Starting /dee2/code/volunteer_pipeline.sh ERR6133403 current disk space = 1547637710848 free memory = 1595155752 ERR6133403 SRAfilesize 201a46b3788a3a7a5d7f688b6d73170e ERR6133403.sra ERR6133403.sra file validated ERR6133403 is single end ERR6133403 is conventional basespace ERR6133403 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133403_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 28.893 33.0 27.0 33.0 15.0 37.0 2 33.367 33.0 33.0 37.0 27.0 37.0 3 33.71525 37.0 33.0 37.0 27.0 37.0 4 34.068 37.0 33.0 37.0 27.0 37.0 5 34.1295 37.0 33.0 37.0 27.0 37.0 6 34.5465 37.0 33.0 37.0 27.0 37.0 7 35.251 37.0 33.0 40.0 27.0 40.0 8 35.35225 37.0 33.0 40.0 27.0 40.0 9 35.5825 37.0 33.0 40.0 33.0 40.0 10-11 35.493125 37.0 33.0 40.0 30.0 40.0 12-13 35.249875 37.0 33.0 40.0 27.0 40.0 14-15 35.215374999999995 37.0 33.0 40.0 27.0 40.0 16-17 34.962375 37.0 33.0 37.0 27.0 40.0 18-19 34.86987499999999 37.0 33.0 37.0 27.0 40.0 20-21 34.153999999999996 37.0 33.0 37.0 27.0 40.0 22-23 34.091375 37.0 33.0 37.0 27.0 40.0 24-25 33.659 37.0 33.0 37.0 24.5 40.0 26-27 33.3085 37.0 33.0 37.0 22.0 40.0 28-29 33.092875 37.0 33.0 37.0 22.0 40.0 30-31 32.678875000000005 37.0 33.0 37.0 22.0 40.0 32-33 32.347624999999994 35.0 33.0 37.0 22.0 40.0 34-35 31.62925 33.0 27.0 37.0 15.0 40.0 36-37 31.100875000000002 33.0 27.0 37.0 15.0 37.0 38-39 31.48975 33.0 27.0 37.0 22.0 40.0 40-41 31.62075 33.0 27.0 37.0 22.0 40.0 42-43 31.233375 33.0 27.0 37.0 15.0 40.0 44-45 31.060499999999998 33.0 27.0 37.0 15.0 40.0 46-47 30.32775 33.0 27.0 37.0 15.0 37.0 48-49 30.181875 33.0 27.0 37.0 15.0 37.0 50-51 29.868125 33.0 27.0 37.0 15.0 37.0 52-53 29.646124999999998 33.0 27.0 37.0 15.0 37.0 54-55 29.33625 33.0 27.0 37.0 15.0 37.0 56-57 28.8035 33.0 27.0 37.0 15.0 37.0 58-59 28.528875 33.0 27.0 33.0 15.0 37.0 60-61 28.053874999999998 33.0 27.0 33.0 15.0 37.0 62-63 27.62725 33.0 22.0 33.0 15.0 37.0 64-65 27.286125 33.0 22.0 33.0 15.0 37.0 66-67 26.70675 30.0 22.0 33.0 6.0 37.0 68-69 26.530875 27.0 22.0 33.0 10.5 35.0 70-71 28.372802672955977 33.0 27.0 33.0 15.0 37.0 72-73 28.878538761433497 33.0 27.0 33.0 15.0 37.0 74-75 28.64941670562105 33.0 27.0 33.0 15.0 37.0 76-77 28.262216315320032 33.0 27.0 33.0 15.0 37.0 78-79 27.719699128606308 33.0 27.0 33.0 10.5 37.0 80-81 26.917184747583242 33.0 24.5 33.0 6.0 37.0 82-83 26.103215781507764 33.0 22.0 33.0 2.0 37.0 84-85 25.28420321683783 33.0 22.0 33.0 2.0 37.0 86-87 24.344018873161254 33.0 15.0 33.0 2.0 37.0 88-89 23.679433805162365 33.0 15.0 33.0 2.0 33.0 90-91 22.453788509575354 27.0 2.0 33.0 2.0 35.0 92-93 21.365667499306134 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 78.0 21 106.0 22 126.0 23 164.0 24 183.0 25 194.0 26 217.0 27 221.0 28 261.0 29 277.0 30 267.0 31 260.0 32 281.0 33 271.0 34 281.0 35 328.0 36 286.0 37 166.0 38 33.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 67.45 8.375 7.825 16.35 2 48.05 25.8 15.625 10.525 3 29.15 38.175 18.825 13.850000000000001 4 29.599999999999998 25.324999999999996 23.7 21.375 5 23.849999999999998 26.125 29.25 20.775 6 19.325 33.15 28.299999999999997 19.225 7 30.099999999999998 28.299999999999997 23.724999999999998 17.875 8 26.174999999999997 28.349999999999998 26.974999999999998 18.5 9 23.0 26.674999999999997 30.9 19.425 10-11 24.2375 27.05 29.1125 19.6 12-13 23.05 29.5375 29.3375 18.075 14-15 21.15 27.437499999999996 31.15 20.2625 16-17 23.2125 30.362499999999997 25.3 21.125 18-19 23.0875 25.674999999999997 30.625000000000004 20.6125 20-21 24.2625 25.124999999999996 29.4 21.212500000000002 22-23 26.75 24.45 27.3125 21.4875 24-25 23.5 26.950000000000003 29.575000000000003 19.975 26-27 23.5 25.412499999999998 30.4625 20.625 28-29 23.425 28.325 28.025 20.225 30-31 25.7875 27.212500000000002 27.400000000000002 19.6 32-33 24.825 25.45 29.45 20.275000000000002 34-35 23.5625 29.9 27.0 19.537499999999998 36-37 23.974999999999998 27.287499999999998 26.2625 22.475 38-39 25.637500000000003 25.4875 28.712500000000002 20.1625 40-41 24.775 25.85 27.712500000000002 21.6625 42-43 24.85 28.65 28.237499999999997 18.2625 44-45 21.6125 28.537499999999998 29.1625 20.6875 46-47 23.9375 27.0875 27.925 21.05 48-49 23.4875 26.775 28.4125 21.325 50-51 21.85 27.987499999999997 29.625 20.5375 52-53 24.625 27.025 27.5875 20.7625 54-55 23.0 28.525 29.425 19.05 56-57 24.099999999999998 27.987499999999997 28.675 19.2375 58-59 23.2125 28.9875 27.275 20.525 60-61 24.7375 28.3125 28.462500000000002 18.4875 62-63 21.712500000000002 29.175 29.1125 20.0 64-65 22.575 31.5 26.987499999999997 18.9375 66-67 24.1125 28.799999999999997 27.3125 19.775000000000002 68-69 21.175 28.425 27.8375 22.5625 70-71 23.79937304075235 27.987460815047022 27.94984326018809 20.26332288401254 72-73 23.846447184441338 26.846320071183428 29.70636837422143 19.600864370153808 74-75 23.860417203193407 28.13546227143961 28.521761524594385 19.482359000772597 76-77 22.384555178711192 27.6024002087138 28.632924602139315 21.38012001043569 78-79 22.94389438943894 28.171617161716174 29.848184818481847 19.036303630363037 80-81 23.294086165373294 31.054321648381055 27.361519935777363 18.290072250468288 82-83 22.014115092290986 27.931596091205215 28.270901194353964 21.78338762214984 84-85 21.477900552486187 26.75414364640884 30.82872928176796 20.93922651933702 86-87 21.981681931723564 30.210935331668054 27.088537330002776 20.718845406605606 88-89 21.31557035803497 30.141548709408827 28.615043019705798 19.927837912850404 90-91 22.814321398834306 30.641132389675267 26.82486816541771 19.719678046072715 92-93 20.094365806272553 33.263946711074105 26.90813211212878 19.733555370524563 >>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 0.5 17 1.5 18 2.5 19 4.0 20 4.5 21 3.0 22 2.5 23 4.0 24 5.0 25 9.5 26 16.0 27 20.5 28 25.0 29 30.0 30 39.5 31 61.5 32 79.5 33 84.5 34 88.5 35 106.0 36 134.5 37 170.0 38 216.5 39 218.5 40 219.0 41 230.0 42 230.0 43 239.5 44 223.0 45 203.0 46 175.0 47 149.5 48 138.0 49 134.0 50 135.5 51 129.5 52 121.5 53 126.0 54 145.5 55 118.0 56 83.5 57 85.0 58 65.0 59 34.0 60 21.0 61 18.0 62 16.5 63 12.5 64 8.0 65 7.5 66 6.0 67 4.5 68 6.5 69 11.5 70 10.0 71 6.0 72 6.5 73 5.0 74 1.5 75 0.5 76 0.5 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 25.0 71 23.0 72 37.0 73 17.0 74 30.0 75 20.0 76 30.0 77 21.0 78 19.0 79 28.0 80 26.0 81 25.0 82 30.0 83 32.0 84 34.0 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 3603.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.175 #Duplication Level Percentage of deduplicated Percentage of total 1 92.19699392388871 72.075 2 3.5817077070674768 5.6000000000000005 3 1.5669971218420211 3.675 4 0.5116725295810681 1.6 5 0.7355292612727854 2.875 6 0.35177486408698433 1.6500000000000001 7 0.25583626479053406 1.4000000000000001 8 0.09593859929645027 0.6 9 0.03197953309881676 0.22499999999999998 >10 0.6715701950751519 10.299999999999999 >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 fail #Sequence Count Percentage Possible Source GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 45 1.125 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 31 0.775 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 31 0.775 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 27 0.675 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 26 0.65 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 22 0.5499999999999999 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 19 0.475 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 19 0.475 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 17 0.42500000000000004 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 16 0.4 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 15 0.375 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 15 0.375 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 15 0.375 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 14 0.35000000000000003 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 13 0.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 11 0.27499999999999997 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 11 0.27499999999999997 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 11 0.27499999999999997 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 9 0.22499999999999998 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 8 0.2 No Hit TGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 8 0.2 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGA 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 6 0.15 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 6 0.15 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 6 0.15 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 6 0.15 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit CAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGG 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit GGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCA 5 0.125 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 5 0.125 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 5 0.125 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 5 0.125 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAA 5 0.125 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 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 0.0125 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40947 READS because READLEN < 1 Read 40947 spots for ERR6133403.sra Written 40947 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra Rejected 40939 READS because READLEN < 1 Read 40939 spots for ERR6133403.sra Written 40939 spots for ERR6133403.sra SRR ids: ['ERR6133403.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vhq3113p ERR6133403.sra spots: 818788 blocks: [[1, 40939], [40940, 81878], [81879, 122817], [122818, 163756], [163757, 204695], [204696, 245634], [245635, 286573], [286574, 327512], [327513, 368451], [368452, 409390], [409391, 450329], [450330, 491268], [491269, 532207], [532208, 573146], [573147, 614085], [614086, 655024], [655025, 695963], [695964, 736902], [736903, 777841], [777842, 818788]] ERR6133403 file size 178131 ERR6133403 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 ERR6133403 ERR6133403_1.fastq Input file: ERR6133403_1.fastq trimmed: ERR6133403-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 03:15:05 2024 >> started Sat Dec 7 03:15:05 2024 >> done (0.583s) 818788 reads processed; of these: 8 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 818777 (100.00%) reads available; of these: 210637 (25.73%) trimmed reads available after processing 608140 (74.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 19 7 0.00% 20 2 0.00% 21 2 0.00% 22 3 0.00% 23 1 0.00% 24 2 0.00% 25 0 0.00% 26 0 0.00% 27 2 0.00% 28 10 0.00% 29 8 0.00% 30 2 0.00% 31 3 0.00% 32 4 0.00% 33 2 0.00% 34 4 0.00% 35 2 0.00% 36 3 0.00% 37 4 0.00% 38 6 0.00% 39 6 0.00% 40 16 0.00% 41 5 0.00% 42 9 0.00% 43 5 0.00% 44 17 0.00% 45 25 0.00% 46 30 0.00% 47 53 0.01% 48 65 0.01% 49 84 0.01% 50 104 0.01% 51 130 0.02% 52 176 0.02% 53 288 0.04% 54 327 0.04% 55 448 0.05% 56 621 0.08% 57 956 0.12% 58 743 0.09% 59 835 0.10% 60 973 0.12% 61 1189 0.15% 62 1252 0.15% 63 1317 0.16% 64 1489 0.18% 65 1421 0.17% 66 1517 0.19% 67 1534 0.19% 68 1491 0.18% 69 1552 0.19% 70 6282 0.77% 71 6500 0.79% 72 7511 0.92% 73 7784 0.95% 74 7989 0.98% 75 8590 1.05% 76 8621 1.05% 77 9203 1.12% 78 10151 1.24% 79 10645 1.30% 80 11012 1.34% 81 12731 1.55% 82 13847 1.69% 83 14093 1.72% 84 15605 1.91% 85 10577 1.29% 86 11086 1.35% 87 12300 1.50% 88 13805 1.69% 89 15011 1.83% 90 16068 1.96% 91 17556 2.14% 92 14264 1.74% 93 538801 65.81% 818777 reads passed initial QC criterion=sequence-density sequence-density=3.79 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=24 prefix-density=3.89 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.05 sequence-density-rank=20 fanout-score=8.92 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=3.0 sequence=GATCGATCCATTGATGTGGATGCGATGCCATGGAGTATATGTACTCGCTATTTTCCAGTACTGCATGCCGGATGGCTCGATGTGAATTTGTAATAAGCAATAGAAGTTTCTACCATTTTCTGACGTGGGGTTGTACTTGTGATGCGTAATTTGGTCATCTTGTGACCAAAAGACATCAACTATATAATTATAATACCATTTTCATCAAGACTC 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 03:15:17 Started mapping on | Dec 07 03:15:17 Finished on | Dec 07 03:15:23 Mapping speed, Million of reads per hour | 491.27 Number of input reads | 818777 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 380631 Uniquely mapped reads % | 46.49% Average mapped length | 88.19 Number of splices: Total | 11721 Number of splices: Annotated (sjdb) | 9429 Number of splices: GT/AG | 11170 Number of splices: GC/AG | 264 Number of splices: AT/AC | 18 Number of splices: Non-canonical | 269 Mismatch rate per base, % | 0.81% Deletion rate per base | 0.03% Deletion average length | 1.73 Insertion rate per base | 0.01% Insertion average length | 1.63 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 343419 % of reads mapped to multiple loci | 41.94% Number of reads mapped to too many loci | 41800 % of reads mapped to too many loci | 5.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.63% % of reads unmapped: other | 0.83% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 94727 94727 94727 N_multimapping 343419 343419 343419 N_noFeature 32407 35950 364083 N_ambiguous 15509 2507 70 UnstrandedReadsAssigned:332715 PositiveStrandReadsAssigned:342174 NegativeStrandReadsAssigned:16478 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133403 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: ERR6133403-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 818,777 reads, 567,460 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 848 rounds 52973 ERR6133403.ke.tsv 35125 ERR6133403.se.tsv 88098 total ==> ERR6133403.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 2 3.44004 PNS24243 293 194 0 0 KQK14069 1603 1504 0 0 KQK14071 474 375 0 0 ==> ERR6133403.se.tsv <== BRADI_1g14170v3 0 BRADI_1g53295v3 7 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 4 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR6133403 completed mapping pipeline successfully