Starting /dee2/code/volunteer_pipeline.sh ERR9452013 current disk space = 1548596412416 free memory = 1600069176 ERR9452013 SRAfilesize c4cb71b1259829cb783244189c126882 ERR9452013.sra ERR9452013.sra file validated ERR9452013 is single end ERR9452013 is conventional basespace ERR9452013 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452013_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.055 37.0 37.0 37.0 37.0 37.0 2 36.321 37.0 37.0 37.0 37.0 37.0 3 36.489 37.0 37.0 37.0 37.0 37.0 4 36.447 37.0 37.0 37.0 37.0 37.0 5 36.4185 37.0 37.0 37.0 37.0 37.0 6 36.474 37.0 37.0 37.0 37.0 37.0 7 36.5 37.0 37.0 37.0 37.0 37.0 8 36.3925 37.0 37.0 37.0 37.0 37.0 9 36.413 37.0 37.0 37.0 37.0 37.0 10 36.428 37.0 37.0 37.0 37.0 37.0 11 36.5055 37.0 37.0 37.0 37.0 37.0 12 36.4525 37.0 37.0 37.0 37.0 37.0 13 36.432 37.0 37.0 37.0 37.0 37.0 14 36.3555 37.0 37.0 37.0 37.0 37.0 15 36.4615 37.0 37.0 37.0 37.0 37.0 16 36.367 37.0 37.0 37.0 37.0 37.0 17 36.351 37.0 37.0 37.0 37.0 37.0 18 36.529 37.0 37.0 37.0 37.0 37.0 19 36.4085 37.0 37.0 37.0 37.0 37.0 20 36.5255 37.0 37.0 37.0 37.0 37.0 21 36.4285 37.0 37.0 37.0 37.0 37.0 22 36.4055 37.0 37.0 37.0 37.0 37.0 23 36.5185 37.0 37.0 37.0 37.0 37.0 24 36.505 37.0 37.0 37.0 37.0 37.0 25 36.5345 37.0 37.0 37.0 37.0 37.0 26 36.4765 37.0 37.0 37.0 37.0 37.0 27 36.4695 37.0 37.0 37.0 37.0 37.0 28 36.461 37.0 37.0 37.0 37.0 37.0 29 36.505 37.0 37.0 37.0 37.0 37.0 30 36.581 37.0 37.0 37.0 37.0 37.0 31 36.5555 37.0 37.0 37.0 37.0 37.0 32 36.4515 37.0 37.0 37.0 37.0 37.0 33 36.4815 37.0 37.0 37.0 37.0 37.0 34 36.481 37.0 37.0 37.0 37.0 37.0 35 36.5195 37.0 37.0 37.0 37.0 37.0 36 36.424 37.0 37.0 37.0 37.0 37.0 37 36.4485 37.0 37.0 37.0 37.0 37.0 38 36.4675 37.0 37.0 37.0 37.0 37.0 39 36.494 37.0 37.0 37.0 37.0 37.0 40 36.384 37.0 37.0 37.0 37.0 37.0 41 36.441 37.0 37.0 37.0 37.0 37.0 42 36.3805 37.0 37.0 37.0 37.0 37.0 43 36.3455 37.0 37.0 37.0 37.0 37.0 44 36.2935 37.0 37.0 37.0 37.0 37.0 45 36.225 37.0 37.0 37.0 37.0 37.0 46 36.436 37.0 37.0 37.0 37.0 37.0 47 36.442 37.0 37.0 37.0 37.0 37.0 48 36.4495 37.0 37.0 37.0 37.0 37.0 49 36.4555 37.0 37.0 37.0 37.0 37.0 50 36.518 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 3.0 24 2.0 25 7.0 26 2.0 27 9.0 28 15.0 29 20.0 30 19.0 31 25.0 32 45.0 33 62.0 34 75.0 35 149.0 36 1459.0 37 2107.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 19.184290030211482 27.492447129909365 23.96777442094663 29.35548841893253 2 23.785678517776667 30.771156735102657 24.01101652478718 21.4321482223335 3 29.4 29.599999999999998 16.325 24.675 4 31.175000000000004 32.625 17.325 18.875 5 23.05 29.475 18.224999999999998 29.25 6 28.225 24.349999999999998 25.974999999999998 21.45 7 26.825 31.874999999999996 22.025 19.275000000000002 8 23.625 27.925 26.3 22.15 9 23.775 28.975 22.650000000000002 24.6 10 36.675000000000004 23.575 18.95 20.8 11 23.625 26.900000000000002 26.700000000000003 22.775000000000002 12 25.05 25.974999999999998 26.924999999999997 22.05 13 26.25 23.3 19.35 31.1 14 30.575000000000003 32.6 19.825 17.0 15 25.525 33.275 22.650000000000002 18.55 16 21.675 28.325 30.2 19.8 17 24.349999999999998 26.650000000000002 31.624999999999996 17.375 18 29.725 24.9 25.35 20.025000000000002 19 36.875 29.7 18.525 14.899999999999999 20 26.6 33.875 25.575 13.950000000000001 21 24.175 39.2 18.475 18.15 22 26.150000000000002 35.425000000000004 20.025000000000002 18.4 23 33.275 34.625 18.025 14.075 24 30.55 35.4 17.849999999999998 16.2 25 31.1 36.475 15.45 16.975 26 33.525 28.675 17.9 19.900000000000002 27 32.824999999999996 39.15 9.375 18.65 28 38.75 34.050000000000004 12.25 14.95 29 35.475 36.025 9.45 19.05 30 33.275 41.875 7.000000000000001 17.849999999999998 31 41.425 35.75 5.975 16.85 32 35.699999999999996 38.25 7.625 18.425 33 28.549999999999997 43.75 5.7 22.0 34 34.949999999999996 32.95 7.249999999999999 24.85 35 28.050000000000004 38.5 6.5 26.950000000000003 36 26.6 39.25 6.275 27.875 37 24.349999999999998 32.475 9.025 34.150000000000006 38 22.225 34.300000000000004 11.899999999999999 31.574999999999996 39 22.5 25.825 14.825 36.85 40 23.025000000000002 29.049999999999997 18.025 29.9 41 18.8 24.65 20.474999999999998 36.075 42 21.099999999999998 26.724999999999998 19.025 33.15 43 22.875 24.675 25.900000000000002 26.55 44 19.925 24.75 21.075 34.25 45 12.3 31.175000000000004 23.724999999999998 32.800000000000004 46 17.025000000000002 28.449999999999996 19.85 34.675 47 15.024999999999999 23.625 21.85 39.5 48 12.7 27.400000000000002 23.075000000000003 36.825 49 13.950000000000001 24.925 15.775 45.35 50 14.875 24.175 22.1 38.85 >>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 0.0 18 0.0 19 0.5 20 1.0 21 1.0 22 1.0 23 1.0 24 1.0 25 1.0 26 1.0 27 1.0 28 1.0 29 0.5 30 0.0 31 0.5 32 1.0 33 1.0 34 1.0 35 2.0 36 3.0 37 17.0 38 31.0 39 61.5 40 92.0 41 115.0 42 138.0 43 157.5 44 177.0 45 312.5 46 448.0 47 595.5 48 743.0 49 589.5 50 436.0 51 455.5 52 475.0 53 506.5 54 538.0 55 505.5 56 473.0 57 360.5 58 248.0 59 166.0 60 84.0 61 67.5 62 51.0 63 37.0 64 23.0 65 19.0 66 15.0 67 14.5 68 14.0 69 8.5 70 3.0 71 1.5 72 0.0 73 0.5 74 1.0 75 0.5 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 0.7000000000000001 2 0.15 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 warn #Total Deduplicated Percentage 60.275 #Duplication Level Percentage of deduplicated Percentage of total 1 82.49688925756948 49.725 2 10.825383658233099 13.05 3 2.364164247200332 4.275 4 0.9954375777685608 2.4 5 0.5391953546246371 1.625 6 0.45624222314392365 1.6500000000000001 7 0.3732890916632103 1.575 8 0.45624222314392365 2.1999999999999997 9 0.2073828287017835 1.125 >10 1.1198672749896308 12.5 >50 0.1244296972210701 4.8500000000000005 >100 0.04147656574035669 5.025 >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 CTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 201 5.025 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCG 87 2.175 TruSeq Adapter, Index 7 (97% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 54 1.35 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 53 1.325 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 37 0.9249999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 37 0.9249999999999999 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 30 0.75 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCG 22 0.5499999999999999 TruSeq Adapter, Index 7 (97% over 36bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCC 13 0.325 TruSeq Adapter, Index 5 (97% over 35bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGA 12 0.3 TruSeq Adapter, Index 7 (97% over 37bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 11 0.27499999999999997 No Hit TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 8 0.2 No Hit GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 8 0.2 No Hit TTTGGATTGAAGGGAGCTCTGAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 8 0.2 No Hit GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAAGATCGGAAGAGCACACGTCTGAACT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) ACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCTGAA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCTGA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) AAGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC 6 0.15 No Hit TACCTGGTTGATCCTGCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) AAGGATGTTTTCATTAATCAAGAACAGATCGGAAGAGCACACGTCTGAAC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCC 5 0.125 TruSeq Adapter, Index 5 (97% over 35bp) TTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCAAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TGACAGAAGAGAGTGAGCACAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 5 0.125 No Hit ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGAC 5 0.125 TruSeq Adapter, Index 16 (97% over 38bp) AGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) ACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CGACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) >>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 0.0 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 0.025 0.0 0.0 0.0 0.0 11 0.15 0.0 0.0 0.0 0.0 12 0.4 0.0 0.0 0.0 0.0 13 1.225 0.0 0.0 0.0 0.0 14 4.525 0.0 0.0 0.0 0.0 15 5.55 0.0 0.0 0.0 0.0 16 6.925 0.0 0.0 0.0 0.0 17 10.4 0.0 0.0 0.0 0.0 18 13.8 0.0 0.0 0.0 0.0 19 18.225 0.0 0.0 0.0 0.0 20 25.325 0.0 0.0 0.0 0.0 21 32.0 0.0 0.0 0.0 0.0 22 41.2 0.0 0.0 0.0 0.0 23 52.975 0.0 0.0 0.0 0.0 24 58.75 0.0 0.0 0.0 0.0 25 68.3 0.0 0.0 0.0 0.0 26 75.7 0.0 0.0 0.0 0.0 27 81.175 0.0 0.0 0.0 0.0 28 85.3 0.0 0.0 0.0 0.0 29 88.725 0.0 0.0 0.0 0.0 30 92.175 0.0 0.0 0.0 0.0 31 94.35 0.0 0.0 0.0 0.0 32 95.9 0.0 0.0 0.0 0.0 33 97.0 0.0 0.0 0.0 0.0 34 97.75 0.0 0.0 0.0 0.0 35 97.95 0.0 0.0 0.0 0.0 36 98.125 0.0 0.0 0.0 0.0 37 98.25 0.0 0.0 0.0 0.0 38 98.325 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGGGCTA 20 6.532858E-4 44.544304 1 AGCTCAG 30 1.9553718E-6 43.987503 9 TAGCTCA 30 1.9553718E-6 43.987503 8 TCACCCG 30 1.9553718E-6 43.987503 44 GCTCAGA 30 1.9553718E-6 43.987503 10 CTATAGC 20 6.9617946E-4 43.9875 5 GCTATAG 20 6.9617946E-4 43.9875 4 ATAGCTC 20 6.9617946E-4 43.9875 7 GGCTATA 20 6.9617946E-4 43.9875 3 TATAGCT 20 6.9617946E-4 43.9875 6 GGGCTAT 20 6.9617946E-4 43.9875 2 GTCACCC 35 5.6490517E-6 37.70357 43 CTCAGAT 35 5.6490517E-6 37.70357 11 CAGTCAC 40 1.4126626E-5 32.990623 41 AGTCACC 40 1.4126626E-5 32.990623 42 CTAACGA 45 0.0010861396 24.746836 1 TCAGATC 50 0.002165315 21.99375 12 TAACGAA 55 0.0037675614 19.994318 2 CCAGTCA 70 6.368369E-4 18.851786 40 GAACGAA 65 0.009902255 16.918268 6 >>END_MODULE Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933510 READS because READLEN < 1 Read 933510 spots for ERR9452013.sra Written 933510 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra Rejected 933509 READS because READLEN < 1 Read 933509 spots for ERR9452013.sra Written 933509 spots for ERR9452013.sra SRR ids: ['ERR9452013.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v0cv0sqb ERR9452013.sra spots: 18670181 blocks: [[1, 933509], [933510, 1867018], [1867019, 2800527], [2800528, 3734036], [3734037, 4667545], [4667546, 5601054], [5601055, 6534563], [6534564, 7468072], [7468073, 8401581], [8401582, 9335090], [9335091, 10268599], [10268600, 11202108], [11202109, 12135617], [12135618, 13069126], [13069127, 14002635], [14002636, 14936144], [14936145, 15869653], [15869654, 16803162], [16803163, 17736671], [17736672, 18670181]] ERR9452013 file size 2603793 ERR9452013 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 ERR9452013 ERR9452013_1.fastq Input file: ERR9452013_1.fastq trimmed: ERR9452013-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 22:42:49 2024 >> started Fri Dec 6 22:42:59 2024 >> done (9.935s) 18670181 reads processed; of these: 2803174 (15.01%) short reads filtered out after trimming by size control 707 ( 0.00%) empty reads filtered out after trimming by size control 15866300 (84.98%) reads available; of these: 820198 ( 5.17%) trimmed reads available after processing 15046102 (94.83%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 820198 5.17% 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 15046102 94.83% 15866300 reads passed initial QC criterion=sequence-density sequence-density=93.23 sequence-density-rank=1 fanout-score=21.11 fanout-score-rank=1 prefix-density=93.55 prefix-fanout=21.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGACAACATCTCGTATGCCG criterion=fanout-score sequence-density=93.23 sequence-density-rank=1 fanout-score=21.11 fanout-score-rank=1 prefix-density=93.55 prefix-fanout=21.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGACAACATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGACAACATCTCGTATGCCG -o ERR9452013 - Input file: STDIN trimmed: ERR9452013-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGACAACATCTCGTATGCCG -- 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 22:43:22 2024 >> started Fri Dec 6 22:43:39 2024 >> done (16.928s) 15528719 reads processed; of these: 17044 ( 0.11%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 15511665 (99.89%) reads available; of these: 14647785 (94.43%) trimmed reads available after processing 863880 ( 5.57%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 816609 5.26% 19 1177940 7.59% 20 1465084 9.45% 21 1649457 10.63% 22 2167529 13.97% 23 1264525 8.15% 24 1631117 10.52% 25 1167728 7.53% 26 976736 6.30% 27 758503 4.89% 28 627900 4.05% 29 573995 3.70% 30 375247 2.42% 31 245851 1.58% 32 224847 1.45% 33 139922 0.90% 34 67445 0.43% 35 47309 0.30% 36 18426 0.12% 37 12751 0.08% 38 7910 0.05% 39 6535 0.04% 40 4903 0.03% 41 7486 0.05% 42 2150 0.01% 43 1284 0.01% 44 963 0.01% 45 731 0.00% 46 529 0.00% 47 892 0.01% 48 0 0.00% 49 0 0.00% 50 69361 0.45% criterion=sequence-density sequence-density=1.69 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=10 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=13.66 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=1.0 sequence=TAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACAGATCGG Started job on | Dec 06 22:43:56 Started mapping on | Dec 06 22:43:56 Finished on | Dec 06 22:44:49 Mapping speed, Million of reads per hour | 1076.55 Number of input reads | 15849246 Average input read length | 24 UNIQUE READS: Uniquely mapped reads number | 1565209 Uniquely mapped reads % | 9.88% Average mapped length | 23.38 Number of splices: Total | 69928 Number of splices: Annotated (sjdb) | 34989 Number of splices: GT/AG | 68137 Number of splices: GC/AG | 1481 Number of splices: AT/AC | 18 Number of splices: Non-canonical | 292 Mismatch rate per base, % | 0.56% Deletion rate per base | 0.00% Deletion average length | 1.26 Insertion rate per base | 0.00% Insertion average length | 1.08 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6292938 % of reads mapped to multiple loci | 39.70% Number of reads mapped to too many loci | 7483930 % of reads mapped to too many loci | 47.22% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.96% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7991099 7991099 7991099 N_multimapping 6292938 6292938 6292938 N_noFeature 726028 813469 1461432 N_ambiguous 24367 7292 932 UnstrandedReadsAssigned:814814 PositiveStrandReadsAssigned:744448 NegativeStrandReadsAssigned:102845 Dataset is classified positive stranded MeadianReadLen=23 20thPercentileLength=20 echo kmer=19 ERR9452013 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: ERR9452013-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,849,246 reads, 1,678,245 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 887 rounds 52973 ERR9452013.ke.tsv 35125 ERR9452013.se.tsv 88098 total ==> ERR9452013.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 3.3125 2.00257 PNS24247 1044 945 0 0 PNS24249 1928 1829 3.6875 1.02018 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 509.75 171.501 KQK14071 474 375 32.2146 43.4688 ==> ERR9452013.se.tsv <== BRADI_1g14170v3 729 BRADI_1g53295v3 5 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 14 BRADI_1g09890v3 1 BRADI_1g77505v3 12 BRADI_1g48960v3 0 ERR9452013 completed mapping pipeline successfully