Starting /dee2/code/volunteer_pipeline.sh ERR6133562 current disk space = 1544497528832 free memory = 1604518300 ERR6133562 SRAfilesize 77cdd69e777366b6c77d466693380593 ERR6133562.sra ERR6133562.sra file validated ERR6133562 is single end ERR6133562 is conventional basespace ERR6133562 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133562_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 35.4955 37.0 33.0 37.0 33.0 37.0 2 36.4585 37.0 37.0 37.0 37.0 37.0 3 36.0105 37.0 37.0 37.0 33.0 37.0 4 35.48525 37.0 37.0 37.0 33.0 37.0 5 35.3915 37.0 37.0 37.0 33.0 37.0 6 35.708 37.0 37.0 37.0 33.0 37.0 7 37.56575 40.0 37.0 40.0 33.0 40.0 8 37.649 40.0 37.0 40.0 33.0 40.0 9 37.7395 40.0 37.0 40.0 33.0 40.0 10-11 37.579375 40.0 37.0 40.0 33.0 40.0 12-13 37.517375 38.5 37.0 40.0 33.0 40.0 14-15 37.478 37.0 37.0 40.0 33.0 40.0 16-17 37.424875 37.0 37.0 40.0 33.0 40.0 18-19 37.372 37.0 37.0 40.0 33.0 40.0 20-21 37.2515 37.0 37.0 40.0 33.0 40.0 22-23 37.291125 37.0 37.0 40.0 33.0 40.0 24-25 37.390125 37.0 37.0 40.0 33.0 40.0 26-27 37.388999999999996 37.0 37.0 40.0 33.0 40.0 28-29 37.35875 37.0 37.0 40.0 33.0 40.0 30-31 37.210375 37.0 37.0 40.0 33.0 40.0 32-33 37.062 37.0 37.0 40.0 33.0 40.0 34-35 36.951125000000005 37.0 37.0 40.0 33.0 40.0 36-37 36.807625 37.0 37.0 40.0 33.0 40.0 38-39 36.542375 37.0 37.0 40.0 33.0 40.0 40-41 36.338 37.0 37.0 40.0 33.0 40.0 42-43 36.300250000000005 37.0 37.0 40.0 33.0 40.0 44-45 36.042874999999995 37.0 37.0 40.0 33.0 40.0 46-47 35.844625 37.0 33.0 38.5 33.0 40.0 48-49 35.73775 37.0 33.0 37.0 33.0 40.0 50-51 35.609125000000006 37.0 33.0 37.0 33.0 40.0 52-53 35.212125 37.0 33.0 37.0 33.0 40.0 54-55 35.2705 37.0 33.0 37.0 33.0 40.0 56-57 34.9405 37.0 33.0 37.0 30.0 38.5 58-59 33.79525 37.0 33.0 37.0 27.0 37.0 60-61 34.375625 37.0 33.0 37.0 27.0 37.0 62-63 34.4525 37.0 33.0 37.0 27.0 37.0 64-65 34.3625 37.0 33.0 37.0 27.0 37.0 66-67 34.45375 37.0 33.0 37.0 27.0 37.0 68-69 33.650375 35.0 33.0 37.0 27.0 37.0 70-71 33.79673422633951 35.0 33.0 37.0 27.0 37.0 72-73 34.13581385406772 37.0 33.0 37.0 27.0 37.0 74-75 33.85847579085647 37.0 33.0 37.0 27.0 37.0 76-77 34.12786280818707 37.0 33.0 37.0 27.0 37.0 78-79 34.13667845404269 37.0 33.0 37.0 27.0 37.0 80-81 33.93416849625713 37.0 33.0 37.0 27.0 37.0 82-83 33.94238391595263 37.0 33.0 37.0 27.0 37.0 84-85 33.92629590604403 37.0 33.0 37.0 27.0 37.0 86-87 33.79196704428425 37.0 33.0 37.0 27.0 37.0 88-89 34.00901132852729 37.0 33.0 37.0 27.0 37.0 90-91 33.66426364572605 37.0 33.0 37.0 27.0 37.0 92-93 33.526004119464474 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 11.0 22 16.0 23 25.0 24 23.0 25 28.0 26 27.0 27 46.0 28 57.0 29 68.0 30 84.0 31 99.0 32 130.0 33 171.0 34 223.0 35 415.0 36 888.0 37 961.0 38 702.0 39 19.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 84.275 3.2 4.45 8.075000000000001 2 67.425 18.425 8.95 5.2 3 34.55 36.7 15.5 13.25 4 33.050000000000004 28.299999999999997 18.275 20.375 5 25.35 30.25 26.450000000000003 17.95 6 18.575 38.824999999999996 26.0 16.6 7 34.1 30.3 19.825 15.775 8 27.675 29.599999999999998 25.05 17.675 9 25.35 29.15 27.325 18.175 10-11 23.7375 27.987499999999997 28.199999999999996 20.075000000000003 12-13 26.625 25.650000000000002 27.575 20.150000000000002 14-15 22.787499999999998 30.2 28.8625 18.15 16-17 24.5125 30.475 25.374999999999996 19.6375 18-19 23.9375 26.0 28.3125 21.75 20-21 25.6125 26.1 28.5625 19.725 22-23 28.212500000000002 23.8875 26.35 21.55 24-25 24.637500000000003 25.4875 28.5625 21.3125 26-27 24.962500000000002 25.874999999999996 30.8 18.3625 28-29 25.0375 27.6625 27.5875 19.7125 30-31 27.150000000000002 25.912499999999998 27.1125 19.825 32-33 24.837500000000002 26.6125 28.237499999999997 20.3125 34-35 24.2875 26.987499999999997 27.35 21.375 36-37 24.9 25.7 26.8375 22.5625 38-39 26.973601901663958 24.38383585637433 30.476667083698235 18.16589515826348 40-41 25.532181317305287 25.344352617079892 28.33708990733784 20.786376158276983 42-43 25.04689258471927 29.661122921095412 26.84756783793923 18.444416656246094 44-45 23.625 26.5 29.5 20.375 46-47 25.662499999999998 23.5375 27.800000000000004 23.0 48-49 25.0125 24.4 30.112499999999997 20.474999999999998 50-51 22.7 26.900000000000002 29.762499999999996 20.6375 52-53 24.736842105263158 26.102756892230577 27.982456140350877 21.17794486215539 54-55 25.4 26.887499999999996 28.549999999999997 19.162499999999998 56-57 26.4625 25.5 28.125 19.9125 58-59 23.65 24.837500000000002 29.912499999999998 21.6 60-61 26.387500000000003 25.587500000000002 28.875 19.15 62-63 21.125 29.2375 32.025 17.6125 64-65 22.85 27.750000000000004 29.775000000000002 19.625 66-67 24.3625 28.325 29.299999999999997 18.0125 68-69 22.3 27.437499999999996 28.212500000000002 22.05 70-71 24.96872654490868 25.756817613209908 28.233675256442332 21.04078058543908 72-73 26.279391424619643 24.783100716710678 29.322268326417706 19.61523953225198 74-75 23.71212121212121 28.156565656565657 29.128787878787875 19.002525252525253 76-77 22.351748606183477 26.15306639635073 29.054738976178406 22.44044602128738 78-79 24.631230925737537 25.661241098677518 29.64140386571719 20.066124109867754 80-81 22.769623484365027 30.453095086151883 29.32992980216975 17.44735162731334 82-83 23.895505186323472 26.136509156101933 28.85132539377641 21.11666026379818 84-85 23.28960905349794 23.765432098765434 32.4974279835391 20.44753086419753 86-87 21.70442842430484 27.536045314109163 30.754376930998973 20.005149330587024 88-89 21.09938208032956 29.81462409886715 29.28681771369722 19.799176107106074 90-91 26.544799176107105 26.364572605561275 28.746138002059734 18.344490216271886 92-93 22.245108135942328 29.853244078269825 29.59577754891864 18.305870236869207 >>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 0.5 12 1.0 13 0.5 14 0.0 15 0.5 16 1.5 17 14.0 18 14.0 19 3.0 20 4.5 21 4.0 22 5.5 23 6.0 24 6.0 25 6.0 26 9.0 27 13.5 28 19.5 29 26.0 30 35.0 31 42.0 32 48.0 33 64.5 34 82.5 35 99.0 36 115.0 37 143.0 38 182.5 39 171.0 40 175.0 41 206.0 42 206.5 43 213.5 44 193.0 45 183.0 46 181.0 47 149.0 48 140.5 49 165.5 50 182.0 51 172.5 52 150.5 53 158.5 54 168.5 55 117.5 56 68.0 57 60.5 58 55.0 59 39.0 60 28.5 61 31.0 62 28.5 63 25.0 64 26.0 65 21.0 66 16.5 67 15.0 68 11.0 69 8.5 70 7.5 71 6.0 72 4.5 73 2.0 74 1.0 75 1.5 76 1.0 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 0.5 86 1.0 87 0.5 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 0.0 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 0.08750000000000001 40-41 0.17500000000000002 42-43 0.0375 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.25 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 6.0 71 14.0 72 7.0 73 8.0 74 10.0 75 5.0 76 8.0 77 6.0 78 8.0 79 6.0 80 9.0 81 7.0 82 3.0 83 11.0 84 8.0 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 3884.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.775 #Duplication Level Percentage of deduplicated Percentage of total 1 92.9926068788171 72.32499999999999 2 4.082288653166184 6.35 3 0.9321761491481839 2.175 4 0.6428801028608165 2.0 5 0.12857602057216327 0.5 6 0.06428801028608164 0.3 7 0.16072002571520413 0.8750000000000001 8 0.19286403085824494 1.2 9 0.09643201542912247 0.675 >10 0.6428801028608165 10.0 >50 0.06428801028608164 3.5999999999999996 >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 81 2.025 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 63 1.575 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 44 1.0999999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 34 0.8500000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 31 0.775 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 30 0.75 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 28 0.7000000000000001 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 27 0.675 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 25 0.625 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 24 0.6 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 21 0.525 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 19 0.475 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 16 0.4 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 11 0.27499999999999997 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 11 0.27499999999999997 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 9 0.22499999999999998 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit GAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCA 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 7 0.17500000000000002 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 5 0.125 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 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 0.025 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 pass >>END_MODULE Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341645 READS because READLEN < 1 Read 341645 spots for ERR6133562.sra Written 341645 spots for ERR6133562.sra Rejected 341652 READS because READLEN < 1 Read 341652 spots for ERR6133562.sra Written 341652 spots for ERR6133562.sra SRR ids: ['ERR6133562.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v7nqv3sy ERR6133562.sra spots: 6832907 blocks: [[1, 341645], [341646, 683290], [683291, 1024935], [1024936, 1366580], [1366581, 1708225], [1708226, 2049870], [2049871, 2391515], [2391516, 2733160], [2733161, 3074805], [3074806, 3416450], [3416451, 3758095], [3758096, 4099740], [4099741, 4441385], [4441386, 4783030], [4783031, 5124675], [5124676, 5466320], [5466321, 5807965], [5807966, 6149610], [6149611, 6491255], [6491256, 6832907]] ERR6133562 file size 1512919 ERR6133562 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 ERR6133562 ERR6133562_1.fastq Input file: ERR6133562_1.fastq trimmed: ERR6133562-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 08:41:34 2024 >> started Sat Dec 7 08:41:38 2024 >> done (3.442s) 6832907 reads processed; of these: 167 ( 0.00%) short reads filtered out after trimming by size control 45 ( 0.00%) empty reads filtered out after trimming by size control 6832695 (100.00%) reads available; of these: 135421 ( 1.98%) trimmed reads available after processing 6697274 (98.02%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 38 0.00% 19 36 0.00% 20 27 0.00% 21 25 0.00% 22 33 0.00% 23 13 0.00% 24 14 0.00% 25 5 0.00% 26 13 0.00% 27 19 0.00% 28 34 0.00% 29 28 0.00% 30 16 0.00% 31 24 0.00% 32 17 0.00% 33 28 0.00% 34 29 0.00% 35 181 0.00% 36 1108 0.02% 37 29 0.00% 38 28 0.00% 39 100 0.00% 40 68 0.00% 41 43 0.00% 42 17 0.00% 43 16 0.00% 44 25 0.00% 45 16 0.00% 46 12 0.00% 47 17 0.00% 48 19 0.00% 49 15 0.00% 50 20 0.00% 51 28 0.00% 52 13 0.00% 53 10 0.00% 54 10 0.00% 55 9 0.00% 56 8 0.00% 57 14 0.00% 58 14 0.00% 59 7 0.00% 60 11 0.00% 61 14 0.00% 62 5 0.00% 63 3 0.00% 64 4 0.00% 65 11 0.00% 66 20 0.00% 67 29 0.00% 68 56 0.00% 69 162 0.00% 70 12853 0.19% 71 12001 0.18% 72 13854 0.20% 73 12391 0.18% 74 13009 0.19% 75 12864 0.19% 76 11421 0.17% 77 11732 0.17% 78 13274 0.19% 79 15208 0.22% 80 13886 0.20% 81 14585 0.21% 82 16677 0.24% 83 18280 0.27% 84 14976 0.22% 85 251 0.00% 86 517 0.01% 87 843 0.01% 88 1472 0.02% 89 2931 0.04% 90 6245 0.09% 91 18246 0.27% 92 99663 1.46% 93 6492975 95.03% 6832695 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=7.38 fanout-score-rank=17 prefix-density=0.56 prefix-fanout=4.6 sequence=ATGCATGCATGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=82.12 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=7.2 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCA Started job on | Dec 07 08:41:51 Started mapping on | Dec 07 08:41:51 Finished on | Dec 07 08:42:00 Mapping speed, Million of reads per hour | 2733.08 Number of input reads | 6832695 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 4460256 Uniquely mapped reads % | 65.28% Average mapped length | 92.02 Number of splices: Total | 204414 Number of splices: Annotated (sjdb) | 165995 Number of splices: GT/AG | 194055 Number of splices: GC/AG | 4621 Number of splices: AT/AC | 191 Number of splices: Non-canonical | 5547 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.81 Insertion rate per base | 0.03% Insertion average length | 1.54 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2217028 % of reads mapped to multiple loci | 32.45% Number of reads mapped to too many loci | 54996 % of reads mapped to too many loci | 0.80% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.42% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 155411 155411 155411 N_multimapping 2217028 2217028 2217028 N_noFeature 320719 364261 4255452 N_ambiguous 180263 18996 570 UnstrandedReadsAssigned:3959274 PositiveStrandReadsAssigned:4076999 NegativeStrandReadsAssigned:204234 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133562 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: ERR6133562-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,832,695 reads, 5,610,070 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,140 rounds 52973 ERR6133562.ke.tsv 35125 ERR6133562.se.tsv 88098 total ==> ERR6133562.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 144 24.7857 PNS24243 293 194 0 0 KQK14069 1603 1504 123.968 19.4649 KQK14071 474 375 1.03232 0.650092 ==> ERR6133562.se.tsv <== BRADI_1g14170v3 125 BRADI_1g53295v3 50 BRADI_1g59795v3 47 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 64 BRADI_1g74790v3 43 BRADI_1g09890v3 0 BRADI_1g77505v3 140 BRADI_1g48960v3 0 ERR6133562 completed mapping pipeline successfully