Starting /dee2/code/volunteer_pipeline.sh ERR9452007 current disk space = 1548671348736 free memory = 1385857192 ERR9452007 SRAfilesize 244d9ed05ef53c48c6936415a398ee5d ERR9452007.sra ERR9452007.sra file validated ERR9452007 is single end ERR9452007 is conventional basespace ERR9452007 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR9452007_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 36.29625 37.0 37.0 37.0 37.0 37.0 2 36.4935 37.0 37.0 37.0 37.0 37.0 3 36.67325 37.0 37.0 37.0 37.0 37.0 4 36.686 37.0 37.0 37.0 37.0 37.0 5 36.6405 37.0 37.0 37.0 37.0 37.0 6 36.5615 37.0 37.0 37.0 37.0 37.0 7 36.69 37.0 37.0 37.0 37.0 37.0 8 36.6135 37.0 37.0 37.0 37.0 37.0 9 36.6445 37.0 37.0 37.0 37.0 37.0 10 36.69 37.0 37.0 37.0 37.0 37.0 11 36.628 37.0 37.0 37.0 37.0 37.0 12 36.638 37.0 37.0 37.0 37.0 37.0 13 36.7175 37.0 37.0 37.0 37.0 37.0 14 36.6495 37.0 37.0 37.0 37.0 37.0 15 36.5925 37.0 37.0 37.0 37.0 37.0 16 36.5035 37.0 37.0 37.0 37.0 37.0 17 36.5995 37.0 37.0 37.0 37.0 37.0 18 36.602 37.0 37.0 37.0 37.0 37.0 19 36.6245 37.0 37.0 37.0 37.0 37.0 20 36.626 37.0 37.0 37.0 37.0 37.0 21 36.5805 37.0 37.0 37.0 37.0 37.0 22 36.6355 37.0 37.0 37.0 37.0 37.0 23 36.586 37.0 37.0 37.0 37.0 37.0 24 36.586 37.0 37.0 37.0 37.0 37.0 25 36.622 37.0 37.0 37.0 37.0 37.0 26 36.603 37.0 37.0 37.0 37.0 37.0 27 36.6675 37.0 37.0 37.0 37.0 37.0 28 36.6665 37.0 37.0 37.0 37.0 37.0 29 36.677 37.0 37.0 37.0 37.0 37.0 30 36.716 37.0 37.0 37.0 37.0 37.0 31 36.716 37.0 37.0 37.0 37.0 37.0 32 36.655 37.0 37.0 37.0 37.0 37.0 33 36.7105 37.0 37.0 37.0 37.0 37.0 34 36.6995 37.0 37.0 37.0 37.0 37.0 35 36.706 37.0 37.0 37.0 37.0 37.0 36 36.703 37.0 37.0 37.0 37.0 37.0 37 36.7515 37.0 37.0 37.0 37.0 37.0 38 36.703 37.0 37.0 37.0 37.0 37.0 39 36.6745 37.0 37.0 37.0 37.0 37.0 40 36.6315 37.0 37.0 37.0 37.0 37.0 41 36.5965 37.0 37.0 37.0 37.0 37.0 42 36.574 37.0 37.0 37.0 37.0 37.0 43 36.592 37.0 37.0 37.0 37.0 37.0 44 36.6515 37.0 37.0 37.0 37.0 37.0 45 36.6815 37.0 37.0 37.0 37.0 37.0 46 36.6405 37.0 37.0 37.0 37.0 37.0 47 36.576 37.0 37.0 37.0 37.0 37.0 48 36.6915 37.0 37.0 37.0 37.0 37.0 49 36.6515 37.0 37.0 37.0 37.0 37.0 50 36.687 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 8.0 26 4.0 27 3.0 28 9.0 29 11.0 30 14.0 31 23.0 32 24.0 33 39.0 34 45.0 35 85.0 36 1124.0 37 2611.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 18.62276954008545 29.203317416436292 21.73913043478261 30.434782608695656 2 24.975 31.900000000000002 22.725 20.4 3 29.40735183795949 29.307326831707925 16.92923230807702 24.356089022255563 4 32.025 33.45 16.7 17.825 5 22.525000000000002 29.25 18.725 29.5 6 28.875 23.599999999999998 26.700000000000003 20.825 7 26.6 34.075 21.15 18.175 8 22.6 26.924999999999997 28.775000000000002 21.7 9 24.224999999999998 30.075000000000003 24.15 21.55 10 34.25 24.349999999999998 21.325 20.075000000000003 11 23.275000000000002 27.35 26.674999999999997 22.7 12 23.525 27.0 26.924999999999997 22.55 13 24.075 23.150000000000002 21.65 31.125000000000004 14 29.4 33.35 20.200000000000003 17.05 15 25.0 34.4 22.225 18.375 16 22.15 30.5 28.525 18.825 17 23.799999999999997 30.975 30.525000000000002 14.7 18 28.275 27.025 24.825 19.875 19 35.325 31.025000000000002 18.15 15.5 20 31.15 33.25 22.35 13.25 21 27.375 40.65 15.825 16.150000000000002 22 27.575 38.4 16.25 17.775 23 35.6 37.2 14.075 13.125 24 33.324999999999996 36.725 15.85 14.099999999999998 25 33.900000000000006 37.75 12.625 15.725 26 36.325 29.825000000000003 13.8 20.05 27 34.2 40.0 7.3999999999999995 18.4 28 37.15 36.025 9.0 17.825 29 33.75 39.050000000000004 6.425 20.775 30 32.1 42.6 5.225 20.075000000000003 31 38.15 35.575 4.45 21.825 32 33.225 37.55 8.5 20.724999999999998 33 26.025 37.974999999999994 7.875 28.125 34 29.549999999999997 31.275 10.225 28.95 35 25.85 33.775 10.85 29.525000000000002 36 24.875 35.325 9.375 30.425 37 20.875 32.7 13.4 33.025 38 20.625 31.1 14.625 33.650000000000006 39 20.150000000000002 23.925 20.275000000000002 35.65 40 20.4 26.200000000000003 21.625 31.775 41 17.7 22.900000000000002 21.85 37.55 42 18.875 26.575 21.75 32.800000000000004 43 21.3 26.325 23.95 28.425 44 19.05 25.424999999999997 23.1 32.425 45 11.825 30.225 22.85 35.099999999999994 46 15.35 29.849999999999998 19.25 35.55 47 13.025 26.35 21.175 39.45 48 11.35 31.2 21.075 36.375 49 11.95 29.125 20.525 38.4 50 12.3 29.675 22.025 36.0 >>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 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 1.0 27 1.0 28 1.0 29 1.5 30 2.0 31 2.0 32 2.0 33 1.5 34 1.0 35 3.5 36 6.0 37 13.0 38 20.0 39 39.5 40 59.0 41 75.5 42 92.0 43 131.5 44 171.0 45 338.5 46 506.0 47 726.5 48 947.0 49 758.5 50 570.0 51 546.5 52 523.0 53 501.5 54 480.0 55 395.5 56 311.0 57 255.5 58 200.0 59 128.0 60 56.0 61 42.5 62 29.0 63 20.0 64 11.0 65 8.0 66 5.0 67 6.0 68 7.0 69 3.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.525 2 0.0 3 0.025 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 57.65 #Duplication Level Percentage of deduplicated Percentage of total 1 83.04423243712056 47.875 2 10.017346053772767 11.55 3 2.818733738074588 4.875 4 0.997398091934085 2.3 5 0.6071118820468344 1.7500000000000002 6 0.3469210754553339 1.2 7 0.21682567215958368 0.8750000000000001 8 0.17346053772766695 0.8 9 0.17346053772766695 0.8999999999999999 >10 1.3876843018213356 15.475 >50 0.13009540329575023 4.3999999999999995 >100 0.08673026886383348 8.0 >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 190 4.75 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) AGGGCTATAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATA 130 3.25 TruSeq Adapter, Index 3 (97% over 36bp) AACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 70 1.7500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT 55 1.375 TruSeq Adapter, Index 1 (100% over 35bp) TAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCA 51 1.275 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) AACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 49 1.225 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) ACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGT 48 1.2 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 46 1.15 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 28 0.7000000000000001 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) TCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACT 26 0.65 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) CTAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCA 25 0.625 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 24 0.6 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) AACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAG 23 0.575 TruSeq Adapter, Index 3 (97% over 37bp) GACACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAAC 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) ATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAAC 23 0.575 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCAGT 21 0.525 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 20 0.5 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATA 18 0.44999999999999996 TruSeq Adapter, Index 3 (97% over 36bp) CGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 18 0.44999999999999996 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GACACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGT 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTC 17 0.42500000000000004 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) TCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 16 0.4 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT 14 0.35000000000000003 TruSeq Adapter, Index 1 (100% over 35bp) GACACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCC 14 0.35000000000000003 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp) CACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CATCCTAACGAACGAACGATTTGAACAGATCGGAAGAGCACACGTCTGAA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 24bp) CTAACGAACGAACGATTTGAAGATCGGAAGAGCACACGTCTGAACTCCAG 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CTCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) CACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTC 12 0.3 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATATCAGATCGGAAGAGCACACGTCTGAACTC 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) CCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 11 0.27499999999999997 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCAGATCGGAAGAGCACACG 10 0.25 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCAGATCGGAAGAGCACACGTCT 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) TTCATGGACGTTGATAAGATCCTTCAGATCGGAAGAGCACACGTCTGAAC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 25bp) CTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGAAGATCGGAAGAGCACACGTCTGAACTCCA 10 0.25 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TCGTGTTGCATTCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAT 9 0.22499999999999998 TruSeq Adapter, Index 1 (100% over 35bp) TATGAACTAATTTGAACTGTGAGATCGGAAGAGCACACGTCTGAACTCCA 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGTAGTTCGACCGCGGAATAGATCGGAAGAGCACACGTCTGAACTCCAGT 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) CACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 9 0.22499999999999998 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) AACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGT 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) ACGATTTGAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGC 8 0.2 TruSeq Adapter, Index 3 (97% over 37bp) CCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAG 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) GACACGACTCTCGGCAACGGATATCTCAGATCGGAAGAGCACACGTCTGA 8 0.2 Illumina Multiplexing PCR Primer 2.01 (100% over 23bp) CACGACTCTCGGCAACGGATAAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) ACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) AAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) CACGACTCTCGGCAACGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TGTTGTCTCAAGCTTGCTGCCAGATCGGAAGAGCACACGTCTGAACTCCA 7 0.17500000000000002 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) GGGGATGTAGCTCAGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GACACGACTCTCGGCAACGGATATCTCGGAGATCGGAAGAGCACACGTCT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 21bp) ACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CCTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 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) CAGCCCCACGTCGCACGGATTCGTAGATCGGAAGAGCACACGTCTGAACT 6 0.15 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp) GGTAGTTCGACCGCGGAATTAGATCGGAAGAGCACACGTCTGAACTCCAG 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) AACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GCGTCTGTAGTCCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCAGATCGGAAGAGCACA 5 0.125 No Hit GGGATTGTAGTTCAATTAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp) TAACGAACGAACGATTTGAAAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) CCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) CACCCCAAGATGAGTGCTCTCTCAGATCGGAAGAGCACACGTCTGAACTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp) GGGGACGTAGCTCATAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCAGATCGGAAGAGCACAC 5 0.125 No Hit ACGACTCTCGGCAACGGATAGATCGGAAGAGCACACGTCTGAACTCCAGT 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp) GACACGACTCTCGGCAACGGAGATCGGAAGAGCACACGTCTGAACTCCAG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp) TCCTCGTGTTGCATTCCCAGATCGGAAGAGCACACGTCTGAACTCCAGTC 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp) CACGACTCTCGGCAACGGATATCTCGGCAGATCGGAAGAGCACACGTCTG 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 22bp) AGTTACTAATTCATGATCTGGCAGATCGGAAGAGCACACGTCTGAACTCC 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.075 0.0 0.0 0.0 0.0 10 0.175 0.0 0.0 0.0 0.0 11 0.3 0.0 0.0 0.0 0.0 12 1.175 0.0 0.0 0.0 0.0 13 2.4 0.0 0.0 0.0 0.0 14 7.85 0.0 0.0 0.0 0.0 15 12.05 0.0 0.0 0.0 0.0 16 15.25 0.0 0.0 0.0 0.0 17 20.9 0.0 0.0 0.0 0.0 18 25.925 0.0 0.0 0.0 0.0 19 32.275 0.0 0.0 0.0 0.0 20 39.975 0.0 0.0 0.0 0.0 21 47.95 0.0 0.0 0.0 0.0 22 57.25 0.0 0.0 0.0 0.0 23 67.4 0.0 0.0 0.0 0.0 24 73.1 0.0 0.0 0.0 0.0 25 80.3 0.0 0.0 0.0 0.0 26 85.5 0.0 0.0 0.0 0.0 27 88.975 0.0 0.0 0.0 0.0 28 91.25 0.0 0.0 0.0 0.0 29 92.975 0.0 0.0 0.0 0.0 30 95.025 0.0 0.0 0.0 0.0 31 96.15 0.0 0.0 0.0 0.0 32 96.85 0.0 0.0 0.0 0.0 33 97.5 0.0 0.0 0.0 0.0 34 97.825 0.0 0.0 0.0 0.0 35 98.125 0.0 0.0 0.0 0.0 36 98.325 0.0 0.0 0.0 0.0 37 98.4 0.0 0.0 0.0 0.0 38 98.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACACGAC 20 6.952051E-4 44.000004 2 GACACGA 20 6.952051E-4 44.000004 1 CAAGATC 25 0.002084305 35.2 13 GTCACAT 35 2.6843656E-4 31.428572 44 GGCAACG 40 5.87456E-4 27.500002 11 CGGCAAC 40 5.87456E-4 27.500002 10 TCGGCAA 45 0.0011696975 24.444447 9 TAACGAA 45 0.0011696975 24.444447 2 CTCTCGG 45 0.0011696975 24.444447 6 ACTCTCG 45 0.0011696975 24.444447 5 CACGACT 45 0.0011696975 24.444447 1 TCTCGGC 45 0.0011696975 24.444447 7 CTAACGA 45 0.0011696975 24.444447 1 CTCGGCA 45 0.0011696975 24.444447 8 ACGACTC 45 0.0011696975 24.444447 2 GACTCTC 45 0.0011696975 24.444447 4 CGACTCT 45 0.0011696975 24.444447 3 AGTCACA 50 0.0021617375 22.0 43 GAACGAA 60 0.0062267617 18.333332 6 CAGTCAC 65 0.009886043 16.923079 42 >>END_MODULE Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931124 READS because READLEN < 1 Read 931124 spots for ERR9452007.sra Written 931124 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra Rejected 931108 READS because READLEN < 1 Read 931108 spots for ERR9452007.sra Written 931108 spots for ERR9452007.sra SRR ids: ['ERR9452007.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qh3q3dzg ERR9452007.sra spots: 18622176 blocks: [[1, 931108], [931109, 1862216], [1862217, 2793324], [2793325, 3724432], [3724433, 4655540], [4655541, 5586648], [5586649, 6517756], [6517757, 7448864], [7448865, 8379972], [8379973, 9311080], [9311081, 10242188], [10242189, 11173296], [11173297, 12104404], [12104405, 13035512], [13035513, 13966620], [13966621, 14897728], [14897729, 15828836], [15828837, 16759944], [16759945, 17691052], [17691053, 18622176]] ERR9452007 file size 2597043 ERR9452007 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 ERR9452007 ERR9452007_1.fastq Input file: ERR9452007_1.fastq trimmed: ERR9452007-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 22:32:31 2024 >> started Fri Dec 6 22:32:42 2024 >> done (10.680s) 18622176 reads processed; of these: 4926847 (26.46%) short reads filtered out after trimming by size control 1654 ( 0.01%) empty reads filtered out after trimming by size control 13693675 (73.53%) reads available; of these: 1095755 ( 8.00%) trimmed reads available after processing 12597920 (92.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1095755 8.00% 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 12597920 92.00% 13693675 reads passed initial QC criterion=sequence-density sequence-density=90.73 sequence-density-rank=1 fanout-score=18.39 fanout-score-rank=1 prefix-density=91.00 prefix-fanout=18.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGCGACATCTCGTATGCCG criterion=fanout-score sequence-density=90.73 sequence-density-rank=1 fanout-score=18.39 fanout-score-rank=1 prefix-density=91.00 prefix-fanout=18.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGCGACATCTCGTATGCCG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGCGACATCTCGTATGCCG -o ERR9452007 - Input file: STDIN trimmed: ERR9452007-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATAGCGACATCTCGTATGCCG -- 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 22:33:03 2024 >> started Fri Dec 6 22:33:19 2024 >> done (15.816s) 13392715 reads processed; of these: 17538 ( 0.13%) short reads filtered out after trimming by size control 9 ( 0.00%) empty reads filtered out after trimming by size control 13375168 (99.87%) reads available; of these: 12266389 (91.71%) trimmed reads available after processing 1108779 ( 8.29%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1080299 8.08% 19 1390094 10.39% 20 1508101 11.28% 21 1540524 11.52% 22 1949230 14.57% 23 1046948 7.83% 24 1507021 11.27% 25 837384 6.26% 26 639727 4.78% 27 468122 3.50% 28 374104 2.80% 29 331354 2.48% 30 200312 1.50% 31 123226 0.92% 32 112411 0.84% 33 77246 0.58% 34 42497 0.32% 35 36699 0.27% 36 17118 0.13% 37 13159 0.10% 38 8223 0.06% 39 6776 0.05% 40 4832 0.04% 41 5745 0.04% 42 1991 0.01% 43 1109 0.01% 44 758 0.01% 45 645 0.00% 46 441 0.00% 47 774 0.01% 48 0 0.00% 49 0 0.00% 50 48298 0.36% criterion=sequence-density sequence-density=1.29 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=11 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=16 fanout-score=6.95 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=2.7 sequence=CCGGCGATGCGTCCTGGCCGTATGCGGAACGGCTTTTGCTGGTCCGCCGCTCGGCTCGGGGCGTGGACTGTTGTCGGCCGTGCTGGCGGCCCAAGC Started job on | Dec 06 22:33:39 Started mapping on | Dec 06 22:33:39 Finished on | Dec 06 22:34:18 Mapping speed, Million of reads per hour | 1262.41 Number of input reads | 13676128 Average input read length | 23 UNIQUE READS: Uniquely mapped reads number | 1434281 Uniquely mapped reads % | 10.49% Average mapped length | 22.98 Number of splices: Total | 49916 Number of splices: Annotated (sjdb) | 23089 Number of splices: GT/AG | 48632 Number of splices: GC/AG | 1119 Number of splices: AT/AC | 8 Number of splices: Non-canonical | 157 Mismatch rate per base, % | 0.60% Deletion rate per base | 0.00% Deletion average length | 1.29 Insertion rate per base | 0.00% Insertion average length | 1.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5670467 % of reads mapped to multiple loci | 41.46% Number of reads mapped to too many loci | 6153101 % of reads mapped to too many loci | 44.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.73% % of reads unmapped: other | 0.33% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6571380 6571380 6571380 N_multimapping 5670467 5670467 5670467 N_noFeature 800738 878261 1343234 N_ambiguous 21714 7720 636 UnstrandedReadsAssigned:611829 PositiveStrandReadsAssigned:548300 NegativeStrandReadsAssigned:90411 Dataset is classified positive stranded MeadianReadLen=22 20thPercentileLength=20 echo kmer=19 ERR9452007 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: ERR9452007-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,676,128 reads, 1,274,677 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 857 rounds 52973 ERR9452007.ke.tsv 35125 ERR9452007.se.tsv 88098 total ==> ERR9452007.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 10 5.00439 PNS24243 293 194 0 0 KQK14069 1603 1504 451.155 205.96 KQK14071 474 375 26.0568 47.7084 ==> ERR9452007.se.tsv <== BRADI_1g14170v3 605 BRADI_1g53295v3 12 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 18 BRADI_1g74790v3 10 BRADI_1g09890v3 0 BRADI_1g77505v3 4 BRADI_1g48960v3 0 ERR9452007 completed mapping pipeline successfully