Starting /dee2/code/volunteer_pipeline.sh ERR9452001 current disk space = 1548596666368 free memory = 1603382996 ERR9452001 SRAfilesize 5bf5f7da625ee06da1fd9d5e582fd002 ERR9452001.sra ERR9452001.sra file validated ERR9452001 is single end ERR9452001 is conventional basespace ERR9452001 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452001_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.999 37.0 37.0 37.0 37.0 37.0 2 36.5825 37.0 37.0 37.0 37.0 37.0 3 36.6245 37.0 37.0 37.0 37.0 37.0 4 36.6555 37.0 37.0 37.0 37.0 37.0 5 36.6375 37.0 37.0 37.0 37.0 37.0 6 36.6795 37.0 37.0 37.0 37.0 37.0 7 36.547 37.0 37.0 37.0 37.0 37.0 8 36.5645 37.0 37.0 37.0 37.0 37.0 9 36.5805 37.0 37.0 37.0 37.0 37.0 10 36.6715 37.0 37.0 37.0 37.0 37.0 11 36.6195 37.0 37.0 37.0 37.0 37.0 12 36.673 37.0 37.0 37.0 37.0 37.0 13 36.611 37.0 37.0 37.0 37.0 37.0 14 36.6335 37.0 37.0 37.0 37.0 37.0 15 36.647 37.0 37.0 37.0 37.0 37.0 16 36.635 37.0 37.0 37.0 37.0 37.0 17 36.5615 37.0 37.0 37.0 37.0 37.0 18 36.5955 37.0 37.0 37.0 37.0 37.0 19 36.5685 37.0 37.0 37.0 37.0 37.0 20 36.621 37.0 37.0 37.0 37.0 37.0 21 36.646 37.0 37.0 37.0 37.0 37.0 22 36.5885 37.0 37.0 37.0 37.0 37.0 23 36.594 37.0 37.0 37.0 37.0 37.0 24 36.6295 37.0 37.0 37.0 37.0 37.0 25 36.6075 37.0 37.0 37.0 37.0 37.0 26 36.539 37.0 37.0 37.0 37.0 37.0 27 36.612 37.0 37.0 37.0 37.0 37.0 28 36.694 37.0 37.0 37.0 37.0 37.0 29 36.723 37.0 37.0 37.0 37.0 37.0 30 36.6855 37.0 37.0 37.0 37.0 37.0 31 36.6785 37.0 37.0 37.0 37.0 37.0 32 36.716 37.0 37.0 37.0 37.0 37.0 33 36.6595 37.0 37.0 37.0 37.0 37.0 34 36.6175 37.0 37.0 37.0 37.0 37.0 35 36.672 37.0 37.0 37.0 37.0 37.0 36 36.7145 37.0 37.0 37.0 37.0 37.0 37 36.616 37.0 37.0 37.0 37.0 37.0 38 36.6705 37.0 37.0 37.0 37.0 37.0 39 36.62 37.0 37.0 37.0 37.0 37.0 40 36.6425 37.0 37.0 37.0 37.0 37.0 41 36.5825 37.0 37.0 37.0 37.0 37.0 42 36.5495 37.0 37.0 37.0 37.0 37.0 43 36.647 37.0 37.0 37.0 37.0 37.0 44 36.7105 37.0 37.0 37.0 37.0 37.0 45 36.612 37.0 37.0 37.0 37.0 37.0 46 36.6495 37.0 37.0 37.0 37.0 37.0 47 36.6805 37.0 37.0 37.0 37.0 37.0 48 36.688 37.0 37.0 37.0 37.0 37.0 49 36.666 37.0 37.0 37.0 37.0 37.0 50 36.668 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 3.0 25 1.0 26 5.0 27 4.0 28 8.0 29 12.0 30 11.0 31 22.0 32 22.0 33 42.0 34 55.0 35 117.0 36 1167.0 37 2531.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 20.459132189707365 29.9949545913219 23.30978809283552 26.236125126135217 2 26.150000000000002 28.525 26.400000000000002 18.925 3 29.589794897448723 30.665332666333168 17.883941970985493 21.860930465232617 4 27.85 37.95 16.825000000000003 17.375 5 23.275000000000002 25.324999999999996 21.75 29.65 6 28.875 22.775000000000002 29.65 18.7 7 29.799999999999997 31.95 20.45 17.8 8 21.775 28.275 30.25 19.7 9 21.975 30.075000000000003 22.95 25.0 10 39.7 22.650000000000002 18.825 18.825 11 20.9 27.950000000000003 30.475 20.674999999999997 12 22.15 28.075 28.625 21.15 13 25.575 21.3 19.400000000000002 33.725 14 29.425 33.800000000000004 22.45 14.325 15 25.025 34.449999999999996 23.075000000000003 17.45 16 20.3 29.25 32.975 17.474999999999998 17 21.75 27.35 34.825 16.075 18 28.849999999999998 24.224999999999998 27.175 19.75 19 37.75 27.6 21.224999999999998 13.425 20 25.025 34.150000000000006 26.474999999999998 14.35 21 22.325 39.025 18.775 19.875 22 23.275000000000002 36.85 18.575 21.3 23 34.675 33.675 17.849999999999998 13.8 24 28.15 35.275 20.125 16.45 25 29.9 39.050000000000004 14.674999999999999 16.375 26 35.85 23.525 18.85 21.775 27 28.749999999999996 42.5 11.05 17.7 28 33.75 28.4 19.075 18.775 29 31.374999999999996 31.7 10.65 26.275 30 38.5 36.95 7.7 16.85 31 43.0 34.925 6.25 15.825 32 33.25 40.875 9.2 16.675 33 25.624999999999996 46.925 6.9 20.549999999999997 34 39.900000000000006 29.799999999999997 8.975 21.325 35 28.775000000000002 40.5 6.325 24.4 36 31.95 37.824999999999996 7.1499999999999995 23.075000000000003 37 22.175 32.0 7.5 38.324999999999996 38 22.6 40.400000000000006 8.85 28.15 39 24.25 24.65 13.375 37.724999999999994 40 24.525 35.125 13.925 26.424999999999997 41 20.3 23.724999999999998 18.65 37.325 42 29.65 25.3 15.775 29.275000000000002 43 23.125 25.650000000000002 28.575 22.650000000000002 44 22.05 25.95 17.599999999999998 34.4 45 13.8 30.625000000000004 24.875 30.7 46 22.900000000000002 31.324999999999996 16.2 29.575000000000003 47 15.075 29.475 17.974999999999998 37.475 48 11.15 35.975 20.95 31.924999999999997 49 11.4 23.849999999999998 15.075 49.675000000000004 50 13.525 24.224999999999998 26.275 35.975 >>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 0.5 16 1.0 17 0.5 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.5 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 0.0 34 0.0 35 7.0 36 14.0 37 30.0 38 46.0 39 79.0 40 112.0 41 147.0 42 182.0 43 212.0 44 242.0 45 371.0 46 500.0 47 669.5 48 839.0 49 645.0 50 451.0 51 483.5 52 516.0 53 513.5 54 511.0 55 383.0 56 255.0 57 208.0 58 161.0 59 110.5 60 60.0 61 52.5 62 45.0 63 30.0 64 15.0 65 15.0 66 15.0 67 19.5 68 24.0 69 16.0 70 8.0 71 4.5 72 1.0 73 0.5 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 0.8999999999999999 2 0.0 3 0.05 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 61.6 #Duplication Level Percentage of deduplicated Percentage of total 1 84.17207792207793 51.849999999999994 2 9.821428571428571 12.1 3 2.313311688311688 4.275 4 1.37987012987013 3.4000000000000004 5 0.4058441558441558 1.25 6 0.2435064935064935 0.8999999999999999 7 0.2029220779220779 0.8750000000000001 8 0.040584415584415584 0.2 9 0.16233766233766234 0.8999999999999999 >10 1.0957792207792207 13.225000000000001 >50 0.12175324675324675 4.7 >100 0.040584415584415584 6.325 >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 253 6.325 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACA 81 2.025 TruSeq Adapter, Index 5 (100% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 55 1.375 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 52 1.3 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 42 1.05 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 40 1.0 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 39 0.975 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 33 0.8250000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 33 0.8250000000000001 No Hit GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACACA 27 0.675 TruSeq Adapter, Index 5 (100% over 36bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGAGATCGGAAGAGCAC 19 0.475 No Hit CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTC 16 0.4 No Hit ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 15 0.375 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) TGAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGT 13 0.325 No Hit TGAAGTGTTTGGGGGAACTCAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTAGATCGGAAGAGCACACGTCTGAA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA 10 0.25 No Hit GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) GACACGACTCTCGGCAACGGATATCTCGAGATCGGAAGAGCACACGTCTG 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GCGTCTGTAGTCCAACGGTTAGGATAAGATCGGAAGAGCACACGTCTGAA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGATCGGAA 7 0.17500000000000002 No Hit CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAC 7 0.17500000000000002 TruSeq Adapter, Index 5 (100% over 35bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTAGATCGGAAGAGCACA 7 0.17500000000000002 No Hit TGTCGTGCCAATTCAACATAAACCCCTAGATCGGAAGAGCACACGTCTGA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) AAGCTGAAGCGGAAATGCAATTCTCGGGTGAGATCGGAAGAGCACACGTC 6 0.15 No Hit TTCATGGACGTTGATAAGATCCTTCCAGATCGGAAGAGCACACGTCTGAA 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) AGGGCTATAGCTCAGTTCGGAGATCGGAAGAGCACACGTCTGAACTCCAG 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) ATCCTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) TAACCGTAGTAATTCTAGAGCTAGATCGGAAGAGCACACGTCTGAACTCC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) NTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AAGTATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GACACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACTCTAGTCCGACTTTGTGAAATGACTAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) GAGGCATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTC 5 0.125 No Hit CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) AAAGATGAAAAGGACTTTGAAAAGAGAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) TCCAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) GCGGGTATAGTTTAGTGGTAAAACCCTAGCCTAGATCGGAAGAGCACACG 5 0.125 No Hit >>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 0.05 0.0 0.0 0.0 0.0 10 0.05 0.0 0.0 0.0 0.0 11 0.1 0.0 0.0 0.0 0.0 12 0.25 0.0 0.0 0.0 0.0 13 0.425 0.0 0.0 0.0 0.0 14 3.825 0.0 0.0 0.0 0.0 15 4.6 0.0 0.0 0.0 0.0 16 5.4 0.0 0.0 0.0 0.0 17 7.55 0.0 0.0 0.0 0.0 18 9.775 0.0 0.0 0.0 0.0 19 12.3 0.0 0.0 0.0 0.0 20 17.1 0.0 0.0 0.0 0.0 21 22.95 0.0 0.0 0.0 0.0 22 30.525 0.0 0.0 0.0 0.0 23 41.525 0.0 0.0 0.0 0.0 24 46.925 0.0 0.0 0.0 0.0 25 61.5 0.0 0.0 0.0 0.0 26 67.375 0.0 0.0 0.0 0.0 27 71.575 0.0 0.0 0.0 0.0 28 74.875 0.0 0.0 0.0 0.0 29 78.475 0.0 0.0 0.0 0.0 30 82.75 0.0 0.0 0.0 0.0 31 86.0 0.0 0.0 0.0 0.0 32 88.2 0.0 0.0 0.0 0.0 33 91.75 0.0 0.0 0.0 0.0 34 94.075 0.0 0.0 0.0 0.0 35 95.375 0.0 0.0 0.0 0.0 36 96.625 0.0 0.0 0.0 0.0 37 97.15 0.0 0.0 0.0 0.0 38 97.825 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 20 6.952051E-4 44.000004 9 GACACGA 20 6.952051E-4 44.000004 1 GCTCAGA 20 6.952051E-4 44.000004 10 TAGCTCA 25 3.6958358E-5 44.0 8 ACACGAC 25 0.002084305 35.2 2 CTAACGA 40 1.4099138E-5 33.0 1 GGCAACG 30 0.005095276 29.333332 13 TCGGCAA 30 0.005095276 29.333332 11 CTCTCGG 30 0.005095276 29.333332 8 ACTCTCG 30 0.005095276 29.333332 7 CACGACT 30 0.005095276 29.333332 3 GCAACGG 30 0.005095276 29.333332 14 TCTCGGC 30 0.005095276 29.333332 9 CTCGGCA 30 0.005095276 29.333332 10 ACGACTC 30 0.005095276 29.333332 4 CGGCAAC 30 0.005095276 29.333332 12 AACGGAT 30 0.005095276 29.333332 16 GACTCTC 30 0.005095276 29.333332 6 ACGGATA 30 0.005095276 29.333332 17 CGACTCT 30 0.005095276 29.333332 5 >>END_MODULE Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721606 READS because READLEN < 1 Read 721606 spots for ERR9452001.sra Written 721606 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra Rejected 721603 READS because READLEN < 1 Read 721603 spots for ERR9452001.sra Written 721603 spots for ERR9452001.sra SRR ids: ['ERR9452001.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1qz7gwd7 ERR9452001.sra spots: 14432063 blocks: [[1, 721603], [721604, 1443206], [1443207, 2164809], [2164810, 2886412], [2886413, 3608015], [3608016, 4329618], [4329619, 5051221], [5051222, 5772824], [5772825, 6494427], [6494428, 7216030], [7216031, 7937633], [7937634, 8659236], [8659237, 9380839], [9380840, 10102442], [10102443, 10824045], [10824046, 11545648], [11545649, 12267251], [12267252, 12988854], [12988855, 13710457], [13710458, 14432063]] ERR9452001 file size 2007808 ERR9452001 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 ERR9452001 ERR9452001_1.fastq Input file: ERR9452001_1.fastq trimmed: ERR9452001-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 22:26:40 2024 >> started Fri Dec 6 22:26:45 2024 >> done (4.969s) 14432063 reads processed; of these: 1461340 (10.13%) short reads filtered out after trimming by size control 945 ( 0.01%) empty reads filtered out after trimming by size control 12969778 (89.87%) reads available; of these: 378408 ( 2.92%) trimmed reads available after processing 12591370 (97.08%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 378408 2.92% 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 12591370 97.08% 12969778 reads passed initial QC criterion=sequence-density sequence-density=94.20 sequence-density-rank=1 fanout-score=25.46 fanout-score-rank=1 prefix-density=95.26 prefix-fanout=25.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACACGACCATCTCGTATGCCG criterion=fanout-score sequence-density=94.20 sequence-density-rank=1 fanout-score=25.46 fanout-score-rank=1 prefix-density=95.26 prefix-fanout=25.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACACGACCATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACACGACCATCTCGTATGCCG -o ERR9452001 - Input file: STDIN trimmed: ERR9452001-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACACGACCATCTCGTATGCCG -- 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 22:26:59 2024 >> started Fri Dec 6 22:27:14 2024 >> done (14.333s) 12696730 reads processed; of these: 7046 ( 0.06%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 12689674 (99.94%) reads available; of these: 12252202 (96.55%) trimmed reads available after processing 437472 ( 3.45%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 375626 2.96% 19 594072 4.68% 20 822923 6.48% 21 1004590 7.92% 22 1446756 11.40% 23 831540 6.55% 24 2084162 16.42% 25 864944 6.82% 26 673454 5.31% 27 542498 4.28% 28 500161 3.94% 29 590838 4.66% 30 412842 3.25% 31 325696 2.57% 32 427179 3.37% 33 310006 2.44% 34 214427 1.69% 35 214991 1.69% 36 105711 0.83% 37 81721 0.64% 38 49838 0.39% 39 39296 0.31% 40 27233 0.21% 41 51397 0.41% 42 10460 0.08% 43 5577 0.04% 44 3816 0.03% 45 2921 0.02% 46 2094 0.02% 47 2248 0.02% 48 0 0.00% 49 0 0.00% 50 70657 0.56% criterion=sequence-density sequence-density=4.63 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=8 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGTCAAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=46 fanout-score=8.16 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=1.0 sequence=GGCGGCCCATGAAAATCCGGAGGACCGAGTACCGTTCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGCCAATGGAACAATGTAGGCAAGGGAAGTCGGCAAAACGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGACTGGGCTCGGGGGTCCCGGCCCCAAACCCGTCGGCTGTCGGCGGATTGCTCGAGCTGCTCACGCGGCGAGAGCGGGT Started job on | Dec 06 22:27:30 Started mapping on | Dec 06 22:27:31 Finished on | Dec 06 22:28:14 Mapping speed, Million of reads per hour | 1085.25 Number of input reads | 12962722 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 2283985 Uniquely mapped reads % | 17.62% Average mapped length | 24.34 Number of splices: Total | 38151 Number of splices: Annotated (sjdb) | 21176 Number of splices: GT/AG | 36964 Number of splices: GC/AG | 731 Number of splices: AT/AC | 19 Number of splices: Non-canonical | 437 Mismatch rate per base, % | 0.12% Deletion rate per base | 0.00% Deletion average length | 1.33 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5029400 % of reads mapped to multiple loci | 38.80% Number of reads mapped to too many loci | 5213171 % of reads mapped to too many loci | 40.22% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.79% % of reads unmapped: other | 0.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5649337 5649337 5649337 N_multimapping 5029400 5029400 5029400 N_noFeature 1605990 1730388 2146857 N_ambiguous 23594 10554 522 UnstrandedReadsAssigned:654401 PositiveStrandReadsAssigned:543043 NegativeStrandReadsAssigned:136606 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 ERR9452001 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: ERR9452001-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,962,722 reads, 2,435,761 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,038 rounds 52973 ERR9452001.ke.tsv 35125 ERR9452001.se.tsv 88098 total ==> ERR9452001.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 4 1.25786 PNS24243 293 194 0 0 KQK14069 1603 1504 339.523 97.3976 KQK14071 474 375 3.0501 3.50921 ==> ERR9452001.se.tsv <== BRADI_1g14170v3 433 BRADI_1g53295v3 0 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 10 BRADI_1g74790v3 31 BRADI_1g09890v3 1 BRADI_1g77505v3 13 BRADI_1g48960v3 0 ERR9452001 completed mapping pipeline successfully