Starting /dee2/code/volunteer_pipeline.sh ERR6133399 current disk space = 1547694665728 free memory = 1362670512 ERR6133399 SRAfilesize 0c1dbbce8450d6b52869d85bb1ba11d6 ERR6133399.sra ERR6133399.sra file validated ERR6133399 is single end ERR6133399 is conventional basespace ERR6133399 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133399_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.45425 33.0 27.0 33.0 15.0 37.0 2 33.53525 33.0 33.0 37.0 27.0 37.0 3 33.88325 37.0 33.0 37.0 27.0 37.0 4 34.09875 37.0 33.0 37.0 27.0 37.0 5 34.08725 37.0 33.0 37.0 27.0 37.0 6 34.3325 37.0 33.0 37.0 27.0 37.0 7 35.3445 37.0 33.0 40.0 27.0 40.0 8 35.3365 37.0 33.0 40.0 27.0 40.0 9 35.33075 37.0 33.0 40.0 27.0 40.0 10-11 35.41225 37.0 33.0 40.0 30.0 40.0 12-13 35.224125 37.0 33.0 40.0 27.0 40.0 14-15 35.1815 37.0 33.0 40.0 27.0 40.0 16-17 34.918499999999995 37.0 33.0 37.0 27.0 40.0 18-19 34.847375 37.0 33.0 37.0 27.0 40.0 20-21 34.105375 37.0 33.0 37.0 27.0 40.0 22-23 33.857875 37.0 33.0 37.0 22.0 40.0 24-25 33.65325 37.0 33.0 37.0 22.0 40.0 26-27 33.29 37.0 33.0 37.0 22.0 40.0 28-29 32.842124999999996 37.0 33.0 37.0 22.0 40.0 30-31 32.85187500000001 37.0 33.0 37.0 22.0 40.0 32-33 32.531000000000006 37.0 33.0 37.0 22.0 40.0 34-35 31.629625 33.0 27.0 37.0 18.5 40.0 36-37 31.462625000000003 33.0 27.0 37.0 18.5 40.0 38-39 31.524 33.0 27.0 37.0 22.0 40.0 40-41 31.689625 33.0 27.0 37.0 22.0 40.0 42-43 31.31475 33.0 27.0 37.0 22.0 40.0 44-45 31.105249999999998 33.0 27.0 37.0 18.5 40.0 46-47 30.482125 33.0 27.0 37.0 15.0 37.0 48-49 30.283250000000002 33.0 27.0 37.0 15.0 37.0 50-51 29.969250000000002 33.0 27.0 37.0 15.0 37.0 52-53 29.591375 33.0 27.0 37.0 15.0 37.0 54-55 29.51425 33.0 27.0 37.0 15.0 37.0 56-57 28.87875 33.0 27.0 37.0 15.0 37.0 58-59 28.47975 33.0 27.0 35.0 15.0 37.0 60-61 28.210625 33.0 27.0 33.0 15.0 37.0 62-63 27.854374999999997 33.0 22.0 33.0 15.0 37.0 64-65 27.4045 33.0 22.0 33.0 10.5 37.0 66-67 27.0355 33.0 22.0 33.0 10.5 37.0 68-69 26.558 27.0 22.0 33.0 10.5 35.0 70-71 28.415333333333336 33.0 27.0 33.0 15.0 37.0 72-73 28.792816817333083 33.0 27.0 33.0 15.0 37.0 74-75 28.6841762548135 33.0 27.0 33.0 15.0 37.0 76-77 28.199830906923886 33.0 27.0 33.0 15.0 37.0 78-79 27.71429660039817 33.0 27.0 33.0 10.5 37.0 80-81 27.238101086698585 33.0 27.0 33.0 6.0 37.0 82-83 26.35879280623308 33.0 22.0 33.0 4.0 37.0 84-85 25.62979815529406 33.0 22.0 33.0 2.0 37.0 86-87 24.639662560257097 33.0 15.0 33.0 2.0 37.0 88-89 24.016470273165506 33.0 15.0 33.0 2.0 37.0 90-91 22.9294322442421 27.0 4.0 33.0 2.0 37.0 92-93 21.606052490626674 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 85.0 21 121.0 22 138.0 23 156.0 24 157.0 25 216.0 26 188.0 27 224.0 28 261.0 29 223.0 30 249.0 31 294.0 32 283.0 33 301.0 34 303.0 35 284.0 36 283.0 37 198.0 38 36.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.89999999999999 8.7 6.800000000000001 14.6 2 52.1 21.925 16.025 9.950000000000001 3 31.3 35.775 18.8 14.124999999999998 4 28.7 28.1 21.4 21.8 5 25.4 25.825 29.049999999999997 19.725 6 19.400000000000002 36.375 27.125 17.1 7 30.45 27.150000000000002 23.150000000000002 19.25 8 25.424999999999997 27.825 26.924999999999997 19.825 9 24.825 27.700000000000003 28.125 19.35 10-11 23.849999999999998 27.962500000000002 29.612500000000004 18.575 12-13 23.3125 29.1375 29.7 17.849999999999998 14-15 20.775 30.012499999999996 29.825000000000003 19.3875 16-17 24.1875 28.537499999999998 25.5125 21.762500000000003 18-19 23.35 24.6125 31.9625 20.075000000000003 20-21 24.637500000000003 25.0375 30.1875 20.1375 22-23 26.325 24.175 28.462500000000002 21.0375 24-25 24.1625 25.25 29.362500000000004 21.224999999999998 26-27 23.7625 25.1 30.599999999999998 20.5375 28-29 23.200000000000003 27.3 29.825000000000003 19.675 30-31 26.437500000000004 27.325 26.737499999999997 19.5 32-33 25.2 24.0 29.1375 21.6625 34-35 22.675 30.325000000000003 27.325 19.675 36-37 23.7125 27.1125 26.2125 22.9625 38-39 26.687499999999996 24.275 29.012500000000003 20.025000000000002 40-41 24.4875 25.55 30.075000000000003 19.8875 42-43 24.3875 28.9875 27.85 18.775 44-45 23.65 26.487500000000004 28.975 20.8875 46-47 24.9875 26.55 27.125 21.337500000000002 48-49 23.5375 25.2375 29.049999999999997 22.175 50-51 22.0125 29.262500000000003 27.950000000000003 20.775 52-53 23.1875 26.6625 28.3375 21.8125 54-55 22.7375 26.650000000000002 30.7375 19.875 56-57 24.6625 27.55 27.474999999999998 20.3125 58-59 22.325 28.175 28.725 20.775 60-61 26.025 27.462500000000002 26.55 19.9625 62-63 21.0625 27.1375 31.0375 20.7625 64-65 20.6125 32.1375 27.3625 19.8875 66-67 24.0375 28.15 27.987499999999997 19.825 68-69 20.9125 27.375 28.962500000000002 22.75 70-71 22.332164328657313 27.25450901803607 28.644789579158314 21.7685370741483 72-73 23.79510471864749 26.898814029775426 29.81327277315165 19.492808478425435 74-75 24.735971497646013 28.782287822878228 28.03155617763074 18.45018450184502 76-77 22.431222008957132 25.86052463211772 28.675623800383875 23.032629558541267 78-79 23.323878287777205 28.51985559566787 28.623001547189276 19.533264569365652 80-81 21.908357198646186 31.241864097891174 28.091642801353817 18.758135902108826 82-83 23.56041639214653 27.131374357622875 26.736065357754647 22.572143892475953 84-85 21.569674319273894 25.961025093432994 30.71276027762947 21.75654030966364 86-87 21.264059989287627 29.96786288162828 27.437064809855382 21.33101231922871 88-89 20.822174611676488 26.56668452062132 30.208891269416178 22.40224959828602 90-91 24.812533476164973 28.240492769148368 26.633636850562397 20.313336904124263 92-93 20.982860203535083 30.423138725227638 28.41456882699518 20.179432244242097 >>END_MODULE >>Per sequence GC content fail #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 2.0 17 3.0 18 1.5 19 1.5 20 2.5 21 3.5 22 2.5 23 2.5 24 6.0 25 9.5 26 12.5 27 17.5 28 24.0 29 29.0 30 35.0 31 43.0 32 51.0 33 63.5 34 80.0 35 103.0 36 142.5 37 191.0 38 217.0 39 223.0 40 234.5 41 231.0 42 238.5 43 251.5 44 212.5 45 185.5 46 163.0 47 136.0 48 128.5 49 118.5 50 106.0 51 105.5 52 115.0 53 126.5 54 163.5 55 162.5 56 115.0 57 93.0 58 73.0 59 43.5 60 27.0 61 19.5 62 18.0 63 12.5 64 10.5 65 14.0 66 14.0 67 9.5 68 6.5 69 7.5 70 9.5 71 10.0 72 7.0 73 2.5 74 1.5 75 1.0 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 0.0 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 16.0 71 9.0 72 24.0 73 16.0 74 11.0 75 10.0 76 13.0 77 15.0 78 16.0 79 21.0 80 16.0 81 24.0 82 29.0 83 22.0 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 3734.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.0 #Duplication Level Percentage of deduplicated Percentage of total 1 93.17307692307692 72.675 2 2.628205128205128 4.1000000000000005 3 1.5705128205128205 3.675 4 0.8974358974358974 2.8000000000000003 5 0.3205128205128205 1.25 6 0.2884615384615385 1.35 7 0.19230769230769232 1.05 8 0.16025641025641024 1.0 9 0.09615384615384616 0.675 >10 0.641025641025641 8.674999999999999 >50 0.0 0.0 >100 0.03205128205128205 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 GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 38 0.95 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 29 0.7250000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 25 0.625 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 22 0.5499999999999999 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 22 0.5499999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 21 0.525 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 16 0.4 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 16 0.4 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 15 0.375 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 14 0.35000000000000003 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 13 0.325 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 13 0.325 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 12 0.3 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 12 0.3 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 11 0.27499999999999997 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 11 0.27499999999999997 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 9 0.22499999999999998 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 9 0.22499999999999998 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 8 0.2 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGGGCCGC 8 0.2 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 7 0.17500000000000002 No Hit GTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCA 7 0.17500000000000002 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 7 0.17500000000000002 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 6 0.15 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 6 0.15 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 5 0.125 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 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 0.025 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 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 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 0.0125 0.0 0.0 0.0 66-67 0.025 0.025 0.0 0.0 0.0 68-69 0.025 0.025 0.0 0.0 0.0 70-71 0.025 0.025 0.0 0.0 0.0 72-73 0.025 0.025 0.0 0.0 0.0 74-75 0.025 0.025 0.0 0.0 0.0 76-77 0.025 0.025 0.0 0.0 0.0 78-79 0.025 0.025 0.0 0.0 0.0 80-81 0.025 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66160 READS because READLEN < 1 Read 66160 spots for ERR6133399.sra Written 66160 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra Rejected 66159 READS because READLEN < 1 Read 66159 spots for ERR6133399.sra Written 66159 spots for ERR6133399.sra SRR ids: ['ERR6133399.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_djpls23o ERR6133399.sra spots: 1323181 blocks: [[1, 66159], [66160, 132318], [132319, 198477], [198478, 264636], [264637, 330795], [330796, 396954], [396955, 463113], [463114, 529272], [529273, 595431], [595432, 661590], [661591, 727749], [727750, 793908], [793909, 860067], [860068, 926226], [926227, 992385], [992386, 1058544], [1058545, 1124703], [1124704, 1190862], [1190863, 1257021], [1257022, 1323181]] ERR6133399 file size 289880 ERR6133399 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 ERR6133399 ERR6133399_1.fastq Input file: ERR6133399_1.fastq trimmed: ERR6133399-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 03:09:30 2024 >> started Sat Dec 7 03:09:31 2024 >> done (1.092s) 1323181 reads processed; of these: 16 ( 0.00%) short reads filtered out after trimming by size control 2 ( 0.00%) empty reads filtered out after trimming by size control 1323163 (100.00%) reads available; of these: 339888 (25.69%) trimmed reads available after processing 983275 (74.31%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 2 0.00% 20 2 0.00% 21 2 0.00% 22 1 0.00% 23 0 0.00% 24 1 0.00% 25 0 0.00% 26 0 0.00% 27 1 0.00% 28 5 0.00% 29 50 0.00% 30 0 0.00% 31 1 0.00% 32 4 0.00% 33 1 0.00% 34 2 0.00% 35 1 0.00% 36 1 0.00% 37 4 0.00% 38 2 0.00% 39 6 0.00% 40 7 0.00% 41 7 0.00% 42 10 0.00% 43 13 0.00% 44 25 0.00% 45 21 0.00% 46 38 0.00% 47 48 0.00% 48 85 0.01% 49 74 0.01% 50 142 0.01% 51 183 0.01% 52 295 0.02% 53 394 0.03% 54 521 0.04% 55 699 0.05% 56 964 0.07% 57 1456 0.11% 58 972 0.07% 59 1193 0.09% 60 1465 0.11% 61 1736 0.13% 62 1915 0.14% 63 2015 0.15% 64 2316 0.18% 65 2346 0.18% 66 2412 0.18% 67 2485 0.19% 68 2228 0.17% 69 2251 0.17% 70 7067 0.53% 71 7966 0.60% 72 9086 0.69% 73 9889 0.75% 74 10007 0.76% 75 11223 0.85% 76 11753 0.89% 77 13194 1.00% 78 13661 1.03% 79 14468 1.09% 80 15808 1.19% 81 18617 1.41% 82 19937 1.51% 83 20164 1.52% 84 22781 1.72% 85 17470 1.32% 86 18075 1.37% 87 19840 1.50% 88 23299 1.76% 89 25220 1.91% 90 25765 1.95% 91 28418 2.15% 92 24967 1.89% 93 906082 68.48% 1323163 reads passed initial QC criterion=sequence-density sequence-density=3.61 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=31 prefix-density=3.71 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=18.38 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=3.4 sequence=TGAAGAAATTAGAGTGCTCAAAGCAAGCCATCGCTCTGGATACATTAGCATGGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCGGCGGATGTTGCTTATAGGACTCCGCCGGCACCTTATGAGAAATCAAAGTCTTTGGGTTCCGGGGGGAG 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 03:09:47 Started mapping on | Dec 07 03:09:47 Finished on | Dec 07 03:09:54 Mapping speed, Million of reads per hour | 680.48 Number of input reads | 1323163 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 653744 Uniquely mapped reads % | 49.41% Average mapped length | 88.73 Number of splices: Total | 33921 Number of splices: Annotated (sjdb) | 27648 Number of splices: GT/AG | 32724 Number of splices: GC/AG | 586 Number of splices: AT/AC | 28 Number of splices: Non-canonical | 583 Mismatch rate per base, % | 0.83% Deletion rate per base | 0.04% Deletion average length | 1.67 Insertion rate per base | 0.02% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 553340 % of reads mapped to multiple loci | 41.82% Number of reads mapped to too many loci | 56000 % of reads mapped to too many loci | 4.23% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.80% % of reads unmapped: other | 0.74% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 116079 116079 116079 N_multimapping 553340 553340 553340 N_noFeature 56522 62853 626396 N_ambiguous 24542 3502 117 UnstrandedReadsAssigned:572680 PositiveStrandReadsAssigned:587389 NegativeStrandReadsAssigned:27231 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=86 echo kmer=81 ERR6133399 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: ERR6133399-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,323,163 reads, 905,877 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 890 rounds 52973 ERR6133399.ke.tsv 35125 ERR6133399.se.tsv 88098 total ==> ERR6133399.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 6 6.29108 PNS24243 293 194 0 0 KQK14069 1603 1504 16 15.3038 KQK14071 474 375 0 0 ==> ERR6133399.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 7 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 7 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 24 BRADI_1g48960v3 0 ERR6133399 completed mapping pipeline successfully