.825 30.1375 19.0125 28-29 25.387500000000003 27.85 27.3375 19.425 30-31 28.7 24.6625 26.875 19.7625 32-33 23.1375 27.9125 28.812500000000004 20.1375 34-35 24.4994994994995 26.426426426426424 28.22822822822823 20.845845845845844 36-37 24.425 24.6625 28.8375 22.075 38-39 27.465933241655204 25.61570196274534 28.66608326040755 18.2522815351919 40-41 26.600800400200097 25.737868934467233 26.488244122061033 21.173086543271637 42-43 24.90613266583229 27.571964956195245 27.684605757196497 19.83729662077597 44-45 22.951844903064416 26.07879924953096 30.093808630393998 20.87554721701063 46-47 24.462500000000002 23.674999999999997 28.775000000000002 23.0875 48-49 24.625 25.35 30.425 19.6 50-51 26.075 25.7 28.7375 19.4875 52-53 25.475475475475474 26.58908908908909 27.77777777777778 20.15765765765766 54-55 23.8125 28.8375 28.725 18.625 56-57 25.8625 26.075 28.8625 19.2 58-59 24.1625 25.1875 29.675 20.974999999999998 60-61 25.5625 25.074999999999996 28.487499999999997 20.875 62-63 23.35 27.400000000000002 31.1 18.15 64-65 25.3125 26.0125 30.0875 18.587500000000002 66-67 24.775 26.9125 29.15 19.162499999999998 68-69 23.5625 27.237499999999997 27.450000000000003 21.75 70-71 25.244055068836047 25.53191489361702 28.46057571964956 20.763454317897374 72-73 25.44609198291028 26.476501633576277 28.23573762251822 19.841668760995223 74-75 23.133198789101918 26.892028254288597 30.4364278506559 19.538345105953585 76-77 22.319391634980988 26.89480354879594 29.366286438529787 21.419518377693283 78-79 25.18461930226636 24.560733384262797 30.02291825821238 20.23172905525847 80-81 24.22614479406498 28.523919160910722 28.61345612688667 18.63647991813763 82-83 24.593967517401392 25.225573601443674 30.45888115493684 19.721577726218097 84-85 22.946138870863074 24.802076573653473 31.21349772874757 21.038286826735884 86-87 22.35370611183355 25.74772431729519 32.197659297789336 19.700910273081927 88-89 21.339401820546165 28.66059817945384 31.352405721716515 18.647594278283485 90-91 24.22626788036411 27.88036410923277 29.128738621586475 18.764629388816644 92-93 23.26397919375813 27.698309492847855 29.55786736020806 19.479843953185956 >>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 0.5 17 5.5 18 7.0 19 2.0 20 0.5 21 1.5 22 1.5 23 3.0 24 7.0 25 5.5 26 5.0 27 8.5 28 17.0 29 23.5 30 28.5 31 38.0 32 50.5 33 69.0 34 79.5 35 96.5 36 109.5 37 130.5 38 169.5 39 176.5 40 183.5 41 203.5 42 215.0 43 221.5 44 201.5 45 194.0 46 244.0 47 230.5 48 170.5 49 167.5 50 174.5 51 164.0 52 142.0 53 123.5 54 111.0 55 86.0 56 68.0 57 70.5 58 55.5 59 38.5 60 32.0 61 27.5 62 27.0 63 27.5 64 26.0 65 26.0 66 21.0 67 14.0 68 13.5 69 9.5 70 6.5 71 7.0 72 5.5 73 3.0 74 2.0 75 2.0 76 1.5 77 0.5 78 0.0 79 0.5 80 1.0 81 0.5 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 0.1 36-37 0.0 38-39 0.0125 40-41 0.05 42-43 0.125 44-45 0.0625 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.1 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 10.0 71 8.0 72 6.0 73 7.0 74 10.0 75 8.0 76 12.0 77 7.0 78 10.0 79 6.0 80 14.0 81 14.0 82 18.0 83 10.0 84 15.0 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 3845.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.8 #Duplication Level Percentage of deduplicated Percentage of total 1 93.71980676328504 77.60000000000001 2 3.592995169082126 5.949999999999999 3 1.1171497584541061 2.775 4 0.4227053140096618 1.4000000000000001 5 0.24154589371980675 1.0 6 0.18115942028985507 0.8999999999999999 7 0.12077294685990338 0.7000000000000001 8 0.09057971014492754 0.6 9 0.030193236714975844 0.22499999999999998 >10 0.4528985507246377 7.3 >50 0.030193236714975844 1.55 >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 62 1.55 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 46 1.15 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 28 0.7000000000000001 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 26 0.65 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 22 0.5499999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 20 0.5 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 17 0.42500000000000004 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 16 0.4 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 14 0.35000000000000003 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 14 0.35000000000000003 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 14 0.35000000000000003 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 7 0.17500000000000002 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGAGGAGATCGAGTTGTTACTTGAGAGTTTGTAACCCTTTATCATACCAT 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGGATTGAGATGTCTGGCTGCAGTTTTAGTGTTTACTAAGTTTTGTCTAT 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 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 0.0125 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTGCTC 25 0.0020284592 35.823376 78-79 >>END_MODULE Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227033 READS because READLEN < 1 Read 227033 spots for ERR6133541.sra Written 227033 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra Rejected 227019 READS because READLEN < 1 Read 227019 spots for ERR6133541.sra Written 227019 spots for ERR6133541.sra SRR ids: ['ERR6133541.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0xa_o371 ERR6133541.sra spots: 4540394 blocks: [[1, 227019], [227020, 454038], [454039, 681057], [681058, 908076], [908077, 1135095], [1135096, 1362114], [1362115, 1589133], [1589134, 1816152], [1816153, 2043171], [2043172, 2270190], [2270191, 2497209], [2497210, 2724228], [2724229, 2951247], [2951248, 3178266], [3178267, 3405285], [3405286, 3632304], [3632305, 3859323], [3859324, 4086342], [4086343, 4313361], [4313362, 4540394]] ERR6133541 file size 1003055 ERR6133541 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 ERR6133541 ERR6133541_1.fastq Input file: ERR6133541_1.fastq trimmed: ERR6133541-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 08:14:45 2024 >> started Sat Dec 7 08:14:47 2024 >> done (2.341s) 4540394 reads processed; of these: 80 ( 0.00%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 4540300 (100.00%) reads available; of these: 78009 ( 1.72%) trimmed reads available after processing 4462291 (98.28%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 15 0.00% 20 13 0.00% 21 3 0.00% 22 9 0.00% 23 3 0.00% 24 5 0.00% 25 0 0.00% 26 3 0.00% 27 6 0.00% 28 6 0.00% 29 3 0.00% 30 3 0.00% 31 13 0.00% 32 14 0.00% 33 5 0.00% 34 15 0.00% 35 41 0.00% 36 424 0.01% 37 7 0.00% 38 13 0.00% 39 35 0.00% 40 40 0.00% 41 18 0.00% 42 5 0.00% 43 7 0.00% 44 6 0.00% 45 5 0.00% 46 5 0.00% 47 10 0.00% 48 6 0.00% 49 4 0.00% 50 6 0.00% 51 12 0.00% 52 8 0.00% 53 3 0.00% 54 7 0.00% 55 12 0.00% 56 4 0.00% 57 5 0.00% 58 5 0.00% 59 5 0.00% 60 13 0.00% 61 9 0.00% 62 2 0.00% 63 5 0.00% 64 3 0.00% 65 7 0.00% 66 9 0.00% 67 18 0.00% 68 42 0.00% 69 153 0.00% 70 11580 0.26% 71 11315 0.25% 72 11950 0.26% 73 11311 0.25% 74 11548 0.25% 75 11506 0.25% 76 10698 0.24% 77 11290 0.25% 78 12456 0.27% 79 13855 0.31% 80 12344 0.27% 81 13628 0.30% 82 15186 0.33% 83 16054 0.35% 84 13070 0.29% 85 182 0.00% 86 338 0.01% 87 546 0.01% 88 956 0.02% 89 1872 0.04% 90 4260 0.09% 91 13031 0.29% 92 53260 1.17% 93 4276986 94.20% 4540300 reads passed initial QC criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=4.15 fanout-score-rank=27 prefix-density=1.00 prefix-fanout=3.2 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=228.62 fanout-score-rank=1 prefix-density=0.67 prefix-fanout=7.9 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 08:15:07 Started mapping on | Dec 07 08:15:09 Finished on | Dec 07 08:15:16 Mapping speed, Million of reads per hour | 2335.01 Number of input reads | 4540300 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3432220 Uniquely mapped reads % | 75.59% Average mapped length | 91.88 Number of splices: Total | 136015 Number of splices: Annotated (sjdb) | 110389 Number of splices: GT/AG | 129676 Number of splices: GC/AG | 2935 Number of splices: AT/AC | 52 Number of splices: Non-canonical | 3352 Mismatch rate per base, % | 0.47% Deletion rate per base | 0.04% Deletion average length | 1.74 Insertion rate per base | 0.03% Insertion average length | 1.67 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1007507 % of reads mapped to multiple loci | 22.19% Number of reads mapped to too many loci | 39238 % of reads mapped to too many loci | 0.86% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.29% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 100573 100573 100573 N_multimapping 1007507 1007507 1007507 N_noFeature 216838 250576 3275895 N_ambiguous 138265 15731 390 UnstrandedReadsAssigned:3077117 PositiveStrandReadsAssigned:3165913 NegativeStrandReadsAssigned:155935 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133541 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: ERR6133541-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,540,300 reads, 3,834,539 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,088 rounds 52973 ERR6133541.ke.tsv 35125 ERR6133541.se.tsv 88098 total ==> ERR6133541.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 128 32.4544 PNS24243 293 194 0 0 KQK14069 1603 1504 47 10.8709 KQK14071 474 375 0 0 ==> ERR6133541.se.tsv <== BRADI_1g14170v3 47 BRADI_1g53295v3 58 BRADI_1g59795v3 25 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 47 BRADI_1g74790v3 43 BRADI_1g09890v3 2 BRADI_1g77505v3 107 BRADI_1g48960v3 0 ERR6133541 completed mapping pipeline successfully