Starting /dee2/code/volunteer_pipeline.sh ERR6133396 current disk space = 1547477929984 free memory = 1434837284 ERR6133396 SRAfilesize 17605d6ed57f0b89ac90efaa93d2261f ERR6133396.sra ERR6133396.sra file validated ERR6133396 is single end ERR6133396 is conventional basespace ERR6133396 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133396_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.744 33.0 27.0 33.0 15.0 37.0 2 33.1235 33.0 33.0 37.0 27.0 37.0 3 33.536 37.0 33.0 37.0 27.0 37.0 4 33.67775 37.0 33.0 37.0 27.0 37.0 5 33.8175 37.0 33.0 37.0 27.0 37.0 6 34.253 37.0 33.0 37.0 27.0 37.0 7 35.242 37.0 33.0 37.0 27.0 40.0 8 35.18925 37.0 33.0 40.0 27.0 40.0 9 35.31125 37.0 33.0 37.0 33.0 40.0 10-11 35.213375 37.0 33.0 38.5 27.0 40.0 12-13 34.9755 37.0 33.0 37.0 27.0 40.0 14-15 35.044375 37.0 33.0 37.0 27.0 40.0 16-17 34.911875 37.0 33.0 37.0 27.0 40.0 18-19 34.783375 37.0 33.0 37.0 27.0 40.0 20-21 34.056124999999994 37.0 33.0 37.0 24.5 40.0 22-23 33.5415 37.0 33.0 37.0 22.0 40.0 24-25 33.325500000000005 37.0 33.0 37.0 22.0 40.0 26-27 32.836749999999995 37.0 33.0 37.0 22.0 40.0 28-29 32.609625 33.0 33.0 37.0 22.0 40.0 30-31 32.397625 33.0 33.0 37.0 22.0 40.0 32-33 31.984875 33.0 30.0 37.0 22.0 40.0 34-35 31.203125 33.0 27.0 37.0 15.0 40.0 36-37 30.8265 33.0 27.0 37.0 15.0 38.5 38-39 30.80225 33.0 27.0 37.0 15.0 37.0 40-41 31.00175 33.0 27.0 37.0 18.5 38.5 42-43 30.806375 33.0 27.0 37.0 15.0 40.0 44-45 30.620125 33.0 27.0 37.0 18.5 38.5 46-47 29.955125000000002 33.0 27.0 37.0 15.0 37.0 48-49 29.714375 33.0 27.0 37.0 15.0 37.0 50-51 29.33175 33.0 27.0 37.0 15.0 37.0 52-53 29.098125 33.0 27.0 37.0 15.0 37.0 54-55 29.193 33.0 27.0 37.0 15.0 37.0 56-57 28.509625 33.0 27.0 35.0 15.0 37.0 58-59 28.257125000000002 33.0 24.5 33.0 15.0 37.0 60-61 27.84675 33.0 24.5 33.0 15.0 37.0 62-63 27.472 33.0 22.0 33.0 15.0 37.0 64-65 27.025375 33.0 22.0 33.0 10.5 37.0 66-67 26.693375 27.0 22.0 33.0 6.0 37.0 68-69 25.928 27.0 18.5 33.0 10.5 35.0 70-71 27.845399084295032 33.0 27.0 33.0 15.0 35.0 72-73 28.289697077586624 33.0 27.0 33.0 15.0 37.0 74-75 27.997444334740162 33.0 27.0 33.0 15.0 37.0 76-77 27.930489889877386 33.0 27.0 33.0 15.0 37.0 78-79 27.095654608247735 33.0 24.5 33.0 6.0 37.0 80-81 26.206651604147368 33.0 22.0 33.0 4.0 37.0 82-83 25.36662057256556 33.0 22.0 33.0 2.0 37.0 84-85 24.935966626685545 33.0 18.5 33.0 2.0 37.0 86-87 23.960695187165776 30.0 15.0 33.0 2.0 35.0 88-89 23.40681818181818 30.0 10.5 33.0 2.0 33.0 90-91 21.997593582887703 27.0 2.0 33.0 2.0 33.0 92-93 20.74077540106952 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 104.0 21 160.0 22 145.0 23 155.0 24 178.0 25 211.0 26 251.0 27 263.0 28 239.0 29 253.0 30 256.0 31 247.0 32 269.0 33 262.0 34 288.0 35 258.0 36 251.0 37 184.0 38 26.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.125 8.475000000000001 8.6 13.8 2 52.349999999999994 23.0 14.975 9.675 3 33.725 35.099999999999994 17.849999999999998 13.325000000000001 4 24.3 32.35 22.35 21.0 5 28.9 23.849999999999998 28.025 19.225 6 15.2 40.300000000000004 25.974999999999998 18.525 7 36.7 27.05 18.9 17.349999999999998 8 24.45 25.650000000000002 24.9 25.0 9 20.275000000000002 34.825 26.075 18.825 10-11 21.224999999999998 28.962500000000002 32.0375 17.775 12-13 19.725 31.724999999999998 26.875 21.675 14-15 18.5625 35.6375 27.237499999999997 18.5625 16-17 25.2125 28.6625 22.5 23.625 18-19 23.724999999999998 23.5875 33.625 19.0625 20-21 26.387500000000003 23.175 31.874999999999996 18.5625 22-23 29.362500000000004 21.0 31.25 18.387500000000003 24-25 22.037499999999998 24.55 30.2375 23.175 26-27 25.4 23.150000000000002 28.999999999999996 22.45 28-29 22.037499999999998 29.562500000000004 30.7375 17.6625 30-31 32.25 24.9 24.887500000000003 17.962500000000002 32-33 26.75 22.912499999999998 27.6 22.7375 34-35 20.825 36.3125 24.025 18.8375 36-37 26.924999999999997 26.1125 23.6375 23.325000000000003 38-39 33.5125 21.9625 26.337500000000002 18.1875 40-41 22.5875 23.4625 35.5375 18.4125 42-43 27.474999999999998 29.599999999999998 25.6125 17.3125 44-45 24.75 25.2 31.0375 19.0125 46-47 27.2625 23.8375 25.587500000000002 23.3125 48-49 26.0625 23.075000000000003 27.425 23.4375 50-51 20.875 30.349999999999998 25.837500000000002 22.9375 52-53 21.837500000000002 25.45 24.8125 27.900000000000002 54-55 21.55 24.925 31.45 22.075 56-57 26.9625 30.0375 25.2 17.8 58-59 20.8625 30.562499999999996 29.562500000000004 19.0125 60-61 31.0125 25.5375 25.7375 17.712500000000002 62-63 19.8125 26.1125 31.587500000000002 22.4875 64-65 19.175 37.6 25.4 17.825 66-67 25.362499999999997 30.9 25.025 18.712500000000002 68-69 19.5875 25.8625 29.562500000000004 24.9875 70-71 22.28900576008014 29.539193588780364 24.655647382920108 23.516153268219384 72-73 25.355838266784232 25.64554729814838 30.369064113868244 18.629550321199144 74-75 26.42131979695431 30.063451776649746 25.926395939086294 17.588832487309645 76-77 21.565863659661712 23.449513070220398 25.909789851358276 29.07483341875961 78-79 25.449838187702266 29.009708737864077 27.28802588996764 18.25242718446602 80-81 20.75816993464052 36.993464052287585 25.084967320261438 17.163398692810457 82-83 23.48044397463002 25.726744186046513 25.21141649048626 25.581395348837212 84-85 20.89671737389912 26.75473712303176 32.2257806244996 20.12276487856952 86-87 20.588235294117645 30.04010695187166 24.665775401069517 24.705882352941178 88-89 18.836898395721924 27.018716577540108 31.44385026737968 22.70053475935829 90-91 25.04010695187166 31.390374331550802 24.31818181818182 19.25133689839572 92-93 18.422459893048128 29.906417112299465 29.53208556149733 22.13903743315508 >>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 0.0 17 2.0 18 4.0 19 4.0 20 2.0 21 1.5 22 4.0 23 6.5 24 6.5 25 9.0 26 13.0 27 16.0 28 25.0 29 31.0 30 30.0 31 38.5 32 45.5 33 54.0 34 71.5 35 86.0 36 116.5 37 184.0 38 223.5 39 199.5 40 219.5 41 229.5 42 217.0 43 231.0 44 219.0 45 191.5 46 143.0 47 116.0 48 113.0 49 109.0 50 113.0 51 113.0 52 109.5 53 138.0 54 264.5 55 259.0 56 119.0 57 78.0 58 55.5 59 32.5 60 25.5 61 23.5 62 20.5 63 11.5 64 7.0 65 7.5 66 8.0 67 7.0 68 7.5 69 8.5 70 6.5 71 4.0 72 2.0 73 0.0 74 0.0 75 0.0 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 14.0 71 7.0 72 19.0 73 13.0 74 14.0 75 20.0 76 22.0 77 19.0 78 19.0 79 21.0 80 14.0 81 23.0 82 22.0 83 19.0 84 14.0 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 3740.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 68.75 #Duplication Level Percentage of deduplicated Percentage of total 1 91.85454545454546 63.14999999999999 2 3.272727272727273 4.5 3 1.6363636363636365 3.375 4 0.8727272727272728 2.4 5 0.6181818181818182 2.125 6 0.32727272727272727 1.35 7 0.14545454545454545 0.7000000000000001 8 0.36363636363636365 2.0 9 0.0 0.0 >10 0.8363636363636363 10.775 >50 0.03636363636363636 1.325 >100 0.03636363636363636 8.3 >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 332 8.3 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 53 1.325 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 42 1.05 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 29 0.7250000000000001 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 29 0.7250000000000001 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 29 0.7250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 26 0.65 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 23 0.575 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 23 0.575 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 22 0.5499999999999999 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 19 0.475 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 19 0.475 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 19 0.475 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 16 0.4 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 15 0.375 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 13 0.325 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 13 0.325 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 13 0.325 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 11 0.27499999999999997 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 11 0.27499999999999997 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 10 0.25 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 8 0.2 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 8 0.2 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 8 0.2 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 8 0.2 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 8 0.2 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 8 0.2 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 7 0.17500000000000002 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 7 0.17500000000000002 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 6 0.15 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 6 0.15 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 6 0.15 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 6 0.15 No Hit GATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAA 6 0.15 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit GCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGT 6 0.15 No Hit GGGTATCCATGCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTCATGTT 5 0.125 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 5 0.125 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 5 0.125 No Hit GTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGA 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 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 0.0 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 AGAGCAA 35 5.5606506E-8 73.60714 4 GGAGAGC 40 1.4029138E-7 64.40625 2 GGGAGAG 40 1.4029138E-7 64.40625 1 CAATACA 40 1.4029138E-7 64.40625 8 GAGCAAT 40 1.4029138E-7 64.40625 5 AATACAA 40 1.4029138E-7 64.40625 9 AGCAATA 40 1.4029138E-7 64.40625 6 GCAATAC 45 3.1700074E-7 57.250004 7 GAGAGCA 45 3.1700074E-7 57.250004 3 TGCTGCT 30 2.6342168E-6 42.9375 22-23 GCTGCTA 30 2.6342168E-6 42.9375 22-23 TGCTAGG 30 2.6342168E-6 42.9375 24-25 CTGCTAG 30 2.6342168E-6 42.9375 24-25 GTGCTGC 30 2.6342168E-6 42.9375 20-21 AAAAAAA 25 0.001695651 37.135136 86-87 GCTAGGC 35 7.600218E-6 36.80357 26-27 AGGCGAA 35 7.600218E-6 36.80357 28-29 CTAGGCG 35 7.600218E-6 36.80357 26-27 TACAAGC 35 7.600218E-6 36.80357 10-11 AAGCGTT 35 7.600218E-6 36.80357 14-15 >>END_MODULE Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25928 READS because READLEN < 1 Read 25928 spots for ERR6133396.sra Written 25928 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra Rejected 25913 READS because READLEN < 1 Read 25913 spots for ERR6133396.sra Written 25913 spots for ERR6133396.sra SRR ids: ['ERR6133396.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hjcqtyys ERR6133396.sra spots: 518275 blocks: [[1, 25913], [25914, 51826], [51827, 77739], [77740, 103652], [103653, 129565], [129566, 155478], [155479, 181391], [181392, 207304], [207305, 233217], [233218, 259130], [259131, 285043], [285044, 310956], [310957, 336869], [336870, 362782], [362783, 388695], [388696, 414608], [414609, 440521], [440522, 466434], [466435, 492347], [492348, 518275]] ERR6133396 file size 113173 ERR6133396 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 ERR6133396 ERR6133396_1.fastq Input file: ERR6133396_1.fastq trimmed: ERR6133396-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 03:04:04 2024 >> started Sat Dec 7 03:04:05 2024 >> done (0.717s) 518275 reads processed; of these: 8 ( 0.00%) short reads filtered out after trimming by size control 1 ( 0.00%) empty reads filtered out after trimming by size control 518266 (100.00%) reads available; of these: 137843 (26.60%) trimmed reads available after processing 380423 (73.40%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 0 0.00% 21 0 0.00% 22 1 0.00% 23 1 0.00% 24 1 0.00% 25 0 0.00% 26 0 0.00% 27 1 0.00% 28 1 0.00% 29 22 0.00% 30 0 0.00% 31 1 0.00% 32 1 0.00% 33 2 0.00% 34 1 0.00% 35 0 0.00% 36 2 0.00% 37 1 0.00% 38 7 0.00% 39 6 0.00% 40 4 0.00% 41 6 0.00% 42 4 0.00% 43 6 0.00% 44 7 0.00% 45 17 0.00% 46 19 0.00% 47 20 0.00% 48 26 0.01% 49 41 0.01% 50 50 0.01% 51 63 0.01% 52 101 0.02% 53 146 0.03% 54 217 0.04% 55 271 0.05% 56 380 0.07% 57 562 0.11% 58 431 0.08% 59 492 0.09% 60 661 0.13% 61 717 0.14% 62 789 0.15% 63 859 0.17% 64 956 0.18% 65 964 0.19% 66 1052 0.20% 67 1046 0.20% 68 910 0.18% 69 929 0.18% 70 3011 0.58% 71 3129 0.60% 72 3717 0.72% 73 3970 0.77% 74 4201 0.81% 75 4584 0.88% 76 4789 0.92% 77 5480 1.06% 78 5652 1.09% 79 5742 1.11% 80 6216 1.20% 81 7037 1.36% 82 7446 1.44% 83 7912 1.53% 84 8739 1.69% 85 6887 1.33% 86 7120 1.37% 87 7886 1.52% 88 9727 1.88% 89 9971 1.92% 90 10736 2.07% 91 11258 2.17% 92 9899 1.91% 93 351359 67.80% 518266 reads passed initial QC criterion=sequence-density sequence-density=2.51 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=23 prefix-density=2.58 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.13 sequence-density-rank=20 fanout-score=102.81 fanout-score-rank=1 prefix-density=12.54 prefix-fanout=1.0 sequence=CCTAGATGGCTCAAGTCCAGTAG 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 03:04:24 Started mapping on | Dec 07 03:04:25 Finished on | Dec 07 03:04:31 Mapping speed, Million of reads per hour | 310.96 Number of input reads | 518266 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 183372 Uniquely mapped reads % | 35.38% Average mapped length | 88.31 Number of splices: Total | 8222 Number of splices: Annotated (sjdb) | 6466 Number of splices: GT/AG | 7796 Number of splices: GC/AG | 131 Number of splices: AT/AC | 6 Number of splices: Non-canonical | 289 Mismatch rate per base, % | 0.87% Deletion rate per base | 0.04% Deletion average length | 1.74 Insertion rate per base | 0.02% Insertion average length | 1.85 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 292490 % of reads mapped to multiple loci | 56.44% Number of reads mapped to too many loci | 12544 % of reads mapped to too many loci | 2.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.37% % of reads unmapped: other | 0.39% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 42404 42404 42404 N_multimapping 292490 292490 292490 N_noFeature 17495 19543 175440 N_ambiguous 7142 1253 40 UnstrandedReadsAssigned:158735 PositiveStrandReadsAssigned:162576 NegativeStrandReadsAssigned:7892 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=86 echo kmer=81 ERR6133396 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: ERR6133396-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 518,266 reads, 320,913 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 725 rounds 52973 ERR6133396.ke.tsv 35125 ERR6133396.se.tsv 88098 total ==> ERR6133396.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 4 11.8369 PNS24243 293 194 0 0 KQK14069 1603 1504 2 5.39902 KQK14071 474 375 0 0 ==> ERR6133396.se.tsv <== BRADI_1g14170v3 2 BRADI_1g53295v3 3 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 0 ERR6133396 completed mapping pipeline successfully