Starting /dee2/code/volunteer_pipeline.sh ERR9452005 current disk space = 1548680876032 free memory = 1597524544 ERR9452005 SRAfilesize 73c068e8bf8252d7f5bf2e0e18e4e57a ERR9452005.sra ERR9452005.sra file validated ERR9452005 is single end ERR9452005 is conventional basespace ERR9452005 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452005_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 35.98075 37.0 37.0 37.0 37.0 37.0 2 36.5365 37.0 37.0 37.0 37.0 37.0 3 36.5815 37.0 37.0 37.0 37.0 37.0 4 36.5565 37.0 37.0 37.0 37.0 37.0 5 36.5385 37.0 37.0 37.0 37.0 37.0 6 36.6065 37.0 37.0 37.0 37.0 37.0 7 36.702 37.0 37.0 37.0 37.0 37.0 8 36.59 37.0 37.0 37.0 37.0 37.0 9 36.5585 37.0 37.0 37.0 37.0 37.0 10 36.583 37.0 37.0 37.0 37.0 37.0 11 36.5955 37.0 37.0 37.0 37.0 37.0 12 36.6 37.0 37.0 37.0 37.0 37.0 13 36.625 37.0 37.0 37.0 37.0 37.0 14 36.5685 37.0 37.0 37.0 37.0 37.0 15 36.61 37.0 37.0 37.0 37.0 37.0 16 36.63 37.0 37.0 37.0 37.0 37.0 17 36.54 37.0 37.0 37.0 37.0 37.0 18 36.719 37.0 37.0 37.0 37.0 37.0 19 36.637 37.0 37.0 37.0 37.0 37.0 20 36.5935 37.0 37.0 37.0 37.0 37.0 21 36.6045 37.0 37.0 37.0 37.0 37.0 22 36.436 37.0 37.0 37.0 37.0 37.0 23 36.5515 37.0 37.0 37.0 37.0 37.0 24 36.44 37.0 37.0 37.0 37.0 37.0 25 36.4095 37.0 37.0 37.0 37.0 37.0 26 36.3085 37.0 37.0 37.0 37.0 37.0 27 36.369 37.0 37.0 37.0 37.0 37.0 28 36.363 37.0 37.0 37.0 37.0 37.0 29 36.1635 37.0 37.0 37.0 37.0 37.0 30 35.9995 37.0 37.0 37.0 37.0 37.0 31 35.844 37.0 37.0 37.0 37.0 37.0 32 36.0255 37.0 37.0 37.0 37.0 37.0 33 35.68 37.0 37.0 37.0 37.0 37.0 34 35.908 37.0 37.0 37.0 37.0 37.0 35 36.185 37.0 37.0 37.0 37.0 37.0 36 36.293 37.0 37.0 37.0 37.0 37.0 37 36.3325 37.0 37.0 37.0 37.0 37.0 38 36.393 37.0 37.0 37.0 37.0 37.0 39 36.3365 37.0 37.0 37.0 37.0 37.0 40 36.426 37.0 37.0 37.0 37.0 37.0 41 36.396 37.0 37.0 37.0 37.0 37.0 42 36.4265 37.0 37.0 37.0 37.0 37.0 43 36.5675 37.0 37.0 37.0 37.0 37.0 44 36.5265 37.0 37.0 37.0 37.0 37.0 45 36.524 37.0 37.0 37.0 37.0 37.0 46 36.646 37.0 37.0 37.0 37.0 37.0 47 36.612 37.0 37.0 37.0 37.0 37.0 48 36.6415 37.0 37.0 37.0 37.0 37.0 49 36.6335 37.0 37.0 37.0 37.0 37.0 50 36.6385 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 3.0 26 6.0 27 9.0 28 10.0 29 13.0 30 14.0 31 14.0 32 32.0 33 41.0 34 72.0 35 179.0 36 2265.0 37 1342.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.64748927580116 29.825889477668433 23.76987130961393 27.756749936916474 2 25.15 29.825000000000003 23.95 21.075 3 29.475 29.875 17.849999999999998 22.8 4 31.175000000000004 34.8 16.675 17.349999999999998 5 22.975 28.549999999999997 20.175 28.299999999999997 6 29.525000000000002 23.525 25.424999999999997 21.525 7 27.025 31.924999999999997 21.975 19.075 8 23.25 27.35 25.874999999999996 23.525 9 23.674999999999997 29.075 23.95 23.3 10 34.35 21.7 20.200000000000003 23.75 11 24.575 25.35 28.625 21.45 12 24.075 26.3 26.150000000000002 23.474999999999998 13 26.525 23.175 21.3 28.999999999999996 14 29.275000000000002 32.05 21.775 16.900000000000002 15 26.174999999999997 31.574999999999996 22.3 19.950000000000003 16 21.95 28.975 28.749999999999996 20.325 17 24.975 28.849999999999998 30.525000000000002 15.65 18 26.950000000000003 28.050000000000004 25.15 19.85 19 36.5 28.349999999999998 19.325 15.825 20 28.4 30.975 24.525 16.1 21 24.975 39.4 17.974999999999998 17.65 22 26.224999999999998 35.25 19.475 19.05 23 33.300000000000004 35.375 17.775 13.55 24 30.2 35.5 18.75 15.55 25 31.275 36.6 14.85 17.275 26 34.625 28.599999999999998 16.225 20.549999999999997 27 32.574999999999996 38.3 12.1 17.025000000000002 28 35.15 31.924999999999997 14.7 18.224999999999998 29 32.9 36.475 9.125 21.5 30 36.925000000000004 37.175000000000004 7.049999999999999 18.85 31 40.1 37.1 6.225 16.575 32 33.725 40.050000000000004 8.774999999999999 17.45 33 29.475 41.25 6.275 23.0 34 35.0 33.25 9.049999999999999 22.7 35 29.45 37.55 6.675000000000001 26.325 36 29.025000000000002 37.875 7.55 25.55 37 22.925 33.7 8.625 34.75 38 22.6 35.725 10.325 31.35 39 22.775000000000002 26.900000000000002 15.45 34.875 40 22.85 30.599999999999998 15.375 31.175000000000004 41 19.5 24.45 19.425 36.625 42 24.425 26.1 18.525 30.95 43 22.55 24.625 25.624999999999996 27.200000000000003 44 19.6 26.424999999999997 21.075 32.9 45 15.425 28.449999999999996 23.150000000000002 32.975 46 19.325 29.849999999999998 19.650000000000002 31.175000000000004 47 14.725 28.249999999999996 19.7 37.325 48 12.675 32.300000000000004 20.775 34.25 49 15.2 25.45 16.825000000000003 42.525 50 14.124999999999998 25.074999999999996 21.95 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 0.5 6 1.0 7 0.5 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 0.5 26 1.0 27 0.5 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.5 34 1.0 35 7.5 36 14.0 37 26.5 38 39.0 39 66.0 40 93.0 41 118.5 42 144.0 43 172.5 44 201.0 45 327.5 46 454.0 47 589.5 48 725.0 49 572.5 50 420.0 51 458.5 52 497.0 53 558.0 54 619.0 55 498.5 56 378.0 57 291.0 58 204.0 59 153.5 60 103.0 61 76.5 62 50.0 63 36.0 64 22.0 65 18.0 66 14.0 67 14.0 68 14.0 69 9.0 70 4.0 71 3.0 72 2.0 73 1.0 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 0.9249999999999999 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 warn #Total Deduplicated Percentage 65.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 84.69154607768469 55.60000000000001 2 9.558263518659558 12.55 3 2.513328255902513 4.95 4 0.8758568164508759 2.3 5 0.49504950495049505 1.625 6 0.30464584920030463 1.2 7 0.15232292460015232 0.7000000000000001 8 0.07616146230007616 0.4 9 0.07616146230007616 0.44999999999999996 >10 1.1805026656511806 13.825000000000001 >50 0.03808073115003808 2.35 >100 0.03808073115003808 4.05 >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 162 4.05 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGC 94 2.35 TruSeq Adapter, Index 1 (97% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 46 1.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 34 0.8500000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 33 0.8250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 32 0.8 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGC 23 0.575 TruSeq Adapter, Index 1 (97% over 36bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 16 0.4 TruSeq Adapter, Index 2 (97% over 35bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 16 0.4 No Hit CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 13 0.325 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 11 0.27499999999999997 No Hit CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 10 0.25 No Hit ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 7 0.17500000000000002 No Hit AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA 6 0.15 No Hit CGTGGACTGTTGTCGGCCGTGAGATCGGAAGAGCACACGTCTGAACTCCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACTCC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) ATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCCACAGGCTTTCTTGAACTGAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) ATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCAGATCGGAAGAGCACACGTC 5 0.125 No Hit TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGATATAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) >>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 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10 0.025 0.0 0.0 0.0 0.0 11 0.125 0.0 0.0 0.0 0.0 12 0.275 0.0 0.0 0.0 0.0 13 0.725 0.0 0.0 0.0 0.0 14 4.475 0.0 0.0 0.0 0.0 15 5.925 0.0 0.0 0.0 0.0 16 7.85 0.0 0.0 0.0 0.0 17 10.65 0.0 0.0 0.0 0.0 18 14.075 0.0 0.0 0.0 0.0 19 18.0 0.0 0.0 0.0 0.0 20 23.0 0.0 0.0 0.0 0.0 21 29.825 0.0 0.0 0.0 0.0 22 38.0 0.0 0.0 0.0 0.0 23 47.7 0.0 0.0 0.0 0.0 24 54.375 0.0 0.0 0.0 0.0 25 65.55 0.0 0.0 0.0 0.0 26 71.775 0.0 0.0 0.0 0.0 27 76.625 0.0 0.0 0.0 0.0 28 80.5 0.0 0.0 0.0 0.0 29 83.95 0.0 0.0 0.0 0.0 30 87.275 0.0 0.0 0.0 0.0 31 89.7 0.0 0.0 0.0 0.0 32 91.55 0.0 0.0 0.0 0.0 33 93.25 0.0 0.0 0.0 0.0 34 94.675 0.0 0.0 0.0 0.0 35 95.6 0.0 0.0 0.0 0.0 36 96.2 0.0 0.0 0.0 0.0 37 96.5 0.0 0.0 0.0 0.0 38 96.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTCCAG 95 0.004922664 13.894736 44 AACTCCA 145 2.2987671E-5 13.655173 44 GAACTCC 175 1.3518654E-4 11.314286 43 TGAACTC 195 3.710021E-4 10.153847 42 CTGAACT 235 0.0020731473 8.425531 41 TCTGAAC 265 0.0061811972 7.4716988 40 >>END_MODULE Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746313 READS because READLEN < 1 Read 746313 spots for ERR9452005.sra Written 746313 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra Rejected 746304 READS because READLEN < 1 Read 746304 spots for ERR9452005.sra Written 746304 spots for ERR9452005.sra SRR ids: ['ERR9452005.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_at8tn8xe ERR9452005.sra spots: 14926089 blocks: [[1, 746304], [746305, 1492608], [1492609, 2238912], [2238913, 2985216], [2985217, 3731520], [3731521, 4477824], [4477825, 5224128], [5224129, 5970432], [5970433, 6716736], [6716737, 7463040], [7463041, 8209344], [8209345, 8955648], [8955649, 9701952], [9701953, 10448256], [10448257, 11194560], [11194561, 11940864], [11940865, 12687168], [12687169, 13433472], [13433473, 14179776], [14179777, 14926089]] ERR9452005 file size 2077280 ERR9452005 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 ERR9452005 ERR9452005_1.fastq Input file: ERR9452005_1.fastq trimmed: ERR9452005-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 22:31:05 2024 >> started Fri Dec 6 22:31:14 2024 >> done (8.487s) 14926089 reads processed; of these: 2122054 (14.22%) short reads filtered out after trimming by size control 1019 ( 0.01%) empty reads filtered out after trimming by size control 12803016 (85.78%) reads available; of these: 615630 ( 4.81%) trimmed reads available after processing 12187386 (95.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 615630 4.81% 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 12187386 95.19% 12803016 reads passed initial QC criterion=sequence-density sequence-density=91.71 sequence-density-rank=1 fanout-score=25.06 fanout-score-rank=1 prefix-density=92.42 prefix-fanout=24.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCCATGCATCTCGTATGCCG criterion=fanout-score sequence-density=91.71 sequence-density-rank=1 fanout-score=25.06 fanout-score-rank=1 prefix-density=92.42 prefix-fanout=24.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCCATGCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCCATGCATCTCGTATGCCG -o ERR9452005 - Input file: STDIN trimmed: ERR9452005-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCCATGCATCTCGTATGCCG -- 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 22:31:30 2024 >> started Fri Dec 6 22:31:43 2024 >> done (13.836s) 12524690 reads processed; of these: 16193 ( 0.13%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 12508488 (99.87%) reads available; of these: 11833091 (94.60%) trimmed reads available after processing 675397 ( 5.40%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 616529 4.93% 19 840242 6.72% 20 988809 7.91% 21 1161452 9.29% 22 1472575 11.77% 23 968776 7.74% 24 1639889 13.11% 25 895720 7.16% 26 745274 5.96% 27 603125 4.82% 28 528893 4.23% 29 499076 3.99% 30 366886 2.93% 31 264037 2.11% 32 251754 2.01% 33 200330 1.60% 34 118196 0.94% 35 92230 0.74% 36 45293 0.36% 37 32708 0.26% 38 21617 0.17% 39 18701 0.15% 40 14824 0.12% 41 19940 0.16% 42 7673 0.06% 43 4864 0.04% 44 3416 0.03% 45 2546 0.02% 46 1649 0.01% 47 2062 0.02% 48 0 0.00% 49 0 0.00% 50 79402 0.63% criterion=sequence-density sequence-density=1.98 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=49 fanout-score=7.08 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=1.0 sequence=AGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTC Started job on | Dec 06 22:31:59 Started mapping on | Dec 06 22:31:59 Finished on | Dec 06 22:32:48 Mapping speed, Million of reads per hour | 939.44 Number of input reads | 12786814 Average input read length | 24 UNIQUE READS: Uniquely mapped reads number | 1514678 Uniquely mapped reads % | 11.85% Average mapped length | 24.01 Number of splices: Total | 55046 Number of splices: Annotated (sjdb) | 25941 Number of splices: GT/AG | 53520 Number of splices: GC/AG | 1218 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 295 Mismatch rate per base, % | 0.63% Deletion rate per base | 0.00% Deletion average length | 1.31 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4720949 % of reads mapped to multiple loci | 36.92% Number of reads mapped to too many loci | 6124615 % of reads mapped to too many loci | 47.90% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.94% % of reads unmapped: other | 0.40% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6551187 6551187 6551187 N_multimapping 4720949 4720949 4720949 N_noFeature 866148 943472 1423679 N_ambiguous 21776 7577 703 UnstrandedReadsAssigned:626754 PositiveStrandReadsAssigned:563629 NegativeStrandReadsAssigned:90296 Dataset is classified positive stranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 ERR9452005 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: ERR9452005-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,786,814 reads, 1,277,111 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 886 rounds 52973 ERR9452005.ke.tsv 35125 ERR9452005.se.tsv 88098 total ==> ERR9452005.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 5 2.03405 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 432.478 213.954 KQK14071 474 375 9.24698 18.3473 ==> ERR9452005.se.tsv <== BRADI_1g14170v3 595 BRADI_1g53295v3 4 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 17 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR9452005 completed mapping pipeline successfully