Starting /dee2/code/volunteer_pipeline.sh ERR6133479 current disk space = 1544873119744 free memory = 1474013864 ERR6133479 SRAfilesize be4772d779d2c74fe5310a8cdb60423d ERR6133479.sra ERR6133479.sra file validated ERR6133479 is single end ERR6133479 is conventional basespace ERR6133479 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133479_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.5215 37.0 33.0 37.0 33.0 37.0 2 36.41325 37.0 37.0 37.0 37.0 37.0 3 35.7035 37.0 37.0 37.0 33.0 37.0 4 35.18225 37.0 37.0 37.0 33.0 37.0 5 35.0515 37.0 37.0 37.0 33.0 37.0 6 35.41375 37.0 37.0 37.0 33.0 37.0 7 37.113 37.0 37.0 40.0 33.0 40.0 8 37.11925 37.0 37.0 40.0 33.0 40.0 9 37.20575 37.0 37.0 40.0 33.0 40.0 10-11 37.182 37.0 37.0 40.0 33.0 40.0 12-13 37.07925 37.0 37.0 40.0 33.0 40.0 14-15 37.077125 37.0 37.0 40.0 33.0 40.0 16-17 36.956125 37.0 37.0 40.0 33.0 40.0 18-19 36.770624999999995 37.0 37.0 40.0 33.0 40.0 20-21 36.472875 37.0 37.0 40.0 33.0 40.0 22-23 36.47225 37.0 37.0 40.0 33.0 40.0 24-25 36.389375 37.0 37.0 40.0 33.0 40.0 26-27 36.662625 37.0 37.0 40.0 33.0 40.0 28-29 36.59575 37.0 37.0 40.0 33.0 40.0 30-31 36.57425 37.0 37.0 40.0 33.0 40.0 32-33 36.389875 37.0 37.0 40.0 33.0 40.0 34-35 36.388374999999996 37.0 37.0 40.0 33.0 40.0 36-37 36.228875 37.0 37.0 40.0 33.0 40.0 38-39 36.151250000000005 37.0 37.0 40.0 33.0 40.0 40-41 35.966875 37.0 35.0 40.0 33.0 40.0 42-43 35.939375 37.0 35.0 40.0 33.0 40.0 44-45 35.918625000000006 37.0 35.0 40.0 33.0 40.0 46-47 35.75475 37.0 33.0 37.0 33.0 40.0 48-49 35.647499999999994 37.0 33.0 37.0 33.0 40.0 50-51 35.485 37.0 33.0 37.0 33.0 40.0 52-53 35.1665 37.0 33.0 37.0 33.0 40.0 54-55 35.143249999999995 37.0 33.0 37.0 33.0 38.5 56-57 34.887 37.0 33.0 37.0 33.0 37.0 58-59 33.9435 37.0 33.0 37.0 27.0 37.0 60-61 34.4875 37.0 33.0 37.0 27.0 37.0 62-63 34.4265 37.0 33.0 37.0 27.0 37.0 64-65 34.452124999999995 37.0 33.0 37.0 30.0 37.0 66-67 34.3765 37.0 33.0 37.0 30.0 37.0 68-69 33.6045 35.0 33.0 37.0 27.0 37.0 70-71 33.739110353029545 35.0 33.0 37.0 27.0 37.0 72-73 34.14109317062686 37.0 33.0 37.0 27.0 37.0 74-75 33.993717014325206 37.0 33.0 37.0 27.0 37.0 76-77 33.877756480649566 37.0 33.0 37.0 27.0 37.0 78-79 33.86401426308104 37.0 33.0 37.0 27.0 37.0 80-81 33.730955500517766 37.0 33.0 37.0 27.0 37.0 82-83 33.5614244077147 37.0 33.0 37.0 27.0 37.0 84-85 33.36539513191634 35.0 33.0 37.0 27.0 37.0 86-87 33.25508388408744 35.0 33.0 37.0 27.0 37.0 88-89 33.38459583121505 37.0 33.0 37.0 27.0 37.0 90-91 33.18784951703101 33.0 33.0 37.0 27.0 37.0 92-93 33.1314184036604 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 11.0 21 15.0 22 18.0 23 21.0 24 33.0 25 28.0 26 39.0 27 52.0 28 60.0 29 64.0 30 105.0 31 111.0 32 147.0 33 191.0 34 249.0 35 520.0 36 894.0 37 962.0 38 473.0 39 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.8 2.725 2.5749999999999997 5.8999999999999995 2 73.65 16.375 5.8999999999999995 4.075 3 37.574999999999996 37.55 13.700000000000001 11.175 4 34.325 29.075 17.5 19.1 5 26.924999999999997 29.9 24.75 18.425 6 20.4 38.175 24.85 16.575 7 38.725 28.925 16.950000000000003 15.4 8 29.599999999999998 29.7 22.2 18.5 9 25.4 29.175 28.025 17.4 10-11 25.324999999999996 26.525 29.25 18.9 12-13 28.1125 26.35 26.0 19.537499999999998 14-15 21.325 31.775 27.775 19.125 16-17 24.5625 31.525 24.0125 19.900000000000002 18-19 24.95 27.35 26.875 20.825 20-21 25.5375 25.575 29.762499999999996 19.125 22-23 28.225 22.912499999999998 27.150000000000002 21.712500000000002 24-25 25.474999999999998 25.3 27.1125 22.112499999999997 26-27 26.0375 23.95 30.9375 19.075 28-29 25.8 28.675 26.525 19.0 30-31 27.875 25.0625 26.85 20.2125 32-33 25.0375 26.5 26.724999999999998 21.7375 34-35 24.5 28.275 26.450000000000003 20.775 36-37 25.8 24.224999999999998 27.3625 22.6125 38-39 27.965995749468686 23.777972246530815 29.503687960995123 18.752344043005376 40-41 26.8375 24.375 27.150000000000002 21.637500000000003 42-43 24.975 27.900000000000002 26.7125 20.4125 44-45 24.4125 24.825 29.7375 21.025 46-47 25.35 23.6375 27.6625 23.35 48-49 25.5 25.0 29.475 20.025000000000002 50-51 24.2875 27.150000000000002 28.1125 20.45 52-53 25.37575150300601 25.789078156312623 26.01452905811623 22.82064128256513 54-55 23.50587646911728 26.469117279319832 30.132533133283324 19.892473118279568 56-57 28.069517379344838 25.693923480870218 26.93173293323331 19.30482620655164 58-59 23.7375 26.087500000000002 28.8875 21.2875 60-61 26.450000000000003 23.974999999999998 29.562500000000004 20.0125 62-63 21.425 27.35 31.775 19.45 64-65 23.5625 28.6875 29.012500000000003 18.7375 66-67 25.374999999999996 27.437499999999996 26.9125 20.275000000000002 68-69 21.349999999999998 26.1125 28.849999999999998 23.6875 70-71 24.20565424068051 25.31898924193145 27.995996997748314 22.47935951963973 72-73 26.802959989966133 23.403988461056063 29.085664116392824 20.707387432584976 74-75 23.93817542096004 26.966574516210102 29.71852224176929 19.37672782106057 76-77 22.80966767371601 25.264350453172206 28.323262839879153 23.602719033232628 78-79 24.646821392532793 24.419778002018163 29.98234106962664 20.951059535822402 80-81 22.014406672564135 30.67104764311892 29.255655250853025 18.05889043346392 82-83 23.93617021276596 24.620060790273556 29.926545086119553 21.517223910840933 84-85 22.611788617886177 23.01829268292683 32.40599593495935 21.963922764227643 86-87 22.890188103711235 26.105744789018807 30.859176410777835 20.14489069649212 88-89 21.26334519572954 28.800203355363497 30.643111337061512 19.29334011184545 90-91 26.931875953228268 25.521098118962886 28.990849008642606 18.55617691916624 92-93 21.51753940010168 27.7198779867819 30.973563802745296 19.78901881037112 >>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 1.0 17 8.0 18 9.0 19 2.5 20 2.5 21 2.5 22 3.5 23 3.5 24 2.5 25 3.5 26 5.5 27 9.0 28 14.0 29 18.0 30 26.5 31 31.5 32 43.5 33 64.5 34 69.0 35 65.5 36 89.0 37 135.5 38 176.0 39 186.0 40 176.0 41 183.5 42 202.0 43 212.5 44 194.5 45 183.5 46 200.5 47 188.5 48 185.0 49 178.0 50 164.0 51 166.5 52 142.5 53 134.0 54 164.5 55 126.5 56 63.5 57 63.0 58 51.5 59 46.0 60 48.5 61 43.5 62 39.5 63 33.5 64 28.5 65 24.5 66 21.5 67 16.5 68 15.5 69 14.0 70 6.5 71 4.0 72 3.5 73 6.0 74 7.5 75 5.0 76 3.0 77 1.5 78 0.5 79 0.0 80 0.5 81 0.5 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 0.0125 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 0.2 54-55 0.025 56-57 0.025 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 5.0 72 5.0 73 5.0 74 0.0 75 4.0 76 6.0 77 4.0 78 2.0 79 5.0 80 3.0 81 6.0 82 2.0 83 9.0 84 4.0 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 3934.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.05 #Duplication Level Percentage of deduplicated Percentage of total 1 92.47242050616484 71.25 2 3.9909149902660612 6.15 3 1.2654120700843607 2.9250000000000003 4 0.6164828033744322 1.9 5 0.42180402336145356 1.625 6 0.16223231667748217 0.75 7 0.12978585334198572 0.7000000000000001 8 0.16223231667748217 1.0 9 0.0973393900064893 0.675 >10 0.6164828033744322 8.875 >50 0.03244646333549643 1.4000000000000001 >100 0.03244646333549643 2.75 >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 110 2.75 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 56 1.4000000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 41 1.0250000000000001 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 38 0.95 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 33 0.8250000000000001 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 24 0.6 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 21 0.525 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 19 0.475 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 18 0.44999999999999996 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 17 0.42500000000000004 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 15 0.375 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 14 0.35000000000000003 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 12 0.3 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 10 0.25 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 9 0.22499999999999998 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 8 0.2 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 7 0.17500000000000002 No Hit GGACAGCTCCGTATTAAGATGGACCATATATAAAGTGTCAGCTCAGTTTT 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GGAAATAAGCAACACAAGCTCCAGCACAGCAATGTCTTTGCTTCTGTGAT 6 0.15 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GGAGGTAAAGGAGCACAACAAGGTAATTTGCCCGTCCCAGAAGGTTGCAC 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGGAGATGCTAACTCAGATGCCATGAAGACTGGTTCCTTCTACGGTTAGA 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.025 0.0 0.0 0.0 0.0 14-15 0.037500000000000006 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.0625 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.125 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.1375 0.0 0.0 0.0 0.0 38-39 0.16249999999999998 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.175 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.175 0.0 0.0 0.0 0.0 48-49 0.175 0.0 0.0 0.0 0.0 50-51 0.175 0.0 0.0 0.0 0.0 52-53 0.175 0.0 0.0 0.0 0.0 54-55 0.175 0.0 0.0 0.0 0.0 56-57 0.175 0.0 0.0 0.0 0.0 58-59 0.2 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.2 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra Rejected 92992 READS because READLEN < 1 Read 92992 spots for ERR6133479.sra Written 92992 spots for ERR6133479.sra Rejected 92986 READS because READLEN < 1 Read 92986 spots for ERR6133479.sra Written 92986 spots for ERR6133479.sra SRR ids: ['ERR6133479.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rrjaba0m ERR6133479.sra spots: 1859726 blocks: [[1, 92986], [92987, 185972], [185973, 278958], [278959, 371944], [371945, 464930], [464931, 557916], [557917, 650902], [650903, 743888], [743889, 836874], [836875, 929860], [929861, 1022846], [1022847, 1115832], [1115833, 1208818], [1208819, 1301804], [1301805, 1394790], [1394791, 1487776], [1487777, 1580762], [1580763, 1673748], [1673749, 1766734], [1766735, 1859726]] ERR6133479 file size 410799 ERR6133479 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 ERR6133479 ERR6133479_1.fastq Input file: ERR6133479_1.fastq trimmed: ERR6133479-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 06:58:28 2024 >> started Sat Dec 7 06:58:33 2024 >> done (5.420s) 1859726 reads processed; of these: 268 ( 0.01%) short reads filtered out after trimming by size control 19 ( 0.00%) empty reads filtered out after trimming by size control 1859439 (99.98%) reads available; of these: 32736 ( 1.76%) trimmed reads available after processing 1826703 (98.24%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 19 0.00% 19 51 0.00% 20 17 0.00% 21 30 0.00% 22 44 0.00% 23 5 0.00% 24 10 0.00% 25 10 0.00% 26 13 0.00% 27 11 0.00% 28 74 0.00% 29 95 0.01% 30 23 0.00% 31 30 0.00% 32 21 0.00% 33 29 0.00% 34 26 0.00% 35 113 0.01% 36 439 0.02% 37 5 0.00% 38 23 0.00% 39 95 0.01% 40 37 0.00% 41 45 0.00% 42 4 0.00% 43 9 0.00% 44 24 0.00% 45 12 0.00% 46 15 0.00% 47 7 0.00% 48 10 0.00% 49 4 0.00% 50 6 0.00% 51 30 0.00% 52 6 0.00% 53 4 0.00% 54 1 0.00% 55 5 0.00% 56 10 0.00% 57 20 0.00% 58 7 0.00% 59 4 0.00% 60 6 0.00% 61 5 0.00% 62 2 0.00% 63 4 0.00% 64 3 0.00% 65 1 0.00% 66 6 0.00% 67 3 0.00% 68 10 0.00% 69 31 0.00% 70 2643 0.14% 71 2374 0.13% 72 2376 0.13% 73 2150 0.12% 74 2367 0.13% 75 2369 0.13% 76 2112 0.11% 77 2157 0.12% 78 2218 0.12% 79 2452 0.13% 80 2158 0.12% 81 2308 0.12% 82 2852 0.15% 83 2898 0.16% 84 2180 0.12% 85 71 0.00% 86 131 0.01% 87 239 0.01% 88 393 0.02% 89 739 0.04% 90 1553 0.08% 91 4697 0.25% 92 22689 1.22% 93 1791799 96.36% 1859439 reads passed initial QC criterion=sequence-density sequence-density=0.41 sequence-density-rank=1 fanout-score=2.46 fanout-score-rank=34 prefix-density=0.47 prefix-fanout=2.1 sequence=TGTACATTTGAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=45.68 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=6.2 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGC Started job on | Dec 07 07:00:24 Started mapping on | Dec 07 07:00:25 Finished on | Dec 07 07:00:52 Mapping speed, Million of reads per hour | 247.93 Number of input reads | 1859439 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1284811 Uniquely mapped reads % | 69.10% Average mapped length | 92.36 Number of splices: Total | 63287 Number of splices: Annotated (sjdb) | 52720 Number of splices: GT/AG | 60604 Number of splices: GC/AG | 1570 Number of splices: AT/AC | 47 Number of splices: Non-canonical | 1066 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.91 Insertion rate per base | 0.02% Insertion average length | 2.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 527141 % of reads mapped to multiple loci | 28.35% Number of reads mapped to too many loci | 7973 % of reads mapped to too many loci | 0.43% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.09% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 47487 47487 47487 N_multimapping 527141 527141 527141 N_noFeature 81778 94090 1228936 N_ambiguous 48271 4771 127 UnstrandedReadsAssigned:1154762 PositiveStrandReadsAssigned:1185950 NegativeStrandReadsAssigned:55748 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133479 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: ERR6133479-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,859,439 reads, 1,539,212 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 931 rounds 52973 ERR6133479.ke.tsv 35125 ERR6133479.se.tsv 88098 total ==> ERR6133479.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 44 27.693 PNS24243 293 194 0 0 KQK14069 1603 1504 20 11.483 KQK14071 474 375 0 0 ==> ERR6133479.se.tsv <== BRADI_1g14170v3 20 BRADI_1g53295v3 11 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 10 BRADI_1g74790v3 14 BRADI_1g09890v3 0 BRADI_1g77505v3 37 BRADI_1g48960v3 0 ERR6133479 completed mapping pipeline successfully