Starting /dee2/code/volunteer_pipeline.sh ERR6133528 current disk space = 1544513646592 free memory = 1447519492 ERR6133528 SRAfilesize 6c6dac3d1bbc26ec5e3bed9393fbe908 ERR6133528.sra ERR6133528.sra file validated ERR6133528 is single end ERR6133528 is conventional basespace ERR6133528 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133528_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 33.95975 37.0 33.0 37.0 33.0 37.0 2 36.02675 37.0 37.0 37.0 33.0 37.0 3 35.13025 37.0 33.0 37.0 33.0 37.0 4 35.409 37.0 37.0 37.0 33.0 37.0 5 35.254 37.0 37.0 37.0 33.0 37.0 6 35.59475 37.0 37.0 37.0 33.0 37.0 7 37.389 37.0 37.0 40.0 33.0 40.0 8 37.43125 37.0 37.0 40.0 33.0 40.0 9 37.365 37.0 37.0 40.0 33.0 40.0 10-11 37.39 37.0 37.0 40.0 33.0 40.0 12-13 37.321625 37.0 37.0 40.0 33.0 40.0 14-15 37.439625 37.0 37.0 40.0 33.0 40.0 16-17 37.35425 37.0 37.0 40.0 33.0 40.0 18-19 37.252875 37.0 37.0 40.0 33.0 40.0 20-21 37.119625 37.0 37.0 40.0 33.0 40.0 22-23 37.1335 37.0 37.0 40.0 33.0 40.0 24-25 37.20675 37.0 37.0 40.0 33.0 40.0 26-27 37.072874999999996 37.0 37.0 40.0 33.0 40.0 28-29 36.911 37.0 37.0 40.0 33.0 40.0 30-31 36.832625 37.0 37.0 40.0 33.0 40.0 32-33 36.713499999999996 37.0 37.0 40.0 33.0 40.0 34-35 36.593625 37.0 37.0 40.0 33.0 40.0 36-37 36.411875 37.0 37.0 40.0 33.0 40.0 38-39 36.3865 37.0 37.0 40.0 33.0 40.0 40-41 36.225875 37.0 37.0 40.0 33.0 40.0 42-43 36.106625 37.0 37.0 40.0 33.0 40.0 44-45 35.829 37.0 35.0 38.5 33.0 40.0 46-47 35.429375 37.0 33.0 37.0 33.0 40.0 48-49 35.516000000000005 37.0 33.0 37.0 33.0 40.0 50-51 35.428 37.0 33.0 37.0 33.0 40.0 52-53 35.128625 37.0 33.0 37.0 33.0 40.0 54-55 35.083875 37.0 33.0 37.0 33.0 38.5 56-57 34.837875 37.0 33.0 37.0 33.0 37.0 58-59 34.248 37.0 33.0 37.0 27.0 37.0 60-61 34.431 37.0 33.0 37.0 27.0 37.0 62-63 34.438625 37.0 33.0 37.0 27.0 37.0 64-65 34.394999999999996 37.0 33.0 37.0 27.0 37.0 66-67 34.43775 37.0 33.0 37.0 27.0 37.0 68-69 33.607375000000005 35.0 33.0 37.0 27.0 37.0 70-71 33.71073948422634 35.0 33.0 37.0 27.0 37.0 72-73 34.12978125253028 37.0 33.0 37.0 27.0 37.0 74-75 34.121515047023124 37.0 33.0 37.0 27.0 37.0 76-77 33.939713639789 37.0 33.0 37.0 27.0 37.0 78-79 33.965293259884575 37.0 33.0 37.0 27.0 37.0 80-81 33.92932764052238 37.0 33.0 37.0 27.0 37.0 82-83 33.76100369167707 37.0 33.0 37.0 27.0 37.0 84-85 33.71093867760058 37.0 33.0 37.0 27.0 37.0 86-87 33.78450240567233 37.0 33.0 37.0 27.0 37.0 88-89 33.776778931375034 37.0 33.0 37.0 27.0 37.0 90-91 33.561281337047355 37.0 33.0 37.0 27.0 37.0 92-93 33.52329703722461 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 13.0 21 18.0 22 19.0 23 19.0 24 27.0 25 26.0 26 39.0 27 41.0 28 50.0 29 75.0 30 83.0 31 97.0 32 171.0 33 165.0 34 258.0 35 438.0 36 924.0 37 868.0 38 657.0 39 12.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.3 2.9000000000000004 2.675 6.125 2 73.575 16.725 5.825 3.875 3 39.25 36.3 13.675 10.775 4 33.625 29.475 16.725 20.175 5 24.925 32.074999999999996 25.575 17.424999999999997 6 19.1 39.300000000000004 24.6 17.0 7 37.0 29.775000000000002 17.625 15.6 8 30.599999999999998 30.875000000000004 22.400000000000002 16.125 9 25.900000000000002 28.975 26.775 18.35 10-11 25.362499999999997 27.625 27.787499999999998 19.225 12-13 29.8375 25.837500000000002 26.375 17.95 14-15 21.625 31.937500000000004 29.2375 17.2 16-17 23.599999999999998 31.874999999999996 26.0125 18.512500000000003 18-19 23.63090772693173 28.94473618404601 25.406351587896975 22.018004501125283 20-21 25.950475237618807 27.55127563781891 26.825912956478238 19.672336168084044 22-23 27.1125 23.2125 27.500000000000004 22.175 24-25 27.400000000000002 22.6375 28.449999999999996 21.512500000000003 26-27 26.6 25.6125 29.862499999999997 17.925 28-29 26.015751968996128 28.316039504938118 26.540817602200274 19.127390923865484 30-31 29.275000000000002 26.224999999999998 25.7 18.8 32-33 23.375 28.3125 26.387500000000003 21.925 34-35 24.185871743486974 25.851703406813627 27.680360721442888 22.28206412825651 36-37 25.025 22.7625 29.849999999999998 22.3625 38-39 26.403300412551566 25.978247280910118 29.97874734341793 17.63970496312039 40-41 27.37171464330413 24.918648310387987 25.744680851063826 21.964956195244056 42-43 24.351422484020553 29.301917533525508 25.404185988219076 20.942473994234867 44-45 23.44180225281602 24.831038798498124 29.086357947434294 22.640801001251564 46-47 25.025 22.4375 27.925 24.6125 48-49 25.4875 24.9875 30.2125 19.3125 50-51 27.287499999999998 26.387500000000003 26.8125 19.5125 52-53 25.807259073842303 28.04755944931164 25.944931163954944 20.200250312891114 54-55 22.825 29.775000000000002 27.3 20.1 56-57 26.375 24.0625 28.599999999999998 20.962500000000002 58-59 23.674999999999997 25.1 28.9 22.325 60-61 25.087500000000002 25.0 27.625 22.287499999999998 62-63 21.95 27.9125 31.5125 18.625 64-65 24.1125 26.8375 29.725 19.325 66-67 25.4875 26.8375 27.925 19.75 68-69 23.175 27.075 27.35 22.400000000000002 70-71 25.30647985989492 25.281461095821868 27.020265198899175 22.39179384538404 72-73 26.443692847300515 23.950895653263185 27.934360516096707 21.671050983339597 74-75 22.651448639157156 27.718550106609808 28.96024081274301 20.66976044149003 76-77 23.04697312233107 26.048731474503896 29.176086410449635 21.7282089927154 78-79 24.346076458752517 24.83651911468813 29.124748490945674 21.692655935613683 80-81 23.78732518583848 30.137331485447906 27.630086934610055 18.445256394103566 82-83 24.403484408534275 25.236712536295926 28.87261709380129 21.487185961368514 84-85 24.360921285750443 23.588964819033155 30.334092634776006 21.716021260440392 86-87 22.03089389718916 26.424411243352747 32.818435046847306 18.726259812610788 88-89 20.587490503925043 28.6654849328944 31.526968852874145 19.220055710306408 90-91 27.27272727272727 25.398835148138772 28.057736135730565 19.270701443403393 92-93 22.8285641934667 28.37427196758673 29.66573816155989 19.13142567738668 >>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 0.5 16 1.5 17 8.5 18 8.5 19 1.0 20 0.0 21 3.0 22 3.0 23 4.5 24 7.0 25 4.0 26 5.5 27 12.5 28 22.0 29 26.5 30 26.5 31 28.0 32 42.5 33 65.0 34 66.0 35 69.0 36 88.5 37 115.5 38 158.5 39 159.0 40 152.0 41 181.5 42 194.0 43 194.5 44 185.0 45 177.0 46 246.5 47 247.5 48 179.5 49 189.5 50 188.5 51 163.0 52 140.5 53 152.5 54 156.5 55 100.5 56 61.0 57 60.5 58 59.0 59 49.0 60 37.0 61 33.5 62 33.0 63 26.0 64 23.0 65 29.0 66 26.0 67 20.0 68 20.5 69 16.0 70 9.0 71 7.0 72 5.0 73 2.0 74 1.5 75 2.0 76 1.5 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 0.025 20-21 0.05 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0125 30-31 0.0 32-33 0.0 34-35 0.2 36-37 0.0 38-39 0.0125 40-41 0.125 42-43 0.2625 44-45 0.125 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.125 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 6.0 71 1.0 72 3.0 73 2.0 74 3.0 75 4.0 76 0.0 77 3.0 78 4.0 79 3.0 80 5.0 81 3.0 82 5.0 83 5.0 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 3949.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.97500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 91.59719906635544 68.675 2 4.434811603867956 6.65 3 1.7005668556185394 3.8249999999999997 4 0.9003001000333445 2.7 5 0.266755585195065 1.0 6 0.06668889629876625 0.3 7 0.10003334444814939 0.525 8 0.06668889629876625 0.4 9 0.06668889629876625 0.44999999999999996 >10 0.7002334111370457 10.174999999999999 >50 0.10003334444814939 5.3 >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 GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 91 2.275 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 61 1.525 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 60 1.5 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 36 0.8999999999999999 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 33 0.8250000000000001 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 29 0.7250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 25 0.625 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 25 0.625 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 24 0.6 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 20 0.5 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 19 0.475 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 18 0.44999999999999996 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 17 0.42500000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 15 0.375 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 14 0.35000000000000003 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 14 0.35000000000000003 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 13 0.325 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 13 0.325 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 11 0.27499999999999997 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 10 0.25 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 10 0.25 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 8 0.2 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 6 0.15 No Hit GGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGCAGCACCTGCAAGTGCG 6 0.15 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGACAAGAGGTGGTTCAAGGGCGCAAAGAAGTTCGTCGAGAACGCAGCCG 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 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 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377548 READS because READLEN < 1 Read 377548 spots for ERR6133528.sra Written 377548 spots for ERR6133528.sra Rejected 377551 READS because READLEN < 1 Read 377551 spots for ERR6133528.sra Written 377551 spots for ERR6133528.sra SRR ids: ['ERR6133528.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dqons699 ERR6133528.sra spots: 7550963 blocks: [[1, 377548], [377549, 755096], [755097, 1132644], [1132645, 1510192], [1510193, 1887740], [1887741, 2265288], [2265289, 2642836], [2642837, 3020384], [3020385, 3397932], [3397933, 3775480], [3775481, 4153028], [4153029, 4530576], [4530577, 4908124], [4908125, 5285672], [5285673, 5663220], [5663221, 6040768], [6040769, 6418316], [6418317, 6795864], [6795865, 7173412], [7173413, 7550963]] ERR6133528 file size 1675821 ERR6133528 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 ERR6133528 ERR6133528_1.fastq Input file: ERR6133528_1.fastq trimmed: ERR6133528-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 07:59:20 2024 >> started Sat Dec 7 07:59:24 2024 >> done (4.520s) 7550963 reads processed; of these: 123 ( 0.00%) short reads filtered out after trimming by size control 27 ( 0.00%) empty reads filtered out after trimming by size control 7550813 (100.00%) reads available; of these: 142283 ( 1.88%) trimmed reads available after processing 7408530 (98.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 16 0.00% 19 38 0.00% 20 13 0.00% 21 8 0.00% 22 13 0.00% 23 2 0.00% 24 13 0.00% 25 2 0.00% 26 10 0.00% 27 6 0.00% 28 10 0.00% 29 13 0.00% 30 10 0.00% 31 10 0.00% 32 15 0.00% 33 18 0.00% 34 28 0.00% 35 74 0.00% 36 875 0.01% 37 16 0.00% 38 20 0.00% 39 45 0.00% 40 44 0.00% 41 21 0.00% 42 8 0.00% 43 12 0.00% 44 23 0.00% 45 13 0.00% 46 14 0.00% 47 16 0.00% 48 7 0.00% 49 9 0.00% 50 9 0.00% 51 21 0.00% 52 9 0.00% 53 9 0.00% 54 10 0.00% 55 7 0.00% 56 7 0.00% 57 3 0.00% 58 9 0.00% 59 5 0.00% 60 10 0.00% 61 8 0.00% 62 3 0.00% 63 5 0.00% 64 3 0.00% 65 12 0.00% 66 17 0.00% 67 23 0.00% 68 37 0.00% 69 108 0.00% 70 7816 0.10% 71 6308 0.08% 72 6400 0.08% 73 5833 0.08% 74 6440 0.09% 75 6458 0.09% 76 5788 0.08% 77 5720 0.08% 78 7061 0.09% 79 8889 0.12% 80 7487 0.10% 81 7706 0.10% 82 8724 0.12% 83 9982 0.13% 84 7602 0.10% 85 315 0.00% 86 614 0.01% 87 977 0.01% 88 1807 0.02% 89 3746 0.05% 90 8286 0.11% 91 24279 0.32% 92 98619 1.31% 93 7302219 96.71% 7550813 reads passed initial QC criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=2.34 fanout-score-rank=29 prefix-density=0.48 prefix-fanout=2.1 sequence=TGTACATTTGAACCCTGACTACACATATACACACATATACATGTAATATTATACAATCTGTCGAGTATGTGTTGGTTCATA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=51.74 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=3.7 sequence=GTCGCCGCCTACCGCGAGCTCATCAATGGCGACCTCGTCGTCGACGACGCCGACATCGGATACTAATTGGCGGGCCGTGCGTGCACGCATGGTTGGCTAGTCGGTCGGTCCCCGGTCAGCTGGGCAATGGGGGATGTGAAGGCTTGTGGTGCCTGTGTGGGCTTGGTGTAGGAGCTGATCGATAGGATAAAGGAGGAATGGAAGCTCTCTTGTATCTAAGAAACTGAAATCTTGTATAACTGTACCTCTCTTGTGTGTATTTTGCCAAGTTCAAATTGTTGAG Started job on | Dec 07 07:59:42 Started mapping on | Dec 07 07:59:42 Finished on | Dec 07 07:59:50 Mapping speed, Million of reads per hour | 3397.87 Number of input reads | 7550813 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 5121826 Uniquely mapped reads % | 67.83% Average mapped length | 92.42 Number of splices: Total | 265737 Number of splices: Annotated (sjdb) | 217316 Number of splices: GT/AG | 255854 Number of splices: GC/AG | 5913 Number of splices: AT/AC | 188 Number of splices: Non-canonical | 3782 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.03% Deletion average length | 1.74 Insertion rate per base | 0.02% Insertion average length | 2.13 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2309099 % of reads mapped to multiple loci | 30.58% Number of reads mapped to too many loci | 28758 % of reads mapped to too many loci | 0.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.18% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 119888 119888 119888 N_multimapping 2309099 2309099 2309099 N_noFeature 339912 385431 4900022 N_ambiguous 198092 22051 574 UnstrandedReadsAssigned:4583822 PositiveStrandReadsAssigned:4714344 NegativeStrandReadsAssigned:221230 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133528 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: ERR6133528-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,550,813 reads, 6,402,068 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,064 rounds 52973 ERR6133528.ke.tsv 35125 ERR6133528.se.tsv 88098 total ==> ERR6133528.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 122 18.1829 PNS24243 293 194 0 0 KQK14069 1603 1504 325 44.1869 KQK14071 474 375 0 0 ==> ERR6133528.se.tsv <== BRADI_1g14170v3 325 BRADI_1g53295v3 38 BRADI_1g59795v3 45 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 59 BRADI_1g74790v3 59 BRADI_1g09890v3 0 BRADI_1g77505v3 114 BRADI_1g48960v3 0 ERR6133528 completed mapping pipeline successfully