Starting /dee2/code/volunteer_pipeline.sh ERR6133420 current disk space = 1547141365760 free memory = 1603116968 ERR6133420 SRAfilesize 1161fdf3e53ca59e6ba7d6a7a087ec46 ERR6133420.sra ERR6133420.sra file validated ERR6133420 is single end ERR6133420 is conventional basespace ERR6133420 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133420_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 29.39525 33.0 27.0 33.0 15.0 37.0 2 33.657 33.0 33.0 37.0 27.0 37.0 3 33.77375 37.0 33.0 37.0 27.0 37.0 4 34.0205 37.0 33.0 37.0 27.0 37.0 5 34.086 37.0 33.0 37.0 27.0 37.0 6 34.08025 37.0 33.0 37.0 27.0 37.0 7 35.32625 37.0 33.0 37.0 27.0 40.0 8 35.11175 37.0 33.0 37.0 27.0 40.0 9 35.49975 37.0 33.0 40.0 33.0 40.0 10-11 35.262125 37.0 33.0 38.5 27.0 40.0 12-13 35.015375000000006 37.0 33.0 37.0 27.0 40.0 14-15 35.013125 37.0 33.0 37.0 27.0 40.0 16-17 34.734875 37.0 33.0 37.0 27.0 40.0 18-19 34.61125 37.0 33.0 37.0 27.0 40.0 20-21 33.8885 37.0 33.0 37.0 24.5 40.0 22-23 33.778375 37.0 33.0 37.0 27.0 40.0 24-25 33.39075 37.0 33.0 37.0 22.0 40.0 26-27 33.185625 37.0 33.0 37.0 22.0 40.0 28-29 32.966625 37.0 33.0 37.0 22.0 40.0 30-31 32.869749999999996 37.0 33.0 37.0 22.0 40.0 32-33 32.306625 33.0 33.0 37.0 22.0 40.0 34-35 31.3975 33.0 27.0 37.0 15.0 40.0 36-37 31.094875000000002 33.0 27.0 37.0 18.5 37.0 38-39 31.310625 33.0 27.0 37.0 22.0 37.0 40-41 31.2675 33.0 27.0 37.0 22.0 37.0 42-43 30.954124999999998 33.0 27.0 37.0 18.5 37.0 44-45 30.6905 33.0 27.0 37.0 18.5 38.5 46-47 30.201749999999997 33.0 27.0 37.0 15.0 37.0 48-49 29.968125 33.0 27.0 37.0 15.0 37.0 50-51 29.479625 33.0 27.0 37.0 15.0 37.0 52-53 29.428625 33.0 27.0 37.0 15.0 37.0 54-55 29.209875 33.0 27.0 37.0 15.0 37.0 56-57 28.521375 33.0 24.5 33.0 15.0 37.0 58-59 28.223125000000003 33.0 27.0 33.0 15.0 37.0 60-61 27.926875 33.0 24.5 33.0 15.0 37.0 62-63 27.53875 33.0 22.0 33.0 15.0 37.0 64-65 27.142 33.0 22.0 33.0 10.5 37.0 66-67 26.702375 27.0 22.0 33.0 10.5 37.0 68-69 26.259500000000003 27.0 22.0 33.0 10.5 35.0 70-71 28.15606715342191 33.0 27.0 33.0 15.0 37.0 72-73 28.324888677651394 33.0 27.0 33.0 15.0 37.0 74-75 28.33550411832819 33.0 27.0 33.0 15.0 37.0 76-77 27.974029393093005 33.0 27.0 33.0 15.0 37.0 78-79 27.234461623647668 33.0 24.5 33.0 6.0 37.0 80-81 26.49759331447141 33.0 22.0 33.0 6.0 37.0 82-83 25.900928442556605 33.0 22.0 33.0 2.0 37.0 84-85 25.253723619940054 33.0 18.5 33.0 2.0 37.0 86-87 24.23366570453949 27.0 15.0 33.0 2.0 37.0 88-89 23.635003935974808 30.0 10.5 33.0 2.0 35.0 90-91 22.497244817633167 27.0 2.0 33.0 2.0 33.0 92-93 21.231041721332982 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 90.0 21 105.0 22 160.0 23 170.0 24 150.0 25 199.0 26 230.0 27 236.0 28 251.0 29 285.0 30 278.0 31 291.0 32 287.0 33 294.0 34 278.0 35 284.0 36 229.0 37 157.0 38 26.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.975 7.3 6.575 16.150000000000002 2 52.400000000000006 25.124999999999996 13.275 9.2 3 31.8 38.45 17.25 12.5 4 25.424999999999997 29.975 23.225 21.375 5 28.075 23.775 28.65 19.5 6 17.5 36.625 27.500000000000004 18.375 7 34.775 27.025 19.8 18.4 8 24.474999999999998 26.1 27.775 21.65 9 21.15 32.225 27.725 18.9 10-11 21.7375 28.462500000000002 31.637500000000003 18.1625 12-13 20.7875 30.15 28.6375 20.424999999999997 14-15 17.4 33.025 29.9625 19.6125 16-17 23.8125 30.025000000000002 22.8 23.3625 18-19 23.175 24.75 33.4375 18.637500000000003 20-21 25.7875 24.1125 30.412499999999998 19.6875 22-23 28.6125 20.849999999999998 30.362499999999997 20.175 24-25 22.9875 24.575 29.8375 22.6 26-27 25.1875 22.5 30.337500000000002 21.975 28-29 23.1 29.1625 30.125 17.6125 30-31 29.462500000000002 25.95 25.974999999999998 18.6125 32-33 25.7375 22.7625 28.825 22.675 34-35 21.099999999999998 35.0 25.0375 18.862499999999997 36-37 25.35 25.724999999999998 25.5125 23.4125 38-39 30.4625 24.025 27.537499999999998 17.974999999999998 40-41 24.4125 22.7375 32.25 20.599999999999998 42-43 26.2125 28.825 26.75 18.212500000000002 44-45 23.9 25.387500000000003 31.5 19.2125 46-47 25.874999999999996 25.6 25.7375 22.787499999999998 48-49 24.275 24.8625 28.975 21.8875 50-51 20.6625 28.237499999999997 28.9 22.2 52-53 22.5 27.025 26.237500000000004 24.2375 54-55 21.587500000000002 26.025 31.65 20.7375 56-57 26.375 28.449999999999996 25.837500000000002 19.3375 58-59 22.6125 28.262500000000003 29.4 19.725 60-61 28.8875 26.924999999999997 26.137500000000003 18.05 62-63 19.3875 26.674999999999997 32.4625 21.475 64-65 19.85 34.449999999999996 27.55 18.15 66-67 25.874999999999996 28.462500000000002 25.5625 20.1 68-69 19.125 27.474999999999998 28.962500000000002 24.4375 70-71 22.981599699586933 28.58931030166479 25.68531731130304 22.743772687445237 72-73 23.980875691997987 25.905888273779563 30.447911424257672 19.66532460996477 74-75 26.57714720040537 28.45198885229288 27.425893083354445 17.544970863947302 76-77 21.05397148676171 26.45112016293279 26.489307535641547 26.00560081466395 78-79 24.664021502623832 27.825419173172918 29.054140535005757 18.45641878919749 80-81 20.651474185657268 35.161581048023685 26.22634221707223 17.96060254924681 82-83 23.154885654885653 26.364345114345117 26.026507276507278 24.454261954261955 84-85 21.047120418848166 25.837696335078537 31.884816753926703 21.230366492146597 86-87 20.742587247441616 29.67725006559958 26.882707950669115 22.69745473628969 88-89 20.086591445814747 26.594069797953296 31.55339805825243 21.765940697979534 90-91 24.639202309105222 29.51981107320913 25.163998950406718 20.67698766727893 92-93 19.11571765940698 29.795329309892416 29.61165048543689 21.47730254526371 >>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 3.0 18 3.0 19 1.0 20 0.5 21 1.5 22 2.0 23 6.0 24 8.0 25 11.0 26 15.5 27 15.5 28 21.5 29 28.0 30 33.5 31 50.0 32 68.5 33 74.0 34 69.0 35 75.0 36 109.0 37 165.5 38 206.5 39 202.0 40 214.5 41 236.0 42 258.5 43 288.5 44 249.5 45 190.0 46 160.5 47 135.0 48 126.0 49 119.0 50 109.5 51 120.5 52 115.0 53 115.5 54 207.5 55 205.5 56 99.5 57 73.0 58 53.0 59 27.5 60 21.5 61 19.0 62 14.5 63 13.0 64 14.5 65 11.0 66 6.0 67 6.0 68 9.0 69 10.5 70 8.0 71 5.0 72 4.5 73 3.5 74 1.5 75 0.0 76 0.5 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 0.0 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 11.0 71 10.0 72 10.0 73 16.0 74 12.0 75 6.0 76 14.0 77 8.0 78 13.0 79 10.0 80 13.0 81 22.0 82 14.0 83 12.0 84 18.0 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 3811.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.05 #Duplication Level Percentage of deduplicated Percentage of total 1 92.60929909784872 66.725 2 3.3310201249132545 4.8 3 1.040943789035392 2.25 4 0.9021512838306732 2.6 5 0.520471894517696 1.875 6 0.31228313671061764 1.35 7 0.2081887578070784 1.05 8 0.2081887578070784 1.2 9 0.06939625260235947 0.44999999999999996 >10 0.6939625260235947 9.075 >50 0.06939625260235947 3.125 >100 0.03469812630117974 5.5 >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 220 5.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 68 1.7000000000000002 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 57 1.425 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 46 1.15 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 37 0.9249999999999999 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 34 0.8500000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 30 0.75 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 23 0.575 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 18 0.44999999999999996 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 15 0.375 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 14 0.35000000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 13 0.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 13 0.325 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 12 0.3 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 12 0.3 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 12 0.3 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 11 0.27499999999999997 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 10 0.25 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 10 0.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 10 0.25 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 10 0.25 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 10 0.25 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 9 0.22499999999999998 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 9 0.22499999999999998 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 8 0.2 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 8 0.2 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 8 0.2 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 8 0.2 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 7 0.17500000000000002 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 7 0.17500000000000002 No Hit CAACAACTCTCGTTCTTTACACTTCTTCTTGGCTGCTTGGCCTGTAGTAG 7 0.17500000000000002 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 6 0.15 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 6 0.15 No Hit TACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGC 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGCGTGCCGC 6 0.15 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 6 0.15 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 5 0.125 No Hit GGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAACAACAACTGGA 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 5 0.125 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 5 0.125 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 5 0.125 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 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 fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 25 6.950904E-7 85.950005 7 GGGAGAG 25 6.950904E-7 85.950005 1 CAATACA 25 6.950904E-7 85.950005 8 AGAGCAA 25 6.950904E-7 85.950005 4 GAGAGCA 25 6.950904E-7 85.950005 3 AATACAA 25 6.950904E-7 85.950005 9 AGCAATA 25 6.950904E-7 85.950005 6 GGAGAGC 30 2.0564803E-6 71.625 2 GAGCAAT 30 2.0564803E-6 71.625 5 GATGGCT 25 4.664068E-5 42.975002 56-57 GAGTGCC 25 4.664068E-5 42.975002 42-43 GAAGCGG 25 4.664068E-5 42.975002 32-33 ATGGCTA 25 4.664068E-5 42.975002 58-59 TGCTGCT 25 4.664068E-5 42.975002 22-23 CGAAGCG 25 4.664068E-5 42.975002 32-33 GGCGAAG 25 4.664068E-5 42.975002 30-31 CTAGGCG 25 4.664068E-5 42.975002 26-27 AGTGCCG 25 4.664068E-5 42.975002 42-43 GCTAAAG 25 4.664068E-5 42.975002 60-61 AAGCGTT 25 4.664068E-5 42.975002 14-15 >>END_MODULE Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75205 READS because READLEN < 1 Read 75205 spots for ERR6133420.sra Written 75205 spots for ERR6133420.sra Rejected 75212 READS because READLEN < 1 Read 75212 spots for ERR6133420.sra Written 75212 spots for ERR6133420.sra SRR ids: ['ERR6133420.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jmwbahxw ERR6133420.sra spots: 1504107 blocks: [[1, 75205], [75206, 150410], [150411, 225615], [225616, 300820], [300821, 376025], [376026, 451230], [451231, 526435], [526436, 601640], [601641, 676845], [676846, 752050], [752051, 827255], [827256, 902460], [902461, 977665], [977666, 1052870], [1052871, 1128075], [1128076, 1203280], [1203281, 1278485], [1278486, 1353690], [1353691, 1428895], [1428896, 1504107]] ERR6133420 file size 330339 ERR6133420 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 ERR6133420 ERR6133420_1.fastq Input file: ERR6133420_1.fastq trimmed: ERR6133420-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 04:32:41 2024 >> started Sat Dec 7 04:32:42 2024 >> done (1.022s) 1504107 reads processed; of these: 13 ( 0.00%) short reads filtered out after trimming by size control 1 ( 0.00%) empty reads filtered out after trimming by size control 1504093 (100.00%) reads available; of these: 396001 (26.33%) trimmed reads available after processing 1108092 (73.67%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 9 0.00% 20 5 0.00% 21 1 0.00% 22 2 0.00% 23 2 0.00% 24 1 0.00% 25 1 0.00% 26 1 0.00% 27 0 0.00% 28 4 0.00% 29 7 0.00% 30 4 0.00% 31 4 0.00% 32 10 0.00% 33 3 0.00% 34 0 0.00% 35 1 0.00% 36 5 0.00% 37 4 0.00% 38 3 0.00% 39 19 0.00% 40 24 0.00% 41 6 0.00% 42 5 0.00% 43 12 0.00% 44 16 0.00% 45 21 0.00% 46 42 0.00% 47 53 0.00% 48 78 0.01% 49 115 0.01% 50 158 0.01% 51 217 0.01% 52 258 0.02% 53 364 0.02% 54 568 0.04% 55 739 0.05% 56 966 0.06% 57 1601 0.11% 58 1159 0.08% 59 1327 0.09% 60 1690 0.11% 61 1987 0.13% 62 2150 0.14% 63 2364 0.16% 64 2502 0.17% 65 2665 0.18% 66 2741 0.18% 67 2870 0.19% 68 2677 0.18% 69 2608 0.17% 70 7736 0.51% 71 8299 0.55% 72 9676 0.64% 73 10301 0.68% 74 10953 0.73% 75 11951 0.79% 76 12680 0.84% 77 14137 0.94% 78 14946 0.99% 79 15985 1.06% 80 17039 1.13% 81 19425 1.29% 82 21006 1.40% 83 21792 1.45% 84 24256 1.61% 85 20325 1.35% 86 21017 1.40% 87 23135 1.54% 88 27700 1.84% 89 28962 1.93% 90 30794 2.05% 91 33602 2.23% 92 29332 1.95% 93 1036970 68.94% 1504093 reads passed initial QC criterion=sequence-density sequence-density=2.30 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=27 prefix-density=2.36 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.14 sequence-density-rank=14 fanout-score=78.97 fanout-score-rank=1 prefix-density=11.09 prefix-fanout=1.0 sequence=GATAGTCAAGGGCGCGTTATTAA 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 04:32:55 Started mapping on | Dec 07 04:32:55 Finished on | Dec 07 04:33:02 Mapping speed, Million of reads per hour | 773.53 Number of input reads | 1504093 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 632167 Uniquely mapped reads % | 42.03% Average mapped length | 88.88 Number of splices: Total | 24408 Number of splices: Annotated (sjdb) | 19235 Number of splices: GT/AG | 23358 Number of splices: GC/AG | 436 Number of splices: AT/AC | 22 Number of splices: Non-canonical | 592 Mismatch rate per base, % | 0.81% Deletion rate per base | 0.04% Deletion average length | 1.87 Insertion rate per base | 0.02% Insertion average length | 1.71 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 751339 % of reads mapped to multiple loci | 49.95% Number of reads mapped to too many loci | 40925 % of reads mapped to too many loci | 2.72% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.81% % of reads unmapped: other | 0.48% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 120587 120587 120587 N_multimapping 751339 751339 751339 N_noFeature 53762 59965 604622 N_ambiguous 25552 4176 141 UnstrandedReadsAssigned:552853 PositiveStrandReadsAssigned:568026 NegativeStrandReadsAssigned:27404 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=86 echo kmer=81 ERR6133420 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: ERR6133420-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,504,093 reads, 1,033,543 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 855 rounds 52973 ERR6133420.ke.tsv 35125 ERR6133420.se.tsv 88098 total ==> ERR6133420.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 10 9.1004 PNS24243 293 194 0 0 KQK14069 1603 1504 0 0 KQK14071 474 375 0 0 ==> ERR6133420.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 7 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 11 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 12 BRADI_1g48960v3 0 ERR6133420 completed mapping pipeline successfully