Starting /dee2/code/volunteer_pipeline.sh ERR9452004 current disk space = 1548677726208 free memory = 1603666944 ERR9452004 SRAfilesize 2da31afb6629d012a98afffd803aee0f ERR9452004.sra ERR9452004.sra file validated ERR9452004 is single end ERR9452004 is conventional basespace ERR9452004 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452004_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 36.0825 37.0 37.0 37.0 37.0 37.0 2 36.637 37.0 37.0 37.0 37.0 37.0 3 36.6655 37.0 37.0 37.0 37.0 37.0 4 36.6865 37.0 37.0 37.0 37.0 37.0 5 36.569 37.0 37.0 37.0 37.0 37.0 6 36.618 37.0 37.0 37.0 37.0 37.0 7 36.63 37.0 37.0 37.0 37.0 37.0 8 36.6005 37.0 37.0 37.0 37.0 37.0 9 36.564 37.0 37.0 37.0 37.0 37.0 10 36.6965 37.0 37.0 37.0 37.0 37.0 11 36.638 37.0 37.0 37.0 37.0 37.0 12 36.733 37.0 37.0 37.0 37.0 37.0 13 36.6155 37.0 37.0 37.0 37.0 37.0 14 36.641 37.0 37.0 37.0 37.0 37.0 15 36.6225 37.0 37.0 37.0 37.0 37.0 16 36.5785 37.0 37.0 37.0 37.0 37.0 17 36.489 37.0 37.0 37.0 37.0 37.0 18 36.643 37.0 37.0 37.0 37.0 37.0 19 36.596 37.0 37.0 37.0 37.0 37.0 20 36.599 37.0 37.0 37.0 37.0 37.0 21 36.469 37.0 37.0 37.0 37.0 37.0 22 36.564 37.0 37.0 37.0 37.0 37.0 23 36.588 37.0 37.0 37.0 37.0 37.0 24 36.603 37.0 37.0 37.0 37.0 37.0 25 36.5795 37.0 37.0 37.0 37.0 37.0 26 36.699 37.0 37.0 37.0 37.0 37.0 27 36.6345 37.0 37.0 37.0 37.0 37.0 28 36.6755 37.0 37.0 37.0 37.0 37.0 29 36.668 37.0 37.0 37.0 37.0 37.0 30 36.7485 37.0 37.0 37.0 37.0 37.0 31 36.6895 37.0 37.0 37.0 37.0 37.0 32 36.6805 37.0 37.0 37.0 37.0 37.0 33 36.6795 37.0 37.0 37.0 37.0 37.0 34 36.521 37.0 37.0 37.0 37.0 37.0 35 36.647 37.0 37.0 37.0 37.0 37.0 36 36.667 37.0 37.0 37.0 37.0 37.0 37 36.6545 37.0 37.0 37.0 37.0 37.0 38 36.6655 37.0 37.0 37.0 37.0 37.0 39 36.606 37.0 37.0 37.0 37.0 37.0 40 36.6045 37.0 37.0 37.0 37.0 37.0 41 36.5475 37.0 37.0 37.0 37.0 37.0 42 36.5695 37.0 37.0 37.0 37.0 37.0 43 36.619 37.0 37.0 37.0 37.0 37.0 44 36.55 37.0 37.0 37.0 37.0 37.0 45 36.6085 37.0 37.0 37.0 37.0 37.0 46 36.604 37.0 37.0 37.0 37.0 37.0 47 36.6445 37.0 37.0 37.0 37.0 37.0 48 36.684 37.0 37.0 37.0 37.0 37.0 49 36.57 37.0 37.0 37.0 37.0 37.0 50 36.7015 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 0.0 25 2.0 26 7.0 27 2.0 28 6.0 29 10.0 30 14.0 31 21.0 32 22.0 33 40.0 34 62.0 35 123.0 36 1251.0 37 2439.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 20.37317196167423 27.88703983862834 23.62581946545638 28.113968734241052 2 23.799999999999997 30.225 25.4 20.575 3 28.375 27.375 18.425 25.825 4 27.975 34.075 17.675 20.275000000000002 5 22.725 28.65 20.474999999999998 28.15 6 30.025000000000002 24.025 23.95 22.0 7 28.599999999999998 30.8 21.95 18.65 8 23.1 27.775 24.875 24.25 9 25.124999999999996 27.474999999999998 24.025 23.375 10 32.925 23.75 19.475 23.849999999999998 11 25.3 26.450000000000003 27.675 20.575 12 25.674999999999997 27.800000000000004 23.400000000000002 23.125 13 27.825 23.175 19.775000000000002 29.225 14 29.675 30.9 22.2 17.224999999999998 15 22.95 32.9 23.125 21.025 16 22.5 26.5 30.25 20.75 17 27.525 26.8 30.049999999999997 15.625 18 28.299999999999997 26.1 25.974999999999998 19.625 19 34.625 28.95 20.125 16.3 20 26.974999999999998 32.074999999999996 25.775 15.174999999999999 21 22.175 38.800000000000004 21.5 17.525 22 26.35 32.15 21.175 20.325 23 28.925 35.775 19.725 15.575 24 29.549999999999997 33.275 21.675 15.5 25 29.925 33.324999999999996 16.025 20.724999999999998 26 31.374999999999996 30.099999999999998 18.3 20.225 27 31.65 34.275 15.575 18.5 28 34.949999999999996 33.6 13.525 17.925 29 35.4 34.75 12.7 17.150000000000002 30 35.75 36.675000000000004 11.3 16.275000000000002 31 36.25 38.25 9.175 16.325 32 39.0 35.55 9.025 16.425 33 33.074999999999996 40.5 7.1 19.325 34 35.725 37.925 6.950000000000001 19.400000000000002 35 33.1 38.4 4.875 23.625 36 30.875000000000004 41.099999999999994 5.800000000000001 22.225 37 27.250000000000004 36.975 6.5 29.275000000000002 38 27.3 36.4 7.675 28.625 39 25.174999999999997 31.35 10.8 32.675 40 26.650000000000002 30.599999999999998 11.825 30.925000000000004 41 22.2 28.875 16.425 32.5 42 23.400000000000002 28.349999999999998 15.65 32.6 43 21.075 27.975 20.175 30.775000000000002 44 23.1 27.3 19.6 30.0 45 18.35 27.375 21.55 32.725 46 18.275 28.749999999999996 21.175 31.8 47 16.75 25.424999999999997 21.675 36.15 48 15.7 27.35 23.025000000000002 33.925 49 14.374999999999998 27.900000000000002 20.5 37.225 50 15.9 25.424999999999997 20.525 38.15 >>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 0.0 20 0.0 21 0.5 22 1.0 23 1.0 24 1.0 25 0.5 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 1.0 34 2.0 35 5.5 36 9.0 37 27.0 38 45.0 39 73.0 40 101.0 41 127.5 42 154.0 43 192.0 44 230.0 45 358.5 46 487.0 47 583.0 48 679.0 49 546.5 50 414.0 51 455.5 52 497.0 53 521.5 54 546.0 55 455.5 56 365.0 57 305.5 58 246.0 59 168.0 60 90.0 61 68.0 62 46.0 63 39.0 64 32.0 65 25.0 66 18.0 67 22.0 68 26.0 69 18.5 70 11.0 71 5.5 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 0.8500000000000001 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 66.2 #Duplication Level Percentage of deduplicated Percentage of total 1 83.57250755287009 55.325 2 10.574018126888216 14.000000000000002 3 2.5302114803625377 5.025 4 0.9441087613293051 2.5 5 0.3776435045317221 1.25 6 0.33987915407854985 1.35 7 0.33987915407854985 1.575 8 0.0377643504531722 0.2 9 0.18882175226586104 1.125 >10 1.0574018126888218 13.750000000000002 >50 0.0 0.0 >100 0.0377643504531722 3.9 >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 156 3.9 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 48 1.2 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 34 0.8500000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 29 0.7250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 27 0.675 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 21 0.525 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 20 0.5 No Hit GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 19 0.475 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGC 17 0.42500000000000004 TruSeq Adapter, Index 1 (97% over 36bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 13 0.325 No Hit CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCTGA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AAGTATGAACTAATTTGAACTGTGAAACTAGATCGGAAGAGCACACGTCT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGC 9 0.22499999999999998 TruSeq Adapter, Index 1 (97% over 36bp) GATCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTGAA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) AGATGAAAAGGACTTTGAAAAGAGAGATCGGAAGAGCACACGTCTGAACT 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) AGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAG 7 0.17500000000000002 TruSeq Adapter, Index 2 (97% over 35bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) ACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTCC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 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) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CGACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AGTATGAACTAATTTGAACTGTGAAACTAGATCGGAAGAGCACACGTCTG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) TCGACTCAGAACTGGTACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 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) CTCTAGTCCGACTTTGTGAAATGACAGATCGGAAGAGCACACGTCTGAAC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 5 0.125 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCAGATCGGAAGAGCACACG 5 0.125 No Hit AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTGA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) AGGGCTATAGCTCAGTTCGGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TAACCGTAGTAATTCTAGAGCTAGATCGGAAGAGCACACGTCTGAACTCC 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 0.075 0.0 0.0 0.0 0.0 11 0.15 0.0 0.0 0.0 0.0 12 0.275 0.0 0.0 0.0 0.0 13 0.45 0.0 0.0 0.0 0.0 14 1.5 0.0 0.0 0.0 0.0 15 2.15 0.0 0.0 0.0 0.0 16 2.75 0.0 0.0 0.0 0.0 17 4.0 0.0 0.0 0.0 0.0 18 5.85 0.0 0.0 0.0 0.0 19 8.425 0.0 0.0 0.0 0.0 20 12.45 0.0 0.0 0.0 0.0 21 18.3 0.0 0.0 0.0 0.0 22 24.525 0.0 0.0 0.0 0.0 23 34.05 0.0 0.0 0.0 0.0 24 41.525 0.0 0.0 0.0 0.0 25 49.925 0.0 0.0 0.0 0.0 26 58.1 0.0 0.0 0.0 0.0 27 65.9 0.0 0.0 0.0 0.0 28 72.25 0.0 0.0 0.0 0.0 29 78.2 0.0 0.0 0.0 0.0 30 83.325 0.0 0.0 0.0 0.0 31 87.4 0.0 0.0 0.0 0.0 32 89.875 0.0 0.0 0.0 0.0 33 92.725 0.0 0.0 0.0 0.0 34 94.975 0.0 0.0 0.0 0.0 35 96.45 0.0 0.0 0.0 0.0 36 97.45 0.0 0.0 0.0 0.0 37 97.975 0.0 0.0 0.0 0.0 38 98.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTCCAG 90 6.5507065E-6 19.555557 44 AACTCCA 110 3.707329E-5 16.0 43 GAACTCC 160 9.007967E-4 11.000001 42 TGAACTC 175 0.0019106758 10.057143 41 CTGAACT 225 1.1372316E-4 9.777778 44 TCTGAAC 270 7.1806915E-4 8.148148 43 GTCTGAA 290 0.0014659096 7.5862074 42 CGTCTGA 310 0.0028396088 7.0967746 41 ACGTCTG 325 0.004522727 6.7692313 40 CACGTCT 340 0.0070363535 6.470588 39 ACACGTC 350 0.009334426 6.2857146 38 CACACGT 350 0.009334426 6.2857146 37 >>END_MODULE Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754116 READS because READLEN < 1 Read 754116 spots for ERR9452004.sra Written 754116 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra Rejected 754110 READS because READLEN < 1 Read 754110 spots for ERR9452004.sra Written 754110 spots for ERR9452004.sra SRR ids: ['ERR9452004.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_y3_ojtuz ERR9452004.sra spots: 15082206 blocks: [[1, 754110], [754111, 1508220], [1508221, 2262330], [2262331, 3016440], [3016441, 3770550], [3770551, 4524660], [4524661, 5278770], [5278771, 6032880], [6032881, 6786990], [6786991, 7541100], [7541101, 8295210], [8295211, 9049320], [9049321, 9803430], [9803431, 10557540], [10557541, 11311650], [11311651, 12065760], [12065761, 12819870], [12819871, 13573980], [13573981, 14328090], [14328091, 15082206]] ERR9452004 file size 2099234 ERR9452004 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 ERR9452004 ERR9452004_1.fastq Input file: ERR9452004_1.fastq trimmed: ERR9452004-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 22:31:19 2024 >> started Fri Dec 6 22:31:27 2024 >> done (7.895s) 15082206 reads processed; of these: 930039 ( 6.17%) short reads filtered out after trimming by size control 922 ( 0.01%) empty reads filtered out after trimming by size control 14151245 (93.83%) reads available; of these: 407002 ( 2.88%) trimmed reads available after processing 13744243 (97.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 407002 2.88% 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 13744243 97.12% 14151245 reads passed initial QC criterion=sequence-density sequence-density=95.19 sequence-density-rank=1 fanout-score=27.92 fanout-score-rank=1 prefix-density=95.83 prefix-fanout=27.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCACCTCATCTCGTATGCCG criterion=fanout-score sequence-density=95.19 sequence-density-rank=1 fanout-score=27.92 fanout-score-rank=1 prefix-density=95.83 prefix-fanout=27.7 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCACCTCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCACCTCATCTCGTATGCCG -o ERR9452004 - Input file: STDIN trimmed: ERR9452004-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGCACCTCATCTCGTATGCCG -- 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 22:31:43 2024 >> started Fri Dec 6 22:31:57 2024 >> done (14.601s) 13856428 reads processed; of these: 14733 ( 0.11%) short reads filtered out after trimming by size control 8 ( 0.00%) empty reads filtered out after trimming by size control 13841687 (99.89%) reads available; of these: 13379755 (96.66%) trimmed reads available after processing 461932 ( 3.34%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 412080 2.98% 19 626922 4.53% 20 807421 5.83% 21 990520 7.16% 22 1369476 9.89% 23 1018148 7.36% 24 1367682 9.88% 25 1150872 8.31% 26 1048075 7.57% 27 921452 6.66% 28 833268 6.02% 29 781721 5.65% 30 600033 4.33% 31 457574 3.31% 32 416308 3.01% 33 339576 2.45% 34 223919 1.62% 35 172084 1.24% 36 84196 0.61% 37 52956 0.38% 38 29310 0.21% 39 20840 0.15% 40 14853 0.11% 41 14049 0.10% 42 7077 0.05% 43 4470 0.03% 44 3269 0.02% 45 2456 0.02% 46 1674 0.01% 47 1923 0.01% 48 0 0.00% 49 0 0.00% 50 67483 0.49% criterion=sequence-density sequence-density=2.27 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=17 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=48 fanout-score=11.89 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=1.0 sequence=TAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCC Started job on | Dec 06 22:32:12 Started mapping on | Dec 06 22:32:12 Finished on | Dec 06 22:33:01 Mapping speed, Million of reads per hour | 1038.60 Number of input reads | 14136504 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 1187820 Uniquely mapped reads % | 8.40% Average mapped length | 25.07 Number of splices: Total | 56736 Number of splices: Annotated (sjdb) | 32298 Number of splices: GT/AG | 54993 Number of splices: GC/AG | 1195 Number of splices: AT/AC | 26 Number of splices: Non-canonical | 522 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5279860 % of reads mapped to multiple loci | 37.35% Number of reads mapped to too many loci | 7244990 % of reads mapped to too many loci | 51.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.80% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7668824 7668824 7668824 N_multimapping 5279860 5279860 5279860 N_noFeature 539369 602461 1111427 N_ambiguous 20033 6373 477 UnstrandedReadsAssigned:628418 PositiveStrandReadsAssigned:578986 NegativeStrandReadsAssigned:75916 Dataset is classified positive stranded MeadianReadLen=25 20thPercentileLength=21 echo kmer=19 ERR9452004 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: ERR9452004-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,136,504 reads, 1,422,748 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 913 rounds 52973 ERR9452004.ke.tsv 35125 ERR9452004.se.tsv 88098 total ==> ERR9452004.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 5 2.46054 PNS24243 293 194 0 0 KQK14069 1603 1504 465.385 208.92 KQK14071 474 375 0 0 ==> ERR9452004.se.tsv <== BRADI_1g14170v3 565 BRADI_1g53295v3 10 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 16 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR9452004 completed mapping pipeline successfully