Starting /dee2/code/volunteer_pipeline.sh ERR6133437 current disk space = 1545995292672 free memory = 1594233996 ERR6133437 SRAfilesize 7e70e1caa7d765a4983900b272555113 ERR6133437.sra ERR6133437.sra file validated ERR6133437 is single end ERR6133437 is conventional basespace ERR6133437 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133437_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 35.17525 37.0 33.0 37.0 33.0 37.0 2 36.30075 37.0 37.0 37.0 33.0 37.0 3 35.67325 37.0 37.0 37.0 33.0 37.0 4 35.41225 37.0 37.0 37.0 33.0 37.0 5 35.323 37.0 37.0 37.0 33.0 37.0 6 35.55575 37.0 37.0 37.0 33.0 37.0 7 37.32525 37.0 37.0 40.0 33.0 40.0 8 37.35025 37.0 37.0 40.0 33.0 40.0 9 37.4425 37.0 37.0 40.0 33.0 40.0 10-11 37.35125 37.0 37.0 40.0 33.0 40.0 12-13 37.23325 37.0 37.0 40.0 33.0 40.0 14-15 37.155 37.0 37.0 40.0 33.0 40.0 16-17 37.061875 37.0 37.0 40.0 33.0 40.0 18-19 37.284499999999994 37.0 37.0 40.0 33.0 40.0 20-21 37.45075 37.0 37.0 40.0 33.0 40.0 22-23 37.37875 37.0 37.0 40.0 33.0 40.0 24-25 37.338750000000005 37.0 37.0 40.0 33.0 40.0 26-27 37.147125 37.0 37.0 40.0 33.0 40.0 28-29 37.237125 37.0 37.0 40.0 33.0 40.0 30-31 37.185249999999996 37.0 37.0 40.0 33.0 40.0 32-33 37.056749999999994 37.0 37.0 40.0 33.0 40.0 34-35 36.780375 37.0 37.0 40.0 33.0 40.0 36-37 36.77775 37.0 37.0 40.0 33.0 40.0 38-39 36.73825 37.0 37.0 40.0 33.0 40.0 40-41 36.619625 37.0 37.0 40.0 33.0 40.0 42-43 36.536500000000004 37.0 37.0 40.0 33.0 40.0 44-45 36.248875 37.0 37.0 40.0 33.0 40.0 46-47 36.22325 37.0 37.0 38.5 33.0 40.0 48-49 36.02925 37.0 37.0 37.0 33.0 40.0 50-51 35.808 37.0 35.0 37.0 33.0 40.0 52-53 35.652875 37.0 33.0 37.0 33.0 40.0 54-55 35.556125 37.0 33.0 37.0 33.0 40.0 56-57 35.456625 37.0 33.0 37.0 33.0 38.5 58-59 35.0445 37.0 33.0 37.0 33.0 37.0 60-61 34.854 37.0 33.0 37.0 33.0 37.0 62-63 34.85525 37.0 33.0 37.0 33.0 37.0 64-65 34.367125 37.0 33.0 37.0 30.0 37.0 66-67 34.316374999999994 37.0 33.0 37.0 30.0 37.0 68-69 33.085 35.0 33.0 35.0 30.0 37.0 70-71 33.395707789764174 33.0 33.0 37.0 27.0 37.0 72-73 34.189770333895275 37.0 33.0 37.0 27.0 37.0 74-75 34.47660465992162 37.0 33.0 37.0 33.0 37.0 76-77 34.320690496400594 37.0 33.0 37.0 33.0 37.0 78-79 34.29427695507471 37.0 33.0 37.0 33.0 37.0 80-81 34.214019833228136 37.0 33.0 37.0 30.0 37.0 82-83 33.92348806333427 37.0 33.0 37.0 30.0 37.0 84-85 33.989126510698426 37.0 33.0 37.0 27.0 37.0 86-87 33.92362924281984 37.0 33.0 37.0 30.0 37.0 88-89 33.879112271540464 37.0 33.0 37.0 27.0 37.0 90-91 33.75652741514361 35.0 33.0 37.0 27.0 37.0 92-93 33.50156657963446 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 4.0 22 14.0 23 11.0 24 26.0 25 24.0 26 28.0 27 27.0 28 40.0 29 52.0 30 64.0 31 122.0 32 128.0 33 179.0 34 245.0 35 439.0 36 997.0 37 1054.0 38 522.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.225 3.15 2.5250000000000004 7.1 2 71.5965965965966 16.116116116116117 7.4074074074074066 4.87987987987988 3 36.95 38.125 13.8 11.125 4 34.125 29.599999999999998 17.4 18.875 5 24.55 31.574999999999996 24.325 19.55 6 20.0 38.425 25.825 15.75 7 36.4 28.525 19.125 15.950000000000001 8 29.375 29.299999999999997 25.374999999999996 15.950000000000001 9 26.650000000000002 28.375 27.675 17.299999999999997 10-11 25.2 28.325 27.187499999999996 19.287499999999998 12-13 28.1875 24.9875 26.674999999999997 20.150000000000002 14-15 23.575 28.9875 29.0875 18.35 16-17 25.35 29.75 26.487500000000004 18.4125 18-19 24.85 26.6625 26.187500000000004 22.3 20-21 24.975 26.2125 27.537499999999998 21.275 22-23 24.725 25.2 27.224999999999998 22.85 24-25 26.625 23.7875 28.0875 21.5 26-27 24.7 25.7875 29.849999999999998 19.662499999999998 28-29 24.375 26.7625 28.225 20.6375 30-31 27.3375 25.474999999999998 26.525 20.6625 32-33 24.7875 26.387500000000003 28.462500000000002 20.3625 34-35 25.9625 25.162499999999998 27.875 21.0 36-37 24.2375 23.549999999999997 29.4875 22.725 38-39 24.775 24.7 31.7875 18.7375 40-41 26.2125 25.35 27.0125 21.425 42-43 23.925 28.3875 27.05 20.6375 44-45 24.587500000000002 24.8125 28.5875 22.0125 46-47 23.6875 24.474999999999998 28.1875 23.65 48-49 24.975 23.9 32.1125 19.0125 50-51 24.3125 26.150000000000002 29.625 19.9125 52-53 24.337500000000002 28.000000000000004 27.487499999999997 20.175 54-55 22.287499999999998 27.700000000000003 30.275000000000002 19.7375 56-57 26.4625 24.5125 28.512500000000003 20.5125 58-59 24.025 24.637500000000003 29.375 21.9625 60-61 24.7875 24.025 29.262500000000003 21.925 62-63 21.875 28.575 32.225 17.325 64-65 24.0 26.5875 29.3875 20.025000000000002 66-67 25.387500000000003 27.0625 28.599999999999998 18.95 68-69 23.45 26.924999999999997 28.675 20.95 70-71 25.807663410969194 23.37841222138743 29.338842975206614 21.475081392436763 72-73 25.677208013103186 24.644072067531813 27.7686783419428 21.9100415774222 74-75 23.741919127899607 26.112308277348205 29.243250095069083 20.902522499683105 76-77 22.960417462135677 26.549573628611427 30.20236731576938 20.287641593483517 78-79 22.42416485344938 24.971201843082042 31.652374248048126 20.952259055420452 80-81 23.856167031834 27.33599690681789 30.506508570692098 18.301327490656014 82-83 23.279325988334413 24.964355152300712 30.239792611795203 21.51652624756967 84-85 24.487932159165034 23.28767123287671 30.85453359425962 21.36986301369863 86-87 21.93211488250653 26.566579634464755 32.885117493472585 18.616187989556135 88-89 22.140992167101828 28.720626631853786 30.443864229765012 18.694516971279374 90-91 26.38381201044386 25.221932114882506 29.451697127937337 18.942558746736292 92-93 21.22715404699739 29.007832898172325 30.509138381201044 19.255874673629243 >>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 5.5 18 6.0 19 1.5 20 2.5 21 2.5 22 2.5 23 4.0 24 5.5 25 7.0 26 6.5 27 10.0 28 21.0 29 28.0 30 28.0 31 32.5 32 54.0 33 77.0 34 88.5 35 98.5 36 114.0 37 124.5 38 150.5 39 170.0 40 179.5 41 192.5 42 203.0 43 216.5 44 214.5 45 186.5 46 188.0 47 176.0 48 157.0 49 182.0 50 173.0 51 152.0 52 145.0 53 178.5 54 175.5 55 104.5 56 61.0 57 51.5 58 55.0 59 50.0 60 38.5 61 39.0 62 39.5 63 34.0 64 32.0 65 28.0 66 15.5 67 9.0 68 9.5 69 7.0 70 4.0 71 3.0 72 2.0 73 1.5 74 2.5 75 1.5 76 0.0 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 0.1 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 0.013044612575006522 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 14.0 71 11.0 72 13.0 73 13.0 74 9.0 75 8.0 76 7.0 77 10.0 78 17.0 79 14.0 80 9.0 81 13.0 82 9.0 83 17.0 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 3830.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.77499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.51018489501723 73.8 2 4.544030084612974 7.249999999999999 3 1.0968348480100283 2.625 4 0.5640864932623002 1.7999999999999998 5 0.21936696960200563 0.8750000000000001 6 0.15669069257286117 0.75 7 0.0940144155437167 0.525 8 0.06267627702914447 0.4 9 0.0940144155437167 0.675 >10 0.6267627702914447 9.2 >50 0.031338138514572234 2.1 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 84 2.1 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 38 0.95 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 36 0.8999999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 34 0.8500000000000001 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 26 0.65 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 21 0.525 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 21 0.525 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 19 0.475 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 18 0.44999999999999996 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 17 0.42500000000000004 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 15 0.375 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 14 0.35000000000000003 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 13 0.325 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 12 0.3 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 10 0.25 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 7 0.17500000000000002 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 6 0.15 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 6 0.15 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 6 0.15 No Hit CCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTT 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGT 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 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 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.0625 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 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGAAA 20 0.0028010176 64.828125 1 GGGAGAG 30 1.8348807E-4 57.625 1 GCAATAC 25 0.0067786244 51.8625 7 CAATACA 25 0.0067786244 51.8625 8 GAGCAAT 25 0.0067786244 51.8625 5 AGAGCAA 25 0.0067786244 51.8625 4 AATACAA 25 0.0067786244 51.8625 9 >>END_MODULE Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Rejected 310439 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Read 310439 spots for ERR6133437.sra Written 310439 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra Rejected 310429 READS because READLEN < 1 Read 310429 spots for ERR6133437.sra Written 310429 spots for ERR6133437.sra SRR ids: ['ERR6133437.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vl7rf8t1 ERR6133437.sra spots: 6208590 blocks: [[1, 310429], [310430, 620858], [620859, 931287], [931288, 1241716], [1241717, 1552145], [1552146, 1862574], [1862575, 2173003], [2173004, 2483432], [2483433, 2793861], [2793862, 3104290], [3104291, 3414719], [3414720, 3725148], [3725149, 4035577], [4035578, 4346006], [4346007, 4656435], [4656436, 4966864], [4966865, 5277293], [5277294, 5587722], [5587723, 5898151], [5898152, 6208590]] ERR6133437 file size 1371606 ERR6133437 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 ERR6133437 ERR6133437_1.fastq Input file: ERR6133437_1.fastq trimmed: ERR6133437-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 05:38:17 2024 >> started Sat Dec 7 05:38:20 2024 >> done (3.105s) 6208590 reads processed; of these: 2255 ( 0.04%) short reads filtered out after trimming by size control 40 ( 0.00%) empty reads filtered out after trimming by size control 6206295 (99.96%) reads available; of these: 83711 ( 1.35%) trimmed reads available after processing 6122584 (98.65%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 69 0.00% 19 105 0.00% 20 48 0.00% 21 23 0.00% 22 31 0.00% 23 27 0.00% 24 26 0.00% 25 16 0.00% 26 22 0.00% 27 27 0.00% 28 19 0.00% 29 86 0.00% 30 42 0.00% 31 17 0.00% 32 35 0.00% 33 16 0.00% 34 50 0.00% 35 132 0.00% 36 87 0.00% 37 85 0.00% 38 122 0.00% 39 88 0.00% 40 106 0.00% 41 49 0.00% 42 133 0.00% 43 704 0.01% 44 69 0.00% 45 115 0.00% 46 110 0.00% 47 34 0.00% 48 110 0.00% 49 45 0.00% 50 28 0.00% 51 81 0.00% 52 38 0.00% 53 46 0.00% 54 19 0.00% 55 31 0.00% 56 29 0.00% 57 27 0.00% 58 12 0.00% 59 26 0.00% 60 50 0.00% 61 21 0.00% 62 3 0.00% 63 5 0.00% 64 1 0.00% 65 15 0.00% 66 13 0.00% 67 31 0.00% 68 65 0.00% 69 208 0.00% 70 18873 0.30% 71 17290 0.28% 72 18637 0.30% 73 16837 0.27% 74 17754 0.29% 75 17740 0.29% 76 15285 0.25% 77 15788 0.25% 78 18396 0.30% 79 21787 0.35% 80 18021 0.29% 81 18660 0.30% 82 20938 0.34% 83 23615 0.38% 84 18216 0.29% 85 172 0.00% 86 321 0.01% 87 487 0.01% 88 899 0.01% 89 1961 0.03% 90 4515 0.07% 91 13444 0.22% 92 55236 0.89% 93 5848026 94.23% 6206295 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=36 prefix-density=0.26 prefix-fanout=2.1 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=244.60 fanout-score-rank=1 prefix-density=0.69 prefix-fanout=7.1 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAA Started job on | Dec 07 05:38:32 Started mapping on | Dec 07 05:38:33 Finished on | Dec 07 05:38:39 Mapping speed, Million of reads per hour | 3723.78 Number of input reads | 6206295 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 4502274 Uniquely mapped reads % | 72.54% Average mapped length | 91.84 Number of splices: Total | 200656 Number of splices: Annotated (sjdb) | 164076 Number of splices: GT/AG | 191921 Number of splices: GC/AG | 4359 Number of splices: AT/AC | 123 Number of splices: Non-canonical | 4253 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 1.97 Insertion rate per base | 0.02% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1590239 % of reads mapped to multiple loci | 25.62% Number of reads mapped to too many loci | 25512 % of reads mapped to too many loci | 0.41% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.39% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 113782 113782 113782 N_multimapping 1590239 1590239 1590239 N_noFeature 285479 325310 4312672 N_ambiguous 165916 16033 763 UnstrandedReadsAssigned:4050879 PositiveStrandReadsAssigned:4160931 NegativeStrandReadsAssigned:188839 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133437 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: ERR6133437-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,206,295 reads, 5,292,220 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,123 rounds 52973 ERR6133437.ke.tsv 35125 ERR6133437.se.tsv 88098 total ==> ERR6133437.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 120 22.1034 PNS24243 293 194 0 0 KQK14069 1603 1504 440 73.9328 KQK14071 474 375 0 0 ==> ERR6133437.se.tsv <== BRADI_1g14170v3 439 BRADI_1g53295v3 45 BRADI_1g59795v3 58 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 77 BRADI_1g74790v3 27 BRADI_1g09890v3 0 BRADI_1g77505v3 113 BRADI_1g48960v3 0 ERR6133437 completed mapping pipeline successfully