Starting /dee2/code/volunteer_pipeline.sh ERR6133481 current disk space = 1544881553408 free memory = 1474931808 ERR6133481 SRAfilesize efa7321adcb627daef896e4768c6f99b ERR6133481.sra ERR6133481.sra file validated ERR6133481 is single end ERR6133481 is conventional basespace ERR6133481 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133481_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 pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.5675 37.0 33.0 37.0 33.0 37.0 2 36.42275 37.0 37.0 37.0 37.0 37.0 3 35.891 37.0 37.0 37.0 33.0 37.0 4 35.44 37.0 37.0 37.0 33.0 37.0 5 35.44525 37.0 37.0 37.0 33.0 37.0 6 35.7435 37.0 37.0 37.0 33.0 37.0 7 37.342 37.0 37.0 40.0 33.0 40.0 8 37.47925 40.0 37.0 40.0 33.0 40.0 9 37.47125 37.0 37.0 40.0 33.0 40.0 10-11 37.42100000000001 37.0 37.0 40.0 33.0 40.0 12-13 37.349375 37.0 37.0 40.0 33.0 40.0 14-15 37.40375 37.0 37.0 40.0 33.0 40.0 16-17 37.270125 37.0 37.0 40.0 33.0 40.0 18-19 37.1255 37.0 37.0 40.0 33.0 40.0 20-21 36.881874999999994 37.0 37.0 40.0 33.0 40.0 22-23 36.808125000000004 37.0 37.0 40.0 33.0 40.0 24-25 36.741375000000005 37.0 37.0 40.0 33.0 40.0 26-27 36.961375000000004 37.0 37.0 40.0 33.0 40.0 28-29 36.929874999999996 37.0 37.0 40.0 33.0 40.0 30-31 36.917125 37.0 37.0 40.0 33.0 40.0 32-33 36.81725 37.0 37.0 40.0 33.0 40.0 34-35 36.784125 37.0 37.0 40.0 33.0 40.0 36-37 36.616 37.0 37.0 40.0 33.0 40.0 38-39 36.6545 37.0 37.0 40.0 33.0 40.0 40-41 36.463875 37.0 37.0 40.0 33.0 40.0 42-43 36.40375 37.0 37.0 40.0 33.0 40.0 44-45 36.35425 37.0 37.0 40.0 33.0 40.0 46-47 36.268375000000006 37.0 37.0 40.0 33.0 40.0 48-49 36.217125 37.0 37.0 37.0 33.0 40.0 50-51 36.05575 37.0 37.0 37.0 33.0 40.0 52-53 35.736999999999995 37.0 35.0 37.0 33.0 40.0 54-55 35.577 37.0 33.0 37.0 33.0 40.0 56-57 35.383875 37.0 33.0 37.0 33.0 38.5 58-59 34.384125 37.0 33.0 37.0 27.0 37.0 60-61 34.861875 37.0 33.0 37.0 33.0 37.0 62-63 34.749125 37.0 33.0 37.0 33.0 37.0 64-65 34.693375 37.0 33.0 37.0 33.0 37.0 66-67 34.673500000000004 37.0 33.0 37.0 33.0 37.0 68-69 33.994 35.0 33.0 37.0 30.0 37.0 70-71 34.078865577889445 35.0 33.0 37.0 27.0 37.0 72-73 34.40267111839161 37.0 33.0 37.0 33.0 37.0 74-75 34.306995028210835 37.0 33.0 37.0 30.0 37.0 76-77 34.211911185803444 37.0 33.0 37.0 27.0 37.0 78-79 34.03198976668679 37.0 33.0 37.0 27.0 37.0 80-81 33.99046838825345 37.0 33.0 37.0 27.0 37.0 82-83 33.82600134646046 37.0 33.0 37.0 27.0 37.0 84-85 33.55248048641489 37.0 33.0 37.0 27.0 37.0 86-87 33.5246810870771 37.0 33.0 37.0 27.0 37.0 88-89 33.579866888519135 37.0 33.0 37.0 27.0 37.0 90-91 33.62354409317804 37.0 33.0 37.0 27.0 37.0 92-93 33.5004159733777 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 10.0 22 10.0 23 18.0 24 16.0 25 22.0 26 28.0 27 45.0 28 60.0 29 54.0 30 83.0 31 96.0 32 124.0 33 183.0 34 249.0 35 479.0 36 874.0 37 984.0 38 641.0 39 19.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.05000000000001 3.225 2.9000000000000004 7.825 2 67.875 18.125 8.525 5.475 3 35.175 39.375 15.875 9.575 4 34.300000000000004 27.700000000000003 18.975 19.025 5 25.624999999999996 30.599999999999998 26.125 17.65 6 20.9 36.199999999999996 25.825 17.075000000000003 7 35.449999999999996 29.75 20.0 14.799999999999999 8 29.875 31.7 23.275000000000002 15.15 9 26.700000000000003 29.725 26.924999999999997 16.650000000000002 10-11 26.0625 28.712500000000002 28.0625 17.1625 12-13 26.687499999999996 26.8 29.375 17.1375 14-15 22.325 28.725 29.525000000000002 19.425 16-17 24.5 31.637500000000003 25.4 18.462500000000002 18-19 24.028003500437556 26.390798849856235 28.378547318414803 21.202650331291412 20-21 24.85932224584219 26.872577216456172 27.085156933850197 21.182943603851445 22-23 26.3125 25.45 27.400000000000002 20.837500000000002 24-25 24.8625 26.4125 28.287499999999998 20.4375 26-27 25.2125 25.85 30.1875 18.75 28-29 25.224999999999998 28.575 27.775 18.425 30-31 24.95 26.6125 28.799999999999997 19.6375 32-33 25.825 25.587500000000002 28.799999999999997 19.787499999999998 34-35 25.3 27.212500000000002 27.3 20.1875 36-37 24.390548818602326 27.603450431303912 26.440805100637583 21.565195649456182 38-39 25.90323790473809 25.203150393799223 30.50381297662208 18.389798724840606 40-41 25.703212901612705 25.54069258657332 27.390923865483185 21.365170646330792 42-43 25.174999999999997 28.849999999999998 27.200000000000003 18.775 44-45 22.9625 28.762500000000003 28.8625 19.412499999999998 46-47 25.424999999999997 26.2625 26.9125 21.4 48-49 23.974999999999998 26.9625 29.2 19.8625 50-51 22.35 29.2 28.512500000000003 19.9375 52-53 24.47061771707806 28.643027189575243 26.96403959403583 19.922315499310862 54-55 24.1780222527816 29.566195774471808 27.928491061382672 18.32729091136392 56-57 23.80297537192149 27.853481685210653 28.353544193024128 19.98999874984373 58-59 23.275000000000002 27.025 28.762500000000003 20.9375 60-61 25.7125 27.037499999999998 28.4 18.85 62-63 22.8875 29.7125 29.7 17.7 64-65 23.0 29.625 28.537499999999998 18.8375 66-67 24.0375 28.6375 28.925 18.4 68-69 23.4875 27.0 28.749999999999996 20.7625 70-71 24.598997493734338 26.979949874686714 28.984962406015036 19.43609022556391 72-73 24.62317922735909 27.422419252691576 29.575680810639643 18.37872070930969 74-75 23.431876606683804 27.80205655526992 28.97172236503856 19.794344473007712 76-77 23.679749641413483 27.591602555743904 29.299778328334853 19.42886947450776 78-79 24.06282998944034 28.59028511087645 28.973072861668424 18.373812038014783 80-81 23.80760986066452 30.827974276527332 27.759914255091108 17.60450160771704 82-83 22.272170004086636 27.78912954638333 28.93338782182264 21.005312627707397 84-85 22.23756906077348 27.044198895027627 31.022099447513813 19.696132596685086 86-87 22.28230726566833 29.25679423183583 28.88241819190239 19.578480310593456 88-89 20.452024403771492 31.572379367720465 29.38158624514698 18.594009983361065 90-91 24.889073765945646 29.145867997781476 26.760953965612867 19.20410427066001 92-93 22.601220188574597 32.04381586245147 27.42651136993899 17.928452579034943 >>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 5.5 18 5.0 19 0.5 20 0.0 21 1.0 22 1.0 23 2.5 24 5.5 25 5.0 26 6.0 27 16.5 28 27.0 29 27.5 30 36.0 31 43.5 32 58.5 33 88.5 34 97.0 35 109.5 36 147.5 37 175.5 38 190.0 39 194.5 40 213.5 41 225.5 42 211.5 43 209.5 44 193.0 45 200.5 46 205.5 47 181.5 48 179.0 49 178.0 50 162.5 51 142.0 52 124.5 53 137.0 54 129.0 55 81.0 56 55.5 57 45.5 58 45.0 59 33.5 60 23.0 61 21.5 62 16.5 63 14.0 64 14.0 65 16.5 66 14.5 67 11.5 68 10.5 69 6.0 70 3.5 71 4.0 72 5.5 73 7.0 74 4.5 75 1.5 76 0.5 77 0.5 78 0.5 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 0.0125 20-21 0.0375 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 0.0125 38-39 0.0125 40-41 0.0125 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2375 54-55 0.0125 56-57 0.0125 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 20.0 71 19.0 72 27.0 73 26.0 74 36.0 75 27.0 76 21.0 77 25.0 78 22.0 79 32.0 80 26.0 81 34.0 82 29.0 83 22.0 84 28.0 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 3606.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.375 #Duplication Level Percentage of deduplicated Percentage of total 1 92.4416796267496 74.3 2 4.136858475894246 6.65 3 1.3685847589424573 3.3000000000000003 4 0.5287713841368584 1.7000000000000002 5 0.27993779160186627 1.125 6 0.27993779160186627 1.35 7 0.06220839813374805 0.35000000000000003 8 0.09331259720062209 0.6 9 0.09331259720062209 0.675 >10 0.7153965785381027 9.950000000000001 >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 warn #Sequence Count Percentage Possible Source GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 34 0.8500000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 27 0.675 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 26 0.65 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 24 0.6 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 22 0.5499999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 22 0.5499999999999999 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 21 0.525 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 19 0.475 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 19 0.475 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 17 0.42500000000000004 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 17 0.42500000000000004 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 16 0.4 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 14 0.35000000000000003 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 14 0.35000000000000003 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 13 0.325 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 11 0.27499999999999997 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 10 0.25 No Hit GGGGGAGAAGTCTTATGTTATATATGGTAATCGCCTTGCCTATAGTGCCC 10 0.25 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 10 0.25 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 9 0.22499999999999998 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 7 0.17500000000000002 No Hit GGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAA 7 0.17500000000000002 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 6 0.15 No Hit ATGGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATC 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit GGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATCGG 6 0.15 No Hit GCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGA 6 0.15 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 5 0.125 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit GGAAGAGTCCTCTTAATATTTATCTAATCTTATATAGGTTTCAGTATATT 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 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 0.025 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.0625 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1125 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 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.15 0.0 0.0 0.0 0.0 46-47 0.1875 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.2 0.0 0.0 0.0 0.0 52-53 0.2 0.0 0.0 0.0 0.0 54-55 0.2 0.0 0.0 0.0 0.0 56-57 0.2 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 0.21250000000000002 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.25 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCCGGG 15 9.315068E-4 85.55 2 CGGGTAT 15 9.315068E-4 85.55 5 GCCGGGT 15 9.315068E-4 85.55 3 CCGGGTA 15 9.315068E-4 85.55 4 GGGCCGG 15 9.315068E-4 85.55 1 GGGTATC 20 0.002918006 64.1625 6 GTATCTC 20 0.002918006 64.1625 8 TATCTCT 20 0.002918006 64.1625 9 GGTATCT 20 0.002918006 64.1625 7 >>END_MODULE Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58403 READS because READLEN < 1 Read 58403 spots for ERR6133481.sra Written 58403 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra Rejected 58393 READS because READLEN < 1 Read 58393 spots for ERR6133481.sra Written 58393 spots for ERR6133481.sra SRR ids: ['ERR6133481.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kvt1d3f2 ERR6133481.sra spots: 1167870 blocks: [[1, 58393], [58394, 116786], [116787, 175179], [175180, 233572], [233573, 291965], [291966, 350358], [350359, 408751], [408752, 467144], [467145, 525537], [525538, 583930], [583931, 642323], [642324, 700716], [700717, 759109], [759110, 817502], [817503, 875895], [875896, 934288], [934289, 992681], [992682, 1051074], [1051075, 1109467], [1109468, 1167870]] ERR6133481 file size 254069 ERR6133481 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 ERR6133481 ERR6133481_1.fastq Input file: ERR6133481_1.fastq trimmed: ERR6133481-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 06:58:11 2024 >> started Sat Dec 7 06:58:12 2024 >> done (1.044s) 1167870 reads processed; of these: 1002 ( 0.09%) short reads filtered out after trimming by size control 24 ( 0.00%) empty reads filtered out after trimming by size control 1166844 (99.91%) reads available; of these: 22826 ( 1.96%) trimmed reads available after processing 1144018 (98.04%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 50 0.00% 19 75 0.01% 20 94 0.01% 21 51 0.00% 22 49 0.00% 23 34 0.00% 24 71 0.01% 25 22 0.00% 26 19 0.00% 27 167 0.01% 28 186 0.02% 29 82 0.01% 30 117 0.01% 31 40 0.00% 32 39 0.00% 33 35 0.00% 34 24 0.00% 35 98 0.01% 36 548 0.05% 37 26 0.00% 38 56 0.00% 39 81 0.01% 40 95 0.01% 41 41 0.00% 42 162 0.01% 43 1952 0.17% 44 143 0.01% 45 1375 0.12% 46 216 0.02% 47 36 0.00% 48 66 0.01% 49 17 0.00% 50 10 0.00% 51 32 0.00% 52 13 0.00% 53 18 0.00% 54 13 0.00% 55 16 0.00% 56 9 0.00% 57 14 0.00% 58 19 0.00% 59 13 0.00% 60 19 0.00% 61 5 0.00% 62 2 0.00% 63 0 0.00% 64 3 0.00% 65 3 0.00% 66 5 0.00% 67 13 0.00% 68 20 0.00% 69 58 0.00% 70 8451 0.72% 71 7391 0.63% 72 8050 0.69% 73 7640 0.65% 74 7893 0.68% 75 7513 0.64% 76 6635 0.57% 77 6916 0.59% 78 7784 0.67% 79 8726 0.75% 80 7696 0.66% 81 9004 0.77% 82 10353 0.89% 83 10204 0.87% 84 8872 0.76% 85 37 0.00% 86 57 0.00% 87 78 0.01% 88 173 0.01% 89 343 0.03% 90 803 0.07% 91 2236 0.19% 92 11011 0.94% 93 1022626 87.64% 1166844 reads passed initial QC criterion=sequence-density sequence-density=1.64 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=1.64 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=24 fanout-score=49.96 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=4.1 sequence=ATCGATCGATCCGTGCATCGCCATGATGGTACCCATCGTCCATGGAATGTAGTGCGTGAGAGAGGTTTAAAATGCTGAGGGTGGGTGTAACATGTAAATTTGTACGCGTGCTGCGTGCACGCTTGTAATATTTATTATATTGTGCTCTTAGTGTGCATTGCATCTCTGATCACTC Started job on | Dec 07 06:58:26 Started mapping on | Dec 07 06:58:26 Finished on | Dec 07 06:58:32 Mapping speed, Million of reads per hour | 700.11 Number of input reads | 1166844 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 780332 Uniquely mapped reads % | 66.88% Average mapped length | 90.67 Number of splices: Total | 23604 Number of splices: Annotated (sjdb) | 19831 Number of splices: GT/AG | 22644 Number of splices: GC/AG | 613 Number of splices: AT/AC | 11 Number of splices: Non-canonical | 336 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.04% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 1.89 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 323375 % of reads mapped to multiple loci | 27.71% Number of reads mapped to too many loci | 31446 % of reads mapped to too many loci | 2.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.55% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 63137 63137 63137 N_multimapping 323375 323375 323375 N_noFeature 55867 63896 742463 N_ambiguous 34046 4215 170 UnstrandedReadsAssigned:690419 PositiveStrandReadsAssigned:712221 NegativeStrandReadsAssigned:37699 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133481 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: ERR6133481-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,166,844 reads, 916,167 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 951 rounds 52973 ERR6133481.ke.tsv 35125 ERR6133481.se.tsv 88098 total ==> ERR6133481.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 30 32.8745 PNS24243 293 194 0 0 KQK14069 1603 1504 19 18.9932 KQK14071 474 375 0 0 ==> ERR6133481.se.tsv <== BRADI_1g14170v3 19 BRADI_1g53295v3 6 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 5 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 21 BRADI_1g48960v3 0 ERR6133481 completed mapping pipeline successfully