Starting /dee2/code/volunteer_pipeline.sh ERR6133466 current disk space = 1545107382272 free memory = 1597428012 ERR6133466 SRAfilesize 07dda88c7270015c640ed000976a7605 ERR6133466.sra ERR6133466.sra file validated ERR6133466 is single end ERR6133466 is conventional basespace ERR6133466 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133466_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.838 37.0 33.0 37.0 33.0 37.0 2 36.12675 37.0 37.0 37.0 33.0 37.0 3 35.3515 37.0 33.0 37.0 33.0 37.0 4 35.03 37.0 37.0 37.0 33.0 37.0 5 34.906 37.0 37.0 37.0 33.0 37.0 6 35.32775 37.0 37.0 37.0 33.0 37.0 7 36.7375 37.0 37.0 40.0 33.0 40.0 8 36.9375 37.0 37.0 40.0 33.0 40.0 9 36.93025 37.0 37.0 40.0 33.0 40.0 10-11 36.900375 37.0 37.0 40.0 33.0 40.0 12-13 36.87075 37.0 37.0 40.0 33.0 40.0 14-15 36.852374999999995 37.0 37.0 40.0 33.0 40.0 16-17 36.655249999999995 37.0 37.0 40.0 33.0 40.0 18-19 36.33475 37.0 37.0 40.0 33.0 40.0 20-21 36.18375 37.0 35.0 40.0 33.0 40.0 22-23 35.87875 37.0 33.0 40.0 33.0 40.0 24-25 35.986000000000004 37.0 35.0 40.0 33.0 40.0 26-27 36.263625000000005 37.0 37.0 40.0 33.0 40.0 28-29 36.26325 37.0 37.0 40.0 33.0 40.0 30-31 36.313125 37.0 37.0 40.0 33.0 40.0 32-33 36.2445 37.0 35.0 40.0 33.0 40.0 34-35 36.233374999999995 37.0 37.0 40.0 33.0 40.0 36-37 36.198125000000005 37.0 37.0 40.0 33.0 40.0 38-39 36.070125000000004 37.0 35.0 40.0 33.0 40.0 40-41 35.973375000000004 37.0 33.0 40.0 33.0 40.0 42-43 35.924875 37.0 35.0 40.0 33.0 40.0 44-45 35.688 37.0 33.0 38.5 33.0 40.0 46-47 35.573375 37.0 33.0 37.0 33.0 40.0 48-49 35.633624999999995 37.0 33.0 37.0 33.0 40.0 50-51 35.42275 37.0 33.0 37.0 33.0 40.0 52-53 35.07575 37.0 33.0 37.0 30.0 40.0 54-55 35.038624999999996 37.0 33.0 37.0 33.0 40.0 56-57 34.824375 37.0 33.0 37.0 27.0 40.0 58-59 34.235375000000005 37.0 33.0 37.0 27.0 37.0 60-61 34.41775 37.0 33.0 37.0 27.0 37.0 62-63 34.379625 37.0 33.0 37.0 27.0 37.0 64-65 34.274874999999994 37.0 33.0 37.0 27.0 37.0 66-67 34.0215 37.0 33.0 37.0 27.0 37.0 68-69 33.261875 35.0 33.0 37.0 27.0 37.0 70-71 33.405962637913746 35.0 33.0 37.0 27.0 37.0 72-73 33.756295577336985 37.0 33.0 37.0 27.0 37.0 74-75 33.857029373989604 37.0 33.0 37.0 27.0 37.0 76-77 33.863593168682115 37.0 33.0 37.0 27.0 37.0 78-79 33.795944845426675 37.0 33.0 37.0 27.0 37.0 80-81 33.707760948094986 37.0 33.0 37.0 27.0 37.0 82-83 33.61933454182474 37.0 33.0 37.0 27.0 37.0 84-85 33.39987417155666 37.0 33.0 37.0 27.0 37.0 86-87 33.29626241505488 35.0 33.0 37.0 27.0 37.0 88-89 33.39610559330894 35.0 33.0 37.0 27.0 37.0 90-91 33.24320439100889 33.0 33.0 37.0 27.0 37.0 92-93 33.26803450078411 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 14.0 21 14.0 22 22.0 23 17.0 24 24.0 25 30.0 26 45.0 27 52.0 28 74.0 29 80.0 30 129.0 31 98.0 32 171.0 33 220.0 34 336.0 35 484.0 36 772.0 37 888.0 38 519.0 39 11.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.15 3.4000000000000004 3.6249999999999996 6.825 2 68.7 17.95 7.9 5.45 3 35.0 39.800000000000004 13.750000000000002 11.450000000000001 4 31.424999999999997 29.049999999999997 20.95 18.575 5 25.525 29.175 26.525 18.775 6 19.400000000000002 37.7 26.275 16.625 7 37.225 27.825 19.175 15.775 8 30.7 31.924999999999997 21.0 16.375 9 26.35 28.375 27.275 18.0 10-11 25.4375 28.050000000000004 28.000000000000004 18.512500000000003 12-13 26.8375 27.075 27.800000000000004 18.2875 14-15 21.2 29.9375 29.275000000000002 19.5875 16-17 25.087500000000002 31.45 25.5 17.962500000000002 18-19 24.3625 25.674999999999997 29.312500000000004 20.65 20-21 24.262131065532767 25.887943971985994 28.96448224112056 20.885442721360683 22-23 26.237500000000004 24.85 27.987499999999997 20.925 24-25 24.712500000000002 25.2875 28.5625 21.4375 26-27 24.637500000000003 25.362499999999997 30.099999999999998 19.900000000000002 28-29 24.375 27.375 28.037499999999998 20.2125 30-31 26.400000000000002 25.8 28.4125 19.3875 32-33 23.9125 27.075 28.449999999999996 20.5625 34-35 23.849999999999998 28.1375 27.5875 20.424999999999997 36-37 24.337500000000002 26.2125 27.825 21.625 38-39 25.662499999999998 25.424999999999997 29.212500000000002 19.7 40-41 25.362499999999997 24.5375 28.8625 21.2375 42-43 23.95598899724931 27.956989247311824 28.382095523880967 19.70492623155789 44-45 23.39042380297537 25.978247280910118 30.428803600450056 20.202525315664456 46-47 24.3125 24.425 28.675 22.5875 48-49 24.224999999999998 26.174999999999997 30.162499999999998 19.4375 50-51 21.9375 27.575 29.349999999999998 21.1375 52-53 23.78981690494106 26.761976423375973 27.188362177075497 22.259844494607474 54-55 24.246592472177067 25.534575465799676 30.686507440290107 19.53232462173315 56-57 24.953119139892486 26.003250406300786 29.61620202525316 19.42742842855357 58-59 23.200000000000003 25.95 30.45 20.4 60-61 25.05 25.5 30.4375 19.0125 62-63 21.0625 28.1875 31.4875 19.2625 64-65 22.5875 27.950000000000003 30.175 19.287499999999998 66-67 23.3 28.525 28.9 19.275000000000002 68-69 21.952744093011624 26.840855106888363 29.778722340292536 21.427678459807474 70-71 23.00951427140711 26.489734601902853 29.394091136705057 21.106659989984976 72-73 24.666666666666668 25.68553459119497 29.735849056603776 19.91194968553459 74-75 23.12942366026289 26.6304347826087 30.59908998988878 19.641051567239636 76-77 23.270600203458798 25.305188199389622 29.52695829094608 21.897253306205496 78-79 23.113328216935276 25.748273215656177 31.593757994371963 19.54464057303658 80-81 22.33097231165486 29.233741146168708 29.684481648422405 18.750804893754026 82-83 22.80383519046385 26.172583570873282 30.12438455558435 20.899196683078518 84-85 21.85949334029773 25.176286236615304 32.76312353094803 20.20109689213894 86-87 22.713016204913746 26.52901202300052 31.45582854155776 19.302143230527964 88-89 20.64819654992159 28.358599059069522 31.468897020386827 19.52430737062206 90-91 23.849973863042344 27.39153162571877 29.926816518557242 18.83167799268165 92-93 21.066387872451646 27.91427077888134 31.27286983795086 19.74647151071615 >>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 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 6.5 18 7.5 19 2.5 20 2.5 21 2.5 22 2.5 23 7.5 24 11.0 25 7.0 26 7.0 27 12.5 28 25.0 29 35.5 30 38.0 31 49.5 32 64.5 33 89.0 34 101.5 35 102.0 36 120.0 37 153.0 38 193.0 39 203.0 40 193.0 41 194.0 42 214.5 43 228.5 44 217.5 45 195.0 46 171.5 47 168.0 48 161.5 49 170.5 50 173.0 51 139.0 52 121.0 53 116.5 54 120.5 55 86.5 56 47.5 57 49.0 58 45.0 59 46.5 60 43.0 61 34.5 62 29.0 63 25.0 64 23.0 65 21.0 66 17.5 67 12.5 68 11.5 69 9.0 70 7.5 71 7.0 72 7.0 73 5.0 74 3.0 75 2.0 76 1.0 77 0.5 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 0.0 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 0.05 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 0.025 44-45 0.0125 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.325 54-55 0.0375 56-57 0.0125 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0125 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 12.0 71 10.0 72 6.0 73 10.0 74 12.0 75 10.0 76 16.0 77 10.0 78 10.0 79 15.0 80 13.0 81 11.0 82 12.0 83 21.0 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 3826.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.83980582524272 76.5 2 3.8228155339805823 6.3 3 1.4563106796116505 3.5999999999999996 4 0.5764563106796117 1.9 5 0.24271844660194172 1.0 6 0.33373786407766987 1.6500000000000001 7 0.09101941747572816 0.525 8 0.12135922330097086 0.8 9 0.06067961165048543 0.44999999999999996 >10 0.42475728155339804 5.825 >50 0.030339805825242715 1.4500000000000002 >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 58 1.4500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 41 1.0250000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 28 0.7000000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 22 0.5499999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 19 0.475 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 16 0.4 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 16 0.4 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 14 0.35000000000000003 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 12 0.3 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 11 0.27499999999999997 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 11 0.27499999999999997 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 8 0.2 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 8 0.2 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 8 0.2 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 6 0.15 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 6 0.15 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 6 0.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAG 5 0.125 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 5 0.125 No Hit ACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATG 5 0.125 No Hit GGATTCCGGCGGAACAAACTAAAATCTAGTACTGCTCTTGGATTGGATCT 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 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 0.05 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 0.05 0.0 0.0 0.0 0.0 54-55 0.05 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 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 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 0.1125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97035 READS because READLEN < 1 Read 97035 spots for ERR6133466.sra Written 97035 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra Rejected 97028 READS because READLEN < 1 Read 97028 spots for ERR6133466.sra Written 97028 spots for ERR6133466.sra SRR ids: ['ERR6133466.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_p2w1qb91 ERR6133466.sra spots: 1940567 blocks: [[1, 97028], [97029, 194056], [194057, 291084], [291085, 388112], [388113, 485140], [485141, 582168], [582169, 679196], [679197, 776224], [776225, 873252], [873253, 970280], [970281, 1067308], [1067309, 1164336], [1164337, 1261364], [1261365, 1358392], [1358393, 1455420], [1455421, 1552448], [1552449, 1649476], [1649477, 1746504], [1746505, 1843532], [1843533, 1940567]] ERR6133466 file size 426520 ERR6133466 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 ERR6133466 ERR6133466_1.fastq Input file: ERR6133466_1.fastq trimmed: ERR6133466-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 06:38:19 2024 >> started Sat Dec 7 06:38:20 2024 >> done (1.096s) 1940567 reads processed; of these: 85 ( 0.00%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 1940471 (100.00%) reads available; of these: 27979 ( 1.44%) trimmed reads available after processing 1912492 (98.56%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 22 0.00% 19 30 0.00% 20 10 0.00% 21 18 0.00% 22 14 0.00% 23 2 0.00% 24 7 0.00% 25 2 0.00% 26 4 0.00% 27 8 0.00% 28 12 0.00% 29 56 0.00% 30 6 0.00% 31 13 0.00% 32 19 0.00% 33 8 0.00% 34 5 0.00% 35 56 0.00% 36 217 0.01% 37 8 0.00% 38 17 0.00% 39 75 0.00% 40 55 0.00% 41 19 0.00% 42 3 0.00% 43 6 0.00% 44 12 0.00% 45 7 0.00% 46 4 0.00% 47 4 0.00% 48 3 0.00% 49 10 0.00% 50 9 0.00% 51 21 0.00% 52 10 0.00% 53 4 0.00% 54 6 0.00% 55 8 0.00% 56 1 0.00% 57 6 0.00% 58 4 0.00% 59 6 0.00% 60 10 0.00% 61 6 0.00% 62 1 0.00% 63 0 0.00% 64 6 0.00% 65 3 0.00% 66 2 0.00% 67 7 0.00% 68 29 0.00% 69 71 0.00% 70 7937 0.41% 71 6962 0.36% 72 7415 0.38% 73 6676 0.34% 74 7349 0.38% 75 6864 0.35% 76 6100 0.31% 77 6321 0.33% 78 7132 0.37% 79 8181 0.42% 80 7602 0.39% 81 7414 0.38% 82 7925 0.41% 83 8474 0.44% 84 6722 0.35% 85 82 0.00% 86 124 0.01% 87 176 0.01% 88 307 0.02% 89 729 0.04% 90 1553 0.08% 91 4563 0.24% 92 18457 0.95% 93 1804464 92.99% 1940471 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=3.19 fanout-score-rank=25 prefix-density=0.40 prefix-fanout=2.8 sequence=GTGTTGTGTTGT criterion=fanout-score sequence-density=0.04 sequence-density-rank=12 fanout-score=80.46 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=18.3 sequence=TTTTTTTTTTAAGAATCCTCCATTTTTGTTCTTCCACCCATGCAATAGAGAGCAAATGGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGAGTCATGGAATAATGGTGAATTCAAATGTTTAGTTCTTTAGTATAAGAAGTATAAGAA Started job on | Dec 07 06:38:33 Started mapping on | Dec 07 06:38:33 Finished on | Dec 07 06:38:38 Mapping speed, Million of reads per hour | 1397.14 Number of input reads | 1940471 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1426239 Uniquely mapped reads % | 73.50% Average mapped length | 91.58 Number of splices: Total | 64134 Number of splices: Annotated (sjdb) | 54997 Number of splices: GT/AG | 61768 Number of splices: GC/AG | 1393 Number of splices: AT/AC | 57 Number of splices: Non-canonical | 916 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.03% Deletion average length | 1.77 Insertion rate per base | 0.02% Insertion average length | 2.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 476139 % of reads mapped to multiple loci | 24.54% Number of reads mapped to too many loci | 9494 % of reads mapped to too many loci | 0.49% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.43% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 38093 38093 38093 N_multimapping 476139 476139 476139 N_noFeature 104438 118051 1361474 N_ambiguous 57296 6116 261 UnstrandedReadsAssigned:1264505 PositiveStrandReadsAssigned:1302072 NegativeStrandReadsAssigned:64504 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133466 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: ERR6133466-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,940,471 reads, 1,593,935 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 937 rounds 52973 ERR6133466.ke.tsv 35125 ERR6133466.se.tsv 88098 total ==> ERR6133466.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 26 16.2626 PNS24243 293 194 0 0 KQK14069 1603 1504 39 22.2529 KQK14071 474 375 0 0 ==> ERR6133466.se.tsv <== BRADI_1g14170v3 39 BRADI_1g53295v3 13 BRADI_1g59795v3 14 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 18 BRADI_1g09890v3 0 BRADI_1g77505v3 43 BRADI_1g48960v3 0 ERR6133466 completed mapping pipeline successfully