Starting /dee2/code/volunteer_pipeline.sh ERR9452003 current disk space = 1548639145984 free memory = 1601808388 ERR9452003 SRAfilesize d46e72e81ebb790360fd197fc6f12928 ERR9452003.sra ERR9452003.sra file validated ERR9452003 is single end ERR9452003 is conventional basespace ERR9452003 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452003_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.248 37.0 37.0 37.0 37.0 37.0 2 36.582 37.0 37.0 37.0 37.0 37.0 3 36.6955 37.0 37.0 37.0 37.0 37.0 4 36.673 37.0 37.0 37.0 37.0 37.0 5 36.737 37.0 37.0 37.0 37.0 37.0 6 36.63 37.0 37.0 37.0 37.0 37.0 7 36.6795 37.0 37.0 37.0 37.0 37.0 8 36.6775 37.0 37.0 37.0 37.0 37.0 9 36.724 37.0 37.0 37.0 37.0 37.0 10 36.6705 37.0 37.0 37.0 37.0 37.0 11 36.7745 37.0 37.0 37.0 37.0 37.0 12 36.7225 37.0 37.0 37.0 37.0 37.0 13 36.7175 37.0 37.0 37.0 37.0 37.0 14 36.688 37.0 37.0 37.0 37.0 37.0 15 36.741 37.0 37.0 37.0 37.0 37.0 16 36.659 37.0 37.0 37.0 37.0 37.0 17 36.7005 37.0 37.0 37.0 37.0 37.0 18 36.726 37.0 37.0 37.0 37.0 37.0 19 36.7275 37.0 37.0 37.0 37.0 37.0 20 36.728 37.0 37.0 37.0 37.0 37.0 21 36.794 37.0 37.0 37.0 37.0 37.0 22 36.6535 37.0 37.0 37.0 37.0 37.0 23 36.7955 37.0 37.0 37.0 37.0 37.0 24 36.7795 37.0 37.0 37.0 37.0 37.0 25 36.8015 37.0 37.0 37.0 37.0 37.0 26 36.7355 37.0 37.0 37.0 37.0 37.0 27 36.748 37.0 37.0 37.0 37.0 37.0 28 36.8005 37.0 37.0 37.0 37.0 37.0 29 36.799 37.0 37.0 37.0 37.0 37.0 30 36.8215 37.0 37.0 37.0 37.0 37.0 31 36.7655 37.0 37.0 37.0 37.0 37.0 32 36.727 37.0 37.0 37.0 37.0 37.0 33 36.8025 37.0 37.0 37.0 37.0 37.0 34 36.747 37.0 37.0 37.0 37.0 37.0 35 36.759 37.0 37.0 37.0 37.0 37.0 36 36.755 37.0 37.0 37.0 37.0 37.0 37 36.729 37.0 37.0 37.0 37.0 37.0 38 36.746 37.0 37.0 37.0 37.0 37.0 39 36.6725 37.0 37.0 37.0 37.0 37.0 40 36.661 37.0 37.0 37.0 37.0 37.0 41 36.7405 37.0 37.0 37.0 37.0 37.0 42 36.535 37.0 37.0 37.0 37.0 37.0 43 36.6005 37.0 37.0 37.0 37.0 37.0 44 36.482 37.0 37.0 37.0 37.0 37.0 45 36.5605 37.0 37.0 37.0 37.0 37.0 46 35.934 37.0 37.0 37.0 37.0 37.0 47 36.367 37.0 37.0 37.0 37.0 37.0 48 35.9625 37.0 37.0 37.0 37.0 37.0 49 36.258 37.0 37.0 37.0 37.0 37.0 50 36.4465 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 0.0 26 5.0 27 4.0 28 9.0 29 7.0 30 12.0 31 13.0 32 27.0 33 38.0 34 40.0 35 107.0 36 1302.0 37 2435.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 19.1183879093199 36.90176322418136 18.66498740554156 25.31486146095718 2 42.199999999999996 23.05 16.275000000000002 18.475 3 47.65 21.675 13.0 17.675 4 48.949999999999996 23.275000000000002 14.000000000000002 13.775 5 21.475 29.299999999999997 15.75 33.475 6 22.725 17.65 42.025 17.599999999999998 7 28.65 37.6 19.575 14.174999999999999 8 20.625 19.8 42.675000000000004 16.900000000000002 9 21.625 43.025000000000006 19.525000000000002 15.825 10 44.35 21.05 19.05 15.55 11 20.075000000000003 19.950000000000003 24.075 35.9 12 19.8 20.849999999999998 41.025 18.325 13 19.275000000000002 23.35 15.7 41.675000000000004 14 22.475 47.825 15.275 14.424999999999999 15 40.625 30.55 14.249999999999998 14.575 16 21.325 46.175 17.224999999999998 15.275 17 22.325 27.800000000000004 35.35 14.524999999999999 18 26.05 24.325 15.525 34.1 19 47.875 26.55 11.825 13.750000000000002 20 49.025 27.250000000000004 12.775 10.95 21 28.225 50.824999999999996 8.7 12.25 22 30.125 51.0 8.5 10.375 23 50.075 31.8 7.3 10.825 24 31.775 51.9 5.025 11.3 25 49.425000000000004 32.550000000000004 4.575 13.450000000000001 26 29.65 30.925000000000004 4.55 34.875 27 22.775000000000002 53.925 2.5 20.8 28 26.0 31.775 2.725 39.5 29 21.675 49.575 3.25 25.5 30 20.424999999999997 31.924999999999997 4.675 42.975 31 39.375 23.974999999999998 8.725 27.925 32 19.15 23.9 30.099999999999998 26.85 33 17.2 20.65 15.15 47.0 34 20.549999999999997 18.875 34.55 26.025 35 35.525 21.85 18.175 24.45 36 17.325 41.825 15.85 25.0 37 15.174999999999999 42.199999999999996 18.75 23.875 38 14.575 21.975 19.1 44.35 39 11.475 21.25 37.5 29.775000000000002 40 12.475 21.4 19.0 47.125 41 11.3 20.625 16.900000000000002 51.175000000000004 42 11.700000000000001 41.675000000000004 17.474999999999998 29.15 43 31.6 21.9 17.275 29.225 44 13.15 19.900000000000002 35.35 31.6 45 10.225 25.3 17.275 47.199999999999996 46 13.225000000000001 41.775 12.85 32.15 47 10.549999999999999 26.55 14.899999999999999 48.0 48 14.025000000000002 45.550000000000004 12.925 27.500000000000004 49 35.3 29.299999999999997 12.275 23.125 50 15.825 46.275 16.175 21.725 >>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 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.5 30 1.0 31 1.0 32 1.0 33 0.5 34 0.0 35 0.5 36 1.0 37 2.5 38 4.0 39 8.0 40 12.0 41 18.0 42 24.0 43 52.0 44 80.0 45 183.5 46 287.0 47 475.5 48 664.0 49 577.0 50 490.0 51 843.0 52 1196.0 53 922.5 54 649.0 55 510.0 56 371.0 57 256.5 58 142.0 59 96.0 60 50.0 61 33.0 62 16.0 63 12.5 64 9.0 65 6.0 66 3.0 67 1.5 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 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 0.75 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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 47.75 #Duplication Level Percentage of deduplicated Percentage of total 1 82.87958115183245 39.574999999999996 2 9.947643979057592 9.5 3 2.931937172774869 4.2 4 1.0471204188481675 2.0 5 0.6806282722513088 1.625 6 0.31413612565445026 0.8999999999999999 7 0.20942408376963353 0.7000000000000001 8 0.15706806282722513 0.6 9 0.15706806282722513 0.675 >10 1.3612565445026177 13.65 >50 0.20942408376963353 6.45 >100 0.052356020942408384 4.8500000000000005 >500 0.052356020942408384 15.275 >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 AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 611 15.275 TruSeq Adapter, Index 2 (97% over 36bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 194 4.8500000000000005 TruSeq Adapter, Index 2 (97% over 36bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 68 1.7000000000000002 TruSeq Adapter, Index 2 (97% over 35bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT 67 1.675 TruSeq Adapter, Index 2 (97% over 37bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 64 1.6 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 59 1.4749999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 48 1.2 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 46 1.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 38 0.95 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 37 0.9249999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 27 0.675 TruSeq Adapter, Index 2 (97% over 35bp) TCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 26 0.65 TruSeq Adapter, Index 2 (97% over 35bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATG 21 0.525 TruSeq Adapter, Index 2 (97% over 38bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGT 17 0.42500000000000004 TruSeq Adapter, Index 2 (97% over 39bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGT 14 0.35000000000000003 TruSeq Adapter, Index 2 (97% over 39bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT 13 0.325 TruSeq Adapter, Index 2 (97% over 37bp) CGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 13 0.325 TruSeq Adapter, Index 2 (97% over 36bp) TTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTACA 13 0.325 TruSeq Adapter, Index 2 (97% over 40bp) GTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 13 0.325 TruSeq Adapter, Index 2 (97% over 36bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GGGGATATGGCGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT 11 0.27499999999999997 TruSeq Adapter, Index 2 (97% over 37bp) ATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTAC 10 0.25 TruSeq Adapter, Index 2 (97% over 40bp) CGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 9 0.22499999999999998 TruSeq Adapter, Index 2 (97% over 36bp) CACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATG 9 0.22499999999999998 TruSeq Adapter, Index 2 (97% over 38bp) CTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) AAAGATGGTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 7 0.17500000000000002 TruSeq Adapter, Index 2 (97% over 36bp) GGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 7 0.17500000000000002 TruSeq Adapter, Index 2 (97% over 36bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGA 6 0.15 TruSeq Adapter, Index 2 (97% over 36bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGACGGAACCAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATG 6 0.15 TruSeq Adapter, Index 2 (97% over 38bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TTGTGAAATGACTTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CGGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 5 0.125 TruSeq Adapter, Index 2 (97% over 35bp) GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TGCGGAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT 5 0.125 TruSeq Adapter, Index 2 (97% over 37bp) GTGGACTGTTGTCGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GTGGACTGTTGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT 5 0.125 TruSeq Adapter, Index 2 (97% over 37bp) GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAAGGATCATTGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT 5 0.125 TruSeq Adapter, Index 2 (97% over 37bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGAT 5 0.125 TruSeq Adapter, Index 2 (97% over 37bp) >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.05 0.0 0.0 0.0 0.0 4 0.075 0.0 0.0 0.0 0.0 5 0.1 0.0 0.0 0.0 0.0 6 0.15 0.0 0.0 0.0 0.0 7 0.275 0.0 0.0 0.0 0.0 8 0.775 0.0 0.0 0.0 0.0 9 1.25 0.0 0.0 0.0 0.0 10 1.875 0.0 0.0 0.0 0.0 11 3.9 0.0 0.0 0.0 0.0 12 6.925 0.0 0.0 0.0 0.0 13 12.725 0.0 0.0 0.0 0.0 14 39.075 0.0 0.0 0.0 0.0 15 47.275 0.0 0.0 0.0 0.0 16 54.525 0.0 0.0 0.0 0.0 17 63.45 0.0 0.0 0.0 0.0 18 69.625 0.0 0.0 0.0 0.0 19 76.075 0.0 0.0 0.0 0.0 20 82.225 0.0 0.0 0.0 0.0 21 86.05 0.0 0.0 0.0 0.0 22 89.8 0.0 0.0 0.0 0.0 23 93.175 0.0 0.0 0.0 0.0 24 94.8 0.0 0.0 0.0 0.0 25 96.15 0.0 0.0 0.0 0.0 26 96.65 0.0 0.0 0.0 0.0 27 97.375 0.0 0.0 0.0 0.0 28 97.725 0.0 0.0 0.0 0.0 29 98.0 0.0 0.0 0.0 0.0 30 98.15 0.0 0.0 0.0 0.0 31 98.2 0.0 0.0 0.0 0.0 32 98.35 0.0 0.0 0.0 0.0 33 98.4 0.0 0.0 0.0 0.0 34 98.45 0.0 0.0 0.0 0.0 35 98.45 0.0 0.0 0.0 0.0 36 98.475 0.0 0.0 0.0 0.0 37 98.475 0.0 0.0 0.0 0.0 38 98.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGGGCTA 70 0.0 44.544304 1 GGGGATG 20 6.532858E-4 44.544304 1 CTATAGC 70 0.0 43.9875 5 AGCTCAG 95 0.0 43.9875 9 TAGCTCA 100 0.0 43.9875 8 GCTATAG 70 0.0 43.9875 4 ATAGCTC 70 0.0 43.9875 7 GGGATGT 20 6.9617946E-4 43.9875 2 GGCTATA 70 0.0 43.9875 3 GCTCAGA 90 0.0 43.9875 10 TATAGCT 70 0.0 43.9875 6 GGGCTAT 70 0.0 43.9875 2 CTCAGAT 95 0.0 41.67237 11 TCAGATC 110 0.0 37.989204 12 TGTAGCT 30 1.0856931E-4 36.65625 6 CACAGAT 30 1.0856931E-4 36.65625 44 GTAGCTC 30 1.0856931E-4 36.65625 7 GGATGTA 25 0.0020872154 35.19 3 GATGTAG 25 0.0020872154 35.19 4 ATGTAGC 25 0.0020872154 35.19 5 >>END_MODULE Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816114 READS because READLEN < 1 Read 816114 spots for ERR9452003.sra Written 816114 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra Rejected 816103 READS because READLEN < 1 Read 816103 spots for ERR9452003.sra Written 816103 spots for ERR9452003.sra SRR ids: ['ERR9452003.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4nn49qc4 ERR9452003.sra spots: 16322071 blocks: [[1, 816103], [816104, 1632206], [1632207, 2448309], [2448310, 3264412], [3264413, 4080515], [4080516, 4896618], [4896619, 5712721], [5712722, 6528824], [6528825, 7344927], [7344928, 8161030], [8161031, 8977133], [8977134, 9793236], [9793237, 10609339], [10609340, 11425442], [11425443, 12241545], [12241546, 13057648], [13057649, 13873751], [13873752, 14689854], [14689855, 15505957], [15505958, 16322071]] ERR9452003 file size 2273590 ERR9452003 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 ERR9452003 ERR9452003_1.fastq Input file: ERR9452003_1.fastq trimmed: ERR9452003-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 Fri Dec 6 22:30:47 2024 >> started Fri Dec 6 22:30:55 2024 >> done (7.826s) 16322071 reads processed; of these: 11453378 (70.17%) short reads filtered out after trimming by size control 7264 ( 0.04%) empty reads filtered out after trimming by size control 4861429 (29.78%) reads available; of these: 966513 (19.88%) trimmed reads available after processing 3894916 (80.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 966513 19.88% 19 0 0.00% 20 0 0.00% 21 0 0.00% 22 0 0.00% 23 0 0.00% 24 0 0.00% 25 0 0.00% 26 0 0.00% 27 0 0.00% 28 0 0.00% 29 0 0.00% 30 0 0.00% 31 0 0.00% 32 0 0.00% 33 0 0.00% 34 0 0.00% 35 0 0.00% 36 0 0.00% 37 0 0.00% 38 0 0.00% 39 0 0.00% 40 0 0.00% 41 0 0.00% 42 0 0.00% 43 0 0.00% 44 0 0.00% 45 0 0.00% 46 0 0.00% 47 0 0.00% 48 0 0.00% 49 0 0.00% 50 3894916 80.12% 4861429 reads passed initial QC criterion=sequence-density sequence-density=78.27 sequence-density-rank=1 fanout-score=20.98 fanout-score-rank=1 prefix-density=78.51 prefix-fanout=20.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTACATCTCGTATGCCG criterion=fanout-score sequence-density=78.27 sequence-density-rank=1 fanout-score=20.98 fanout-score-rank=1 prefix-density=78.51 prefix-fanout=20.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTACATCTCGTATGCCG 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: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTACATCTCGTATGCCG -o ERR9452003 - Input file: STDIN trimmed: ERR9452003-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGATGTACATCTCGTATGCCG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Fri Dec 6 22:31:07 2024 >> started Fri Dec 6 22:31:12 2024 >> done (5.203s) 4738355 reads processed; of these: 21727 ( 0.46%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 4716620 (99.54%) reads available; of these: 3745424 (79.41%) trimmed reads available after processing 971196 (20.59%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 952963 20.20% 19 919476 19.49% 20 763205 16.18% 21 627443 13.30% 22 511657 10.85% 23 265001 5.62% 24 249459 5.29% 25 125589 2.66% 26 79151 1.68% 27 50512 1.07% 28 35068 0.74% 29 28311 0.60% 30 18716 0.40% 31 13612 0.29% 32 11728 0.25% 33 8160 0.17% 34 4815 0.10% 35 3787 0.08% 36 1939 0.04% 37 1372 0.03% 38 888 0.02% 39 744 0.02% 40 598 0.01% 41 802 0.02% 42 339 0.01% 43 252 0.01% 44 257 0.01% 45 316 0.01% 46 512 0.01% 47 1459 0.03% 48 0 0.00% 49 0 0.00% 50 38489 0.82% criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=14 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGGATGTAGCTCAGATGGTAGAGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=19 fanout-score=8.49 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.0 sequence=CCGGCGATGCGTCCTGGCCGTATGCGGAACGGCTTTTGCTGGTCCGCCGCTCGGCTCGGGGCGTGGACTGTTGTCGGCCGTGCTGGCGGCCCAAGC Started job on | Dec 06 22:31:28 Started mapping on | Dec 06 22:31:28 Finished on | Dec 06 22:31:52 Mapping speed, Million of reads per hour | 725.95 Number of input reads | 4839694 Average input read length | 21 UNIQUE READS: Uniquely mapped reads number | 403560 Uniquely mapped reads % | 8.34% Average mapped length | 21.29 Number of splices: Total | 16527 Number of splices: Annotated (sjdb) | 8401 Number of splices: GT/AG | 16251 Number of splices: GC/AG | 254 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 19 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.00% Deletion average length | 1.39 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2026492 % of reads mapped to multiple loci | 41.87% Number of reads mapped to too many loci | 2254960 % of reads mapped to too many loci | 46.59% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.03% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2409642 2409642 2409642 N_multimapping 2026492 2026492 2026492 N_noFeature 168997 189799 377861 N_ambiguous 7164 2130 173 UnstrandedReadsAssigned:227399 PositiveStrandReadsAssigned:211631 NegativeStrandReadsAssigned:25526 Dataset is classified positive stranded MeadianReadLen=20 20thPercentileLength=18 echo kmer=19 ERR9452003 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: ERR9452003-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,839,694 reads, 410,675 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 832 rounds 52973 ERR9452003.ke.tsv 35125 ERR9452003.se.tsv 88098 total ==> ERR9452003.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 1.43551 2.82013 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 2.56449 3.0735 PNS24243 293 194 0 0 KQK14069 1603 1504 59.7815 65.3591 KQK14071 474 375 5.15777 22.6161 ==> ERR9452003.se.tsv <== BRADI_1g14170v3 120 BRADI_1g53295v3 3 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 0 ERR9452003 completed mapping pipeline successfully