Starting /dee2/code/volunteer_pipeline.sh ERR6133439 current disk space = 1546013925376 free memory = 1602170904 ERR6133439 SRAfilesize 498436b6b122a9dd8324fa76917517f4 ERR6133439.sra ERR6133439.sra file validated ERR6133439 is single end ERR6133439 is conventional basespace ERR6133439 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133439_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 35.21775 37.0 33.0 37.0 33.0 37.0 2 36.30125 37.0 37.0 37.0 33.0 37.0 3 35.6425 37.0 37.0 37.0 33.0 37.0 4 35.27675 37.0 37.0 37.0 33.0 37.0 5 35.14925 37.0 37.0 37.0 33.0 37.0 6 35.57275 37.0 37.0 37.0 33.0 37.0 7 37.1325 37.0 37.0 40.0 33.0 40.0 8 37.13325 37.0 37.0 40.0 33.0 40.0 9 37.106 37.0 37.0 40.0 33.0 40.0 10-11 37.034875 37.0 37.0 40.0 33.0 40.0 12-13 36.9815 37.0 37.0 40.0 33.0 40.0 14-15 36.995000000000005 37.0 37.0 40.0 33.0 40.0 16-17 36.8785 37.0 37.0 40.0 33.0 40.0 18-19 37.020624999999995 37.0 37.0 40.0 33.0 40.0 20-21 37.32225 37.0 37.0 40.0 33.0 40.0 22-23 37.125625 37.0 37.0 40.0 33.0 40.0 24-25 37.1345 37.0 37.0 40.0 33.0 40.0 26-27 36.987875 37.0 37.0 40.0 33.0 40.0 28-29 37.1175 37.0 37.0 40.0 33.0 40.0 30-31 37.086875 37.0 37.0 40.0 33.0 40.0 32-33 37.073499999999996 37.0 37.0 40.0 33.0 40.0 34-35 36.93425 37.0 37.0 40.0 33.0 40.0 36-37 36.817375 37.0 37.0 40.0 33.0 40.0 38-39 36.67975 37.0 37.0 40.0 33.0 40.0 40-41 36.667874999999995 37.0 37.0 40.0 33.0 40.0 42-43 36.522125 37.0 37.0 40.0 33.0 40.0 44-45 36.3545 37.0 37.0 40.0 33.0 40.0 46-47 36.327124999999995 37.0 37.0 38.5 33.0 40.0 48-49 36.09075 37.0 37.0 37.0 33.0 40.0 50-51 35.954625 37.0 35.0 37.0 33.0 40.0 52-53 35.795 37.0 33.0 37.0 33.0 40.0 54-55 35.666375 37.0 33.0 37.0 33.0 40.0 56-57 35.514875 37.0 33.0 37.0 33.0 38.5 58-59 35.06075 37.0 33.0 37.0 33.0 37.0 60-61 34.92725 37.0 33.0 37.0 33.0 37.0 62-63 34.974625 37.0 33.0 37.0 33.0 37.0 64-65 34.547875 37.0 33.0 37.0 33.0 37.0 66-67 34.488875 37.0 33.0 37.0 33.0 37.0 68-69 33.116 35.0 33.0 35.0 30.0 37.0 70-71 33.49611538703192 35.0 33.0 37.0 27.0 37.0 72-73 34.199659286413066 37.0 33.0 37.0 33.0 37.0 74-75 34.44277452917396 37.0 33.0 37.0 33.0 37.0 76-77 34.35379391956643 37.0 33.0 37.0 33.0 37.0 78-79 34.284765593062474 37.0 33.0 37.0 33.0 37.0 80-81 34.238852029385725 37.0 33.0 37.0 33.0 37.0 82-83 34.013995500319325 37.0 33.0 37.0 27.0 37.0 84-85 34.10597006361344 37.0 33.0 37.0 33.0 37.0 86-87 34.02666666666667 37.0 33.0 37.0 27.0 37.0 88-89 33.9691156462585 37.0 33.0 37.0 30.0 37.0 90-91 33.94163265306122 37.0 33.0 37.0 30.0 37.0 92-93 33.76163265306123 35.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 13.0 22 7.0 23 17.0 24 12.0 25 24.0 26 30.0 27 26.0 28 46.0 29 58.0 30 75.0 31 89.0 32 151.0 33 199.0 34 238.0 35 480.0 36 943.0 37 1065.0 38 513.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 90.225 2.075 2.6 5.1 2 75.08131098323743 14.310733049787341 6.805103827870903 3.802852139104328 3 38.05 39.775 13.125 9.049999999999999 4 32.45 29.175 19.775000000000002 18.6 5 23.875 32.725 24.349999999999998 19.05 6 20.65 37.625 27.250000000000004 14.475 7 38.7 27.85 18.025 15.425 8 31.900000000000002 31.424999999999997 22.875 13.8 9 27.950000000000003 27.700000000000003 27.450000000000003 16.900000000000002 10-11 25.85 28.512500000000003 28.3875 17.25 12-13 28.075 26.2875 29.5375 16.1 14-15 22.0125 29.25 30.837500000000002 17.9 16-17 23.0125 32.925 26.5625 17.5 18-19 23.4625 27.237499999999997 30.0875 19.2125 20-21 23.3375 26.325 30.2375 20.1 22-23 25.324999999999996 24.4125 28.5875 21.675 24-25 24.3 24.349999999999998 29.575000000000003 21.775 26-27 23.962500000000002 25.324999999999996 31.825 18.8875 28-29 23.9375 26.8625 29.15 20.05 30-31 25.0 25.0125 30.1875 19.8 32-33 23.8375 27.0125 28.975 20.175 34-35 23.75 25.9625 29.65 20.6375 36-37 24.474999999999998 26.125 28.487499999999997 20.9125 38-39 25.2125 25.637500000000003 29.7875 19.3625 40-41 24.762500000000003 24.9 29.599999999999998 20.7375 42-43 24.3 27.9375 29.375 18.387500000000003 44-45 22.900000000000002 25.6 31.087500000000002 20.4125 46-47 23.925 25.0125 29.612500000000004 21.45 48-49 22.925 25.8125 31.5125 19.75 50-51 22.975 27.5875 30.175 19.2625 52-53 23.075000000000003 28.1125 28.7375 20.075000000000003 54-55 23.0125 27.5125 30.1375 19.3375 56-57 23.1125 26.4125 31.075000000000003 19.400000000000002 58-59 22.2125 26.4625 30.975 20.349999999999998 60-61 23.3625 27.150000000000002 30.5125 18.975 62-63 21.6125 28.299999999999997 31.775 18.3125 64-65 23.225 27.4125 31.0 18.3625 66-67 22.912499999999998 27.700000000000003 30.362499999999997 19.025 68-69 22.912499999999998 26.525 30.95 19.6125 70-71 23.323724777541045 25.554580774533147 30.392279734302548 20.729414713623264 72-73 24.879594423320658 26.197718631178706 30.773130544993666 18.149556400506974 74-75 22.637644046094753 26.197183098591548 30.460947503201023 20.704225352112676 76-77 22.55104678211424 26.94494701473249 29.83975187386922 20.664254329284052 78-79 23.0145230930263 25.892973963103493 31.83304984953552 19.259453094334685 80-81 22.563153022087025 28.594101309350616 29.49345324692501 19.349292421637347 82-83 22.709003215434084 27.116827438370844 30.640407288317256 19.533762057877812 84-85 22.541706225417062 25.52556625525566 31.98155431981554 19.951173199511732 86-87 22.095238095238095 26.95238095238095 31.700680272108844 19.25170068027211 88-89 19.98639455782313 30.149659863945576 31.22448979591837 18.639455782312925 90-91 23.238095238095237 28.952380952380953 29.333333333333332 18.476190476190478 92-93 19.877551020408163 30.476190476190478 30.7891156462585 18.857142857142858 >>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 3.5 18 3.5 19 1.0 20 1.0 21 2.0 22 2.0 23 4.5 24 9.5 25 8.5 26 12.0 27 16.5 28 27.0 29 37.5 30 39.5 31 51.5 32 70.0 33 100.0 34 115.0 35 130.5 36 147.5 37 168.0 38 203.5 39 208.5 40 212.0 41 223.5 42 214.5 43 204.5 44 212.0 45 208.0 46 201.5 47 188.5 48 155.5 49 133.0 50 139.5 51 138.0 52 108.0 53 116.0 54 111.5 55 71.5 56 57.5 57 56.0 58 44.0 59 32.0 60 33.0 61 28.0 62 19.0 63 19.5 64 19.5 65 15.5 66 13.5 67 10.0 68 9.0 69 7.0 70 3.0 71 2.0 72 2.5 73 2.0 74 1.0 75 0.5 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 0.5 89 0.5 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 0.075 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 0.013561160835367509 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 21.0 71 24.0 72 20.0 73 21.0 74 18.0 75 19.0 76 16.0 77 27.0 78 25.0 79 20.0 80 17.0 81 27.0 82 26.0 83 20.0 84 24.0 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 3675.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.55 #Duplication Level Percentage of deduplicated Percentage of total 1 92.28007181328546 77.10000000000001 2 4.248952722920407 7.1 3 1.765409934171155 4.425 4 0.47875523638539796 1.6 5 0.23937761819269898 1.0 6 0.17953321364452424 0.8999999999999999 7 0.20945541591861158 1.225 8 0.059844404548174746 0.4 9 0.08976660682226212 0.675 >10 0.4488330341113106 5.575 >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 warn #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 26 0.65 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 20 0.5 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 16 0.4 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 15 0.375 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 15 0.375 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 11 0.27499999999999997 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 11 0.27499999999999997 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 10 0.25 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 10 0.25 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 10 0.25 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 9 0.22499999999999998 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 9 0.22499999999999998 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 7 0.17500000000000002 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 7 0.17500000000000002 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 7 0.17500000000000002 No Hit GGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCAT 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit CCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTT 7 0.17500000000000002 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGGACGGACGAGTACTATATATACTACTCCTATATTGCAGTGACAATGGA 6 0.15 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 6 0.15 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 6 0.15 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GGAGGAGAGCGGCGGCGGTCTGTTCAAGATGGCTCAGGGCTTCATGAAGT 5 0.125 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACC 5 0.125 No Hit GAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAACACAGGG 5 0.125 No Hit GGAACAATTATTATATATTTCAAGTTATTTCGGATCTTTCTTAATCTTCA 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 0.0125 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 0.037500000000000006 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 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGCTCG 15 9.207688E-4 85.8 1 >>END_MODULE Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra Rejected 176072 READS because READLEN < 1 Read 176072 spots for ERR6133439.sra Written 176072 spots for ERR6133439.sra Rejected 176069 READS because READLEN < 1 Read 176069 spots for ERR6133439.sra Written 176069 spots for ERR6133439.sra SRR ids: ['ERR6133439.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gea5ssem ERR6133439.sra spots: 3521383 blocks: [[1, 176069], [176070, 352138], [352139, 528207], [528208, 704276], [704277, 880345], [880346, 1056414], [1056415, 1232483], [1232484, 1408552], [1408553, 1584621], [1584622, 1760690], [1760691, 1936759], [1936760, 2112828], [2112829, 2288897], [2288898, 2464966], [2464967, 2641035], [2641036, 2817104], [2817105, 2993173], [2993174, 3169242], [3169243, 3345311], [3345312, 3521383]] ERR6133439 file size 771985 ERR6133439 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 ERR6133439 ERR6133439_1.fastq Input file: ERR6133439_1.fastq trimmed: ERR6133439-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 05:40:57 2024 >> started Sat Dec 7 05:40:58 2024 >> done (1.856s) 3521383 reads processed; of these: 1107 ( 0.03%) short reads filtered out after trimming by size control 23 ( 0.00%) empty reads filtered out after trimming by size control 3520253 (99.97%) reads available; of these: 43164 ( 1.23%) trimmed reads available after processing 3477089 (98.77%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 35 0.00% 19 54 0.00% 20 28 0.00% 21 16 0.00% 22 16 0.00% 23 3 0.00% 24 14 0.00% 25 5 0.00% 26 10 0.00% 27 13 0.00% 28 7 0.00% 29 88 0.00% 30 9 0.00% 31 3 0.00% 32 26 0.00% 33 3 0.00% 34 8 0.00% 35 7 0.00% 36 10 0.00% 37 11 0.00% 38 25 0.00% 39 56 0.00% 40 125 0.00% 41 27 0.00% 42 13 0.00% 43 41 0.00% 44 17 0.00% 45 14 0.00% 46 11 0.00% 47 15 0.00% 48 10 0.00% 49 19 0.00% 50 23 0.00% 51 49 0.00% 52 23 0.00% 53 18 0.00% 54 17 0.00% 55 21 0.00% 56 8 0.00% 57 17 0.00% 58 14 0.00% 59 9 0.00% 60 32 0.00% 61 19 0.00% 62 7 0.00% 63 6 0.00% 64 6 0.00% 65 10 0.00% 66 11 0.00% 67 31 0.00% 68 65 0.00% 69 263 0.01% 70 21896 0.62% 71 20573 0.58% 72 20476 0.58% 73 19151 0.54% 74 20833 0.59% 75 20188 0.57% 76 18324 0.52% 77 18904 0.54% 78 21369 0.61% 79 24141 0.69% 80 21861 0.62% 81 22742 0.65% 82 24582 0.70% 83 24833 0.71% 84 19831 0.56% 85 71 0.00% 86 154 0.00% 87 208 0.01% 88 395 0.01% 89 956 0.03% 90 2129 0.06% 91 6625 0.19% 92 27925 0.79% 93 3160698 89.79% 3520253 reads passed initial QC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=3.21 fanout-score-rank=32 prefix-density=0.46 prefix-fanout=2.9 sequence=GTGTTGTGTTGT criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=231.40 fanout-score-rank=1 prefix-density=0.56 prefix-fanout=6.3 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAA Started job on | Dec 07 05:41:15 Started mapping on | Dec 07 05:41:16 Finished on | Dec 07 05:41:21 Mapping speed, Million of reads per hour | 2534.58 Number of input reads | 3520253 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 2724697 Uniquely mapped reads % | 77.40% Average mapped length | 91.04 Number of splices: Total | 77487 Number of splices: Annotated (sjdb) | 63463 Number of splices: GT/AG | 73352 Number of splices: GC/AG | 2570 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 1536 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 1.72 Insertion rate per base | 0.02% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 726072 % of reads mapped to multiple loci | 20.63% Number of reads mapped to too many loci | 21786 % of reads mapped to too many loci | 0.62% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.31% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 69484 69484 69484 N_multimapping 726072 726072 726072 N_noFeature 204658 233132 2594682 N_ambiguous 114063 12584 567 UnstrandedReadsAssigned:2405976 PositiveStrandReadsAssigned:2478981 NegativeStrandReadsAssigned:129448 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133439 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: ERR6133439-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,520,253 reads, 2,919,567 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 997 rounds 52973 ERR6133439.ke.tsv 35125 ERR6133439.se.tsv 88098 total ==> ERR6133439.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 63 21.8749 PNS24243 293 194 0 0 KQK14069 1603 1504 523 165.659 KQK14071 474 375 0 0 ==> ERR6133439.se.tsv <== BRADI_1g14170v3 523 BRADI_1g53295v3 41 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 21 BRADI_1g74790v3 19 BRADI_1g09890v3 1 BRADI_1g77505v3 68 BRADI_1g48960v3 0 ERR6133439 completed mapping pipeline successfully