Starting /dee2/code/volunteer_pipeline.sh ERR6133351 current disk space = 1548356378624 free memory = 1444429796 ERR6133351 SRAfilesize 350a271d3072fc644be9a6df904035e0 ERR6133351.sra ERR6133351.sra file validated ERR6133351 is single end ERR6133351 is conventional basespace ERR6133351 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133351_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.405 37.0 37.0 37.0 33.0 37.0 2 36.5935 37.0 37.0 37.0 37.0 37.0 3 36.34325 37.0 37.0 37.0 37.0 37.0 4 36.364 37.0 37.0 37.0 37.0 37.0 5 36.411 37.0 37.0 37.0 37.0 37.0 6 36.4905 37.0 37.0 37.0 37.0 37.0 7 38.583 40.0 37.0 40.0 37.0 40.0 8 38.7155 40.0 37.0 40.0 37.0 40.0 9 38.715 40.0 37.0 40.0 37.0 40.0 10-11 38.6725 40.0 37.0 40.0 37.0 40.0 12-13 38.635 40.0 37.0 40.0 37.0 40.0 14-15 38.570625 40.0 37.0 40.0 37.0 40.0 16-17 38.568250000000006 40.0 37.0 40.0 37.0 40.0 18-19 38.60625 40.0 37.0 40.0 37.0 40.0 20-21 38.356625 40.0 37.0 40.0 37.0 40.0 22-23 38.531375 40.0 37.0 40.0 37.0 40.0 24-25 38.50275 40.0 37.0 40.0 37.0 40.0 26-27 38.3905 40.0 37.0 40.0 37.0 40.0 28-29 38.33975 40.0 37.0 40.0 37.0 40.0 30-31 38.350875 40.0 37.0 40.0 37.0 40.0 32-33 38.314375 40.0 37.0 40.0 37.0 40.0 34-35 38.3055 40.0 37.0 40.0 37.0 40.0 36-37 38.114625000000004 40.0 37.0 40.0 37.0 40.0 38-39 37.858000000000004 40.0 37.0 40.0 35.0 40.0 40-41 37.833124999999995 40.0 37.0 40.0 37.0 40.0 42-43 37.822125 37.0 37.0 40.0 35.0 40.0 44-45 37.54275 37.0 37.0 40.0 33.0 40.0 46-47 37.292874999999995 37.0 37.0 40.0 33.0 40.0 48-49 37.264875 37.0 37.0 40.0 33.0 40.0 50-51 37.075874999999996 37.0 37.0 40.0 33.0 40.0 52-53 36.92075 37.0 37.0 40.0 33.0 40.0 54-55 36.703 37.0 37.0 37.0 33.0 40.0 56-57 36.492875 37.0 37.0 37.0 33.0 40.0 58-59 36.173500000000004 37.0 37.0 37.0 33.0 40.0 60-61 35.96725 37.0 37.0 37.0 33.0 40.0 62-63 35.49075 37.0 33.0 37.0 33.0 37.0 64-65 35.264624999999995 37.0 33.0 37.0 33.0 37.0 66-67 35.121375 37.0 33.0 37.0 33.0 37.0 68-69 33.65725 35.0 33.0 37.0 30.0 37.0 70-71 33.48165344762623 33.0 33.0 37.0 27.0 37.0 72-73 33.964416944191306 33.0 33.0 37.0 33.0 37.0 74-75 33.999805758671016 33.0 33.0 37.0 33.0 37.0 76-77 33.657489830650455 33.0 33.0 37.0 30.0 37.0 78-79 33.332193316365064 33.0 33.0 37.0 27.0 37.0 80-81 32.88914999632078 33.0 33.0 37.0 27.0 37.0 82-83 32.92342424860885 33.0 33.0 37.0 27.0 37.0 84-85 32.24957912326131 33.0 33.0 35.0 27.0 37.0 86-87 32.04551686317521 33.0 33.0 33.0 27.0 37.0 88-89 32.03345215245407 33.0 33.0 33.0 27.0 37.0 90-91 31.364820400329037 33.0 30.0 33.0 27.0 37.0 92-93 30.468330134357004 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 2.0 22 2.0 23 6.0 24 9.0 25 8.0 26 15.0 27 21.0 28 16.0 29 32.0 30 39.0 31 42.0 32 65.0 33 95.0 34 207.0 35 581.0 36 1101.0 37 1454.0 38 284.0 39 19.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.025 8.95 7.175 17.849999999999998 2 47.275 26.35 16.275000000000002 10.100000000000001 3 31.15 38.4 17.424999999999997 13.025 4 30.625000000000004 27.425 22.025 19.925 5 23.125 27.575 28.749999999999996 20.549999999999997 6 21.099999999999998 33.550000000000004 27.125 18.224999999999998 7 29.925 27.900000000000002 24.5 17.675 8 28.975 28.199999999999996 25.4 17.424999999999997 9 24.625 26.900000000000002 28.749999999999996 19.725 10-11 25.025 27.0625 28.9375 18.975 12-13 24.0375 27.0 29.812499999999996 19.15 14-15 22.25 27.875 30.587500000000002 19.287499999999998 16-17 23.7625 28.525 27.4125 20.3 18-19 23.9125 26.174999999999997 30.325000000000003 19.5875 20-21 24.2625 25.525 29.75 20.4625 22-23 25.825 24.9875 29.225 19.9625 24-25 24.0625 26.25 29.1875 20.5 26-27 24.0 24.975 30.575000000000003 20.45 28-29 24.325 26.424999999999997 29.212500000000002 20.0375 30-31 24.3 25.637500000000003 29.9875 20.075000000000003 32-33 23.775 25.424999999999997 30.575000000000003 20.225 34-35 23.2625 28.449999999999996 28.449999999999996 19.8375 36-37 23.8625 26.950000000000003 28.6625 20.525 38-39 23.775 24.975 30.7375 20.5125 40-41 24.3875 24.6125 31.087500000000002 19.9125 42-43 24.4 26.35 29.812499999999996 19.4375 44-45 23.225 26.4125 30.8 19.5625 46-47 23.65 26.487500000000004 29.562500000000004 20.3 48-49 23.175 25.45 30.887500000000003 20.4875 50-51 22.4625 27.325 31.137500000000003 19.075 52-53 23.200000000000003 27.150000000000002 29.375 20.275000000000002 54-55 23.275000000000002 27.037499999999998 30.225 19.4625 56-57 23.35 27.237499999999997 29.65 19.7625 58-59 23.400000000000002 27.212500000000002 29.362500000000004 20.025000000000002 60-61 24.7875 26.700000000000003 29.475 19.037499999999998 62-63 22.0875 27.700000000000003 30.4875 19.725 64-65 21.8875 29.4 30.275000000000002 18.4375 66-67 24.0375 27.0 28.787499999999998 20.175 68-69 21.8 27.1 30.8125 20.2875 70-71 23.543415612078686 26.888861044981834 30.672848014033328 18.894875328906153 72-73 23.530901722391086 27.0516717325228 30.38247213779129 19.034954407294833 74-75 23.503070624360287 27.226202661207775 29.92579324462641 19.34493346980553 76-77 22.095730918499353 27.309184993531694 29.935316946959894 20.659767141009056 78-79 23.773387413319377 26.80884469449169 31.205024205155045 18.212743687033885 80-81 22.819324950364 28.735936465916613 30.74784910655195 17.69688947716744 82-83 21.957778674196586 26.46228317870109 30.24068844964367 21.339249697458655 84-85 22.225255972696246 25.665529010238906 32.06825938566553 20.040955631399317 86-87 20.9075952837949 28.146421716479296 29.86015903482314 21.08582396490266 88-89 21.606800109679188 28.023032629558543 30.998080614203456 19.372086646558813 90-91 22.251165341376474 29.0649849191116 29.736769947902385 18.947079791609543 92-93 20.948724979435152 29.750479846449135 29.791609542089386 19.509185632026323 >>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 2.0 18 2.0 19 0.5 20 0.5 21 2.0 22 3.0 23 3.0 24 6.5 25 8.0 26 10.0 27 18.0 28 27.0 29 30.5 30 36.0 31 49.5 32 62.0 33 80.0 34 95.0 35 110.0 36 138.0 37 190.5 38 227.5 39 228.0 40 238.0 41 234.5 42 230.5 43 235.5 44 221.0 45 208.0 46 196.5 47 175.0 48 146.5 49 132.5 50 145.5 51 135.5 52 121.5 53 136.5 54 136.0 55 96.0 56 65.0 57 64.5 58 51.5 59 28.0 60 19.0 61 20.0 62 14.0 63 6.0 64 5.0 65 7.5 66 5.0 67 2.0 68 2.5 69 1.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 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 0.0 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 0.0 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 0.02586652871184687 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 19.0 71 23.0 72 20.0 73 15.0 74 30.0 75 19.0 76 16.0 77 25.0 78 23.0 79 20.0 80 25.0 81 34.0 82 25.0 83 28.0 84 31.0 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 3647.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.1 #Duplication Level Percentage of deduplicated Percentage of total 1 94.19279907084785 81.10000000000001 2 3.1068524970963995 5.35 3 1.1033681765389083 2.85 4 0.6097560975609756 2.1 5 0.23228803716608595 1.0 6 0.08710801393728224 0.44999999999999996 7 0.17421602787456447 1.05 8 0.05807200929152149 0.4 9 0.029036004645760744 0.22499999999999998 >10 0.40650406504065045 5.475 >50 0.0 0.0 >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 42 1.05 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 25 0.625 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 17 0.42500000000000004 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 16 0.4 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 16 0.4 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 14 0.35000000000000003 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 12 0.3 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 11 0.27499999999999997 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 11 0.27499999999999997 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 10 0.25 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 7 0.17500000000000002 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 6 0.15 No Hit TATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATA 6 0.15 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 6 0.15 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit GCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATA 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 5 0.125 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 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 0.025 0.0 0.0 0.0 0.0 10-11 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 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 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97171 READS because READLEN < 1 Read 97171 spots for ERR6133351.sra Written 97171 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra Rejected 97166 READS because READLEN < 1 Read 97166 spots for ERR6133351.sra Written 97166 spots for ERR6133351.sra SRR ids: ['ERR6133351.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dh10jm0f ERR6133351.sra spots: 1943325 blocks: [[1, 97166], [97167, 194332], [194333, 291498], [291499, 388664], [388665, 485830], [485831, 582996], [582997, 680162], [680163, 777328], [777329, 874494], [874495, 971660], [971661, 1068826], [1068827, 1165992], [1165993, 1263158], [1263159, 1360324], [1360325, 1457490], [1457491, 1554656], [1554657, 1651822], [1651823, 1748988], [1748989, 1846154], [1846155, 1943325]] ERR6133351 file size 425723 ERR6133351 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 ERR6133351 ERR6133351_1.fastq Input file: ERR6133351_1.fastq trimmed: ERR6133351-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 01:15:54 2024 >> started Sat Dec 7 01:15:55 2024 >> done (1.415s) 1943325 reads processed; of these: 336 ( 0.02%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 1942981 (99.98%) reads available; of these: 28565 ( 1.47%) trimmed reads available after processing 1914416 (98.53%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 26 0.00% 19 62 0.00% 20 20 0.00% 21 19 0.00% 22 28 0.00% 23 23 0.00% 24 15 0.00% 25 10 0.00% 26 20 0.00% 27 11 0.00% 28 48 0.00% 29 18 0.00% 30 19 0.00% 31 22 0.00% 32 51 0.00% 33 28 0.00% 34 16 0.00% 35 31 0.00% 36 15 0.00% 37 16 0.00% 38 25 0.00% 39 61 0.00% 40 95 0.00% 41 28 0.00% 42 20 0.00% 43 19 0.00% 44 19 0.00% 45 12 0.00% 46 12 0.00% 47 13 0.00% 48 6 0.00% 49 10 0.00% 50 25 0.00% 51 55 0.00% 52 19 0.00% 53 11 0.00% 54 9 0.00% 55 8 0.00% 56 12 0.00% 57 15 0.00% 58 12 0.00% 59 10 0.00% 60 9 0.00% 61 19 0.00% 62 1 0.00% 63 0 0.00% 64 3 0.00% 65 1 0.00% 66 3 0.00% 67 7 0.00% 68 13 0.00% 69 51 0.00% 70 9978 0.51% 71 10050 0.52% 72 9972 0.51% 73 9642 0.50% 74 9495 0.49% 75 9404 0.48% 76 9279 0.48% 77 9878 0.51% 78 9863 0.51% 79 10032 0.52% 80 10193 0.52% 81 12279 0.63% 82 12538 0.65% 83 11154 0.57% 84 12898 0.66% 85 23 0.00% 86 31 0.00% 87 78 0.00% 88 165 0.01% 89 406 0.02% 90 959 0.05% 91 3456 0.18% 92 21243 1.09% 93 1758864 90.52% 1942981 reads passed initial QC criterion=sequence-density sequence-density=2.42 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=36 prefix-density=2.43 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=199.20 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=7.1 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:16:15 Started mapping on | Dec 07 01:16:15 Finished on | Dec 07 01:16:25 Mapping speed, Million of reads per hour | 699.47 Number of input reads | 1942981 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1299666 Uniquely mapped reads % | 66.89% Average mapped length | 91.01 Number of splices: Total | 49354 Number of splices: Annotated (sjdb) | 41039 Number of splices: GT/AG | 47907 Number of splices: GC/AG | 908 Number of splices: AT/AC | 38 Number of splices: Non-canonical | 501 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.03% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.27 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 563683 % of reads mapped to multiple loci | 29.01% Number of reads mapped to too many loci | 43550 % of reads mapped to too many loci | 2.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.73% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 79632 79632 79632 N_multimapping 563683 563683 563683 N_noFeature 94371 106618 1245781 N_ambiguous 47220 5570 197 UnstrandedReadsAssigned:1158075 PositiveStrandReadsAssigned:1187478 NegativeStrandReadsAssigned:53688 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133351 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: ERR6133351-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,942,981 reads, 1,509,902 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 940 rounds 52973 ERR6133351.ke.tsv 35125 ERR6133351.se.tsv 88098 total ==> ERR6133351.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 36 23.6414 PNS24243 293 194 0 0 KQK14069 1603 1504 50 29.9534 KQK14071 474 375 0 0 ==> ERR6133351.se.tsv <== BRADI_1g14170v3 51 BRADI_1g53295v3 20 BRADI_1g59795v3 23 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 15 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 48 BRADI_1g48960v3 0 ERR6133351 completed mapping pipeline successfully