Starting /dee2/code/volunteer_pipeline.sh SRR1772235 current disk space = 1552299479040 free memory = 1605409760 SRR1772235 SRAfilesize 4befc26741eb4c5843e9ea8576afd11f SRR1772235.sra SRR1772235.sra file validated SRR1772235 is single end SRR1772235 is conventional basespace SRR1772235 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772235_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.74225 34.0 31.0 34.0 31.0 34.0 2 33.065 34.0 33.0 34.0 31.0 34.0 3 33.045 34.0 33.0 34.0 31.0 34.0 4 36.444 37.0 37.0 37.0 35.0 37.0 5 36.4225 37.0 37.0 37.0 35.0 37.0 6 36.27075 37.0 37.0 37.0 35.0 37.0 7 36.336 37.0 37.0 37.0 35.0 37.0 8 36.3395 37.0 37.0 37.0 35.0 37.0 9 38.14475 39.0 39.0 39.0 37.0 39.0 10 38.19275 39.0 39.0 39.0 37.0 39.0 11 38.12175 39.0 39.0 39.0 35.0 39.0 12 38.0445 39.0 39.0 39.0 35.0 39.0 13 38.06575 39.0 39.0 39.0 35.0 39.0 14 39.522 41.0 39.0 41.0 37.0 41.0 15 39.4755 41.0 39.0 41.0 36.0 41.0 16 39.534 41.0 40.0 41.0 37.0 41.0 17 39.48275 41.0 40.0 41.0 37.0 41.0 18 39.5235 41.0 40.0 41.0 37.0 41.0 19 39.401 41.0 39.0 41.0 36.0 41.0 20 39.3585 41.0 39.0 41.0 36.0 41.0 21 39.34025 41.0 39.0 41.0 36.0 41.0 22 39.39275 41.0 39.0 41.0 36.0 41.0 23 39.3375 41.0 39.0 41.0 36.0 41.0 24 39.28 41.0 39.0 41.0 36.0 41.0 25 39.22975 41.0 39.0 41.0 36.0 41.0 26 39.09325 41.0 39.0 41.0 36.0 41.0 27 38.99225 41.0 39.0 41.0 35.0 41.0 28 38.8055 40.0 38.0 41.0 35.0 41.0 29 38.92125 40.0 39.0 41.0 36.0 41.0 30 38.64725 40.0 38.0 41.0 35.0 41.0 31 38.567 40.0 38.0 41.0 35.0 41.0 32 38.49675 40.0 38.0 41.0 34.0 41.0 33 38.48875 40.0 38.0 41.0 35.0 41.0 34 38.386 40.0 38.0 41.0 34.0 41.0 35 38.748 40.0 39.0 41.0 35.0 41.0 36 38.57275 40.0 38.0 41.0 34.0 41.0 37 38.44725 40.0 38.0 41.0 34.0 41.0 38 38.46075 40.0 38.0 41.0 35.0 41.0 39 38.28725 40.0 38.0 41.0 34.0 41.0 40 38.2665 40.0 38.0 41.0 35.0 41.0 41 38.291 40.0 38.0 41.0 34.0 41.0 42 38.351 40.0 38.0 41.0 34.0 41.0 43 38.20725 40.0 38.0 41.0 34.0 41.0 44 38.0415 40.0 38.0 41.0 33.0 41.0 45 37.82325 40.0 38.0 41.0 33.0 41.0 46 37.875 40.0 38.0 41.0 33.0 41.0 47 37.73225 40.0 38.0 41.0 33.0 41.0 48 37.477 40.0 38.0 41.0 33.0 41.0 49 37.4305 40.0 38.0 41.0 33.0 41.0 50 37.02175 40.0 37.0 41.0 32.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10 0.0 1101 11 0.0 1101 12 0.0 1101 13 0.0 1101 14 0.0 1101 15 0.0 1101 16 0.0 1101 17 0.0 1101 18 0.0 1101 19 0.0 1101 20 0.0 1101 21 0.0 1101 22 0.0 1101 23 0.0 1101 24 0.0 1101 25 0.0 1101 26 0.0 1101 27 0.0 1101 28 0.0 1101 29 0.0 1101 30 0.0 1101 31 0.0 1101 32 0.0 1101 33 0.0 1101 34 0.0 1101 35 0.0 1101 36 0.0 1101 37 0.0 1101 38 0.0 1101 39 0.0 1101 40 0.0 1101 41 0.0 1101 42 0.0 1101 43 0.0 1101 44 0.0 1101 45 0.0 1101 46 0.0 1101 47 0.0 1101 48 0.0 1101 49 0.0 1101 50 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 1.0 15 4.0 16 1.0 17 2.0 18 3.0 19 5.0 20 3.0 21 5.0 22 2.0 23 13.0 24 13.0 25 13.0 26 9.0 27 21.0 28 12.0 29 27.0 30 33.0 31 49.0 32 69.0 33 55.0 34 87.0 35 138.0 36 202.0 37 284.0 38 575.0 39 2373.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.15 11.700000000000001 10.325 35.825 2 25.85 12.075 28.95 33.125 3 37.1935967983992 16.283141570785393 19.484742371185593 27.03851925962982 4 33.074999999999996 23.95 15.225 27.750000000000004 5 31.75 28.275 21.475 18.5 6 24.275 33.0 18.85 23.875 7 10.725 39.15 32.725 17.4 8 19.975 29.725 28.925 21.375 9 22.025 19.55 34.4 24.025 10 16.900000000000002 42.925000000000004 24.8 15.375 11 26.1 32.425 18.05 23.425 12 26.0 29.125 22.5 22.375 13 19.125 37.125 23.775 19.975 14 24.775 30.975 26.700000000000003 17.549999999999997 15 19.05 37.475 21.675 21.8 16 24.6 31.3 21.475 22.625 17 24.275 32.324999999999996 22.25 21.15 18 19.55 34.725 24.349999999999998 21.375 19 21.6 30.325000000000003 25.324999999999996 22.75 20 15.65 33.175 28.675 22.5 21 19.925 26.775 28.4 24.9 22 15.0 40.825 22.95 21.224999999999998 23 20.525 33.900000000000006 25.775 19.8 24 17.599999999999998 34.725 21.6 26.075 25 19.025 31.900000000000002 27.025 22.05 26 18.65 35.075 21.05 25.224999999999998 27 22.400000000000002 28.325 27.975 21.3 28 24.925 38.324999999999996 20.45 16.3 29 27.800000000000004 31.1 21.4 19.7 30 23.275000000000002 32.300000000000004 25.3 19.125 31 28.799999999999997 26.35 21.9 22.95 32 24.075 32.6 22.5 20.825 33 26.881720430107524 31.682920730182545 20.655163790947736 20.78019504876219 34 22.3 37.175000000000004 19.3 21.224999999999998 35 25.324999999999996 34.925 20.674999999999997 19.075 36 26.756689172293076 26.9567391847962 25.381345336334082 20.905226306576644 37 21.111945905334334 27.222639619333833 29.000751314800898 22.664663160530928 38 20.025000000000002 30.25 29.15 20.575 39 27.3 24.825 27.35 20.525 40 17.349999999999998 35.875 24.8 21.975 41 22.1 29.525000000000002 26.625 21.75 42 21.36602451838879 32.69952464348261 24.168126094570926 21.766324743557668 43 21.85 31.65 25.1 21.4 44 20.230057514378593 26.9567391847962 27.031757939484873 25.78144536134033 45 21.022300175394637 29.84214482585818 30.944625407166125 18.190929591581057 46 18.798498122653317 25.406758448060074 34.11764705882353 21.67709637046308 47 22.158237356034054 32.648973460190284 25.7135703555333 19.479218828242363 48 22.455613903475868 33.083270817704424 25.70642660665166 18.754688672168044 49 22.375 34.475 22.575 20.575 50 27.500000000000004 26.55 26.775 19.175 >>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 0.5 18 1.0 19 1.0 20 1.0 21 2.5 22 4.0 23 8.0 24 12.0 25 20.0 26 28.0 27 31.0 28 34.0 29 33.0 30 32.0 31 42.0 32 52.0 33 95.0 34 138.0 35 238.0 36 338.0 37 414.5 38 491.0 39 419.5 40 348.0 41 334.5 42 321.0 43 381.0 44 441.0 45 444.0 46 447.0 47 327.5 48 208.0 49 317.0 50 426.0 51 274.0 52 122.0 53 112.5 54 103.0 55 96.5 56 90.0 57 73.0 58 56.0 59 49.5 60 43.0 61 41.0 62 39.0 63 33.5 64 28.0 65 34.0 66 40.0 67 33.5 68 27.0 69 33.5 70 40.0 71 39.0 72 38.0 73 28.0 74 18.0 75 14.5 76 11.0 77 11.0 78 11.0 79 8.5 80 6.0 81 4.0 82 2.0 83 2.0 84 2.0 85 1.0 86 0.0 87 1.0 88 2.0 89 1.0 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 0.0 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 0.025 34 0.0 35 0.0 36 0.025 37 0.17500000000000002 38 0.0 39 0.0 40 0.0 41 0.0 42 0.075 43 0.0 44 0.025 45 0.22499999999999998 46 0.125 47 0.15 48 0.025 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 52.075 #Duplication Level Percentage of deduplicated Percentage of total 1 85.26164186269803 44.4 2 6.096975516082574 6.35 3 2.7364378300528083 4.275 4 1.4402304368698993 3.0 5 1.2481997119539128 3.25 6 0.3360537686029765 1.05 7 0.28804608737397985 1.05 8 0.28804608737397985 1.2 9 0.14402304368698993 0.675 >10 1.872299567930869 20.325 >50 0.19203072491598655 7.875 >100 0.09601536245799328 6.550000000000001 >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 GCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACG 153 3.8249999999999997 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCAGAAATCTCGTAT 109 2.725 TruSeq Adapter, Index 13 (97% over 38bp) GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 94 2.35 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 83 2.075 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 73 1.825 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 65 1.625 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 40 1.0 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 37 0.9249999999999999 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 36 0.8999999999999999 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 36 0.8999999999999999 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 35 0.8750000000000001 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 34 0.8500000000000001 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 31 0.775 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 29 0.7250000000000001 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 28 0.7000000000000001 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 27 0.675 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 25 0.625 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 25 0.625 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 24 0.6 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 24 0.6 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 24 0.6 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 22 0.5499999999999999 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 22 0.5499999999999999 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 21 0.525 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 21 0.525 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 18 0.44999999999999996 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 17 0.42500000000000004 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 17 0.42500000000000004 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 17 0.42500000000000004 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 17 0.42500000000000004 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 16 0.4 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 15 0.375 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 15 0.375 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 15 0.375 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 14 0.35000000000000003 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 13 0.325 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 12 0.3 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 12 0.3 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 11 0.27499999999999997 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 11 0.27499999999999997 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 11 0.27499999999999997 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 11 0.27499999999999997 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 10 0.25 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 10 0.25 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 10 0.25 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 9 0.22499999999999998 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 9 0.22499999999999998 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 9 0.22499999999999998 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 8 0.2 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 8 0.2 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 8 0.2 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 8 0.2 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 8 0.2 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 8 0.2 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 7 0.17500000000000002 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 7 0.17500000000000002 No Hit TCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGT 7 0.17500000000000002 No Hit CCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAA 7 0.17500000000000002 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 7 0.17500000000000002 No Hit CGGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTG 7 0.17500000000000002 No Hit GCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATC 6 0.15 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 6 0.15 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 6 0.15 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 6 0.15 No Hit GGGACAAATAGCATAAAGAAATGTAACCAACGTTTGTTGGAAAAAGCAAC 6 0.15 No Hit GCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCAT 6 0.15 No Hit GCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTC 6 0.15 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 5 0.125 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 5 0.125 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 5 0.125 No Hit GGCGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAA 5 0.125 No Hit GACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGG 5 0.125 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 5 0.125 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 5 0.125 No Hit CGCGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATT 5 0.125 No Hit CTCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAG 5 0.125 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 5 0.125 No Hit CCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGT 5 0.125 No Hit CATCAGAGAAGCTTCCTTGACCAATAGGGTAAATCAAGAAAACAGCAGTC 5 0.125 No Hit CTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGGCT 5 0.125 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 5 0.125 No Hit GGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAG 5 0.125 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 5 0.125 No Hit CTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTTCC 5 0.125 No Hit GCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTA 5 0.125 No Hit GTGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCG 5 0.125 No Hit ATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAG 5 0.125 No Hit ACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCC 5 0.125 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 5 0.125 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 5 0.125 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 5 0.125 No Hit AGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGG 5 0.125 No Hit TAGCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811739 spots for SRR1772235.sra Written 811739 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra Read 811729 spots for SRR1772235.sra Written 811729 spots for SRR1772235.sra SRR ids: ['SRR1772235.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_isrbplt2 SRR1772235.sra spots: 16234590 blocks: [[1, 811729], [811730, 1623458], [1623459, 2435187], [2435188, 3246916], [3246917, 4058645], [4058646, 4870374], [4870375, 5682103], [5682104, 6493832], [6493833, 7305561], [7305562, 8117290], [8117291, 8929019], [8929020, 9740748], [9740749, 10552477], [10552478, 11364206], [11364207, 12175935], [12175936, 12987664], [12987665, 13799393], [13799394, 14611122], [14611123, 15422851], [15422852, 16234590]] SRR1772235 file size 2802888 SRR1772235 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 SRR1772235 SRR1772235_1.fastq Input file: SRR1772235_1.fastq trimmed: SRR1772235-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 09:49:04 2024 >> started Fri Dec 6 09:49:14 2024 >> done (9.998s) 16234590 reads processed; of these: 2085 ( 0.01%) short reads filtered out after trimming by size control 483245 ( 2.98%) empty reads filtered out after trimming by size control 15749260 (97.01%) reads available; of these: 634390 ( 4.03%) trimmed reads available after processing 15114870 (95.97%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 879 0.01% 19 1323 0.01% 20 2796 0.02% 21 3149 0.02% 22 3798 0.02% 23 4078 0.03% 24 5346 0.03% 25 6051 0.04% 26 6430 0.04% 27 7303 0.05% 28 6697 0.04% 29 11355 0.07% 30 9721 0.06% 31 8720 0.06% 32 13887 0.09% 33 9276 0.06% 34 10187 0.06% 35 11427 0.07% 36 11755 0.07% 37 16748 0.11% 38 13210 0.08% 39 14629 0.09% 40 19722 0.13% 41 19863 0.13% 42 28468 0.18% 43 32517 0.21% 44 49889 0.32% 45 43834 0.28% 46 54192 0.34% 47 65606 0.42% 48 75292 0.48% 49 66242 0.42% 50 15114870 95.97% 15749260 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=22 prefix-density=0.00 prefix-fanout=1.0 sequence=CGCGGGAACTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=14.56 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=1.4 sequence=CTACGCCAAAACTCGGCGCAAAGAACCAACCGGATTGCCCCAGTGGATAAATAAGGAATACAGAAACAAAAACAGCGATTGGACCAGAGAATGAGATTGCATTATAAGGCCGCAATTGAATAGACCGAGCAAGTTCAAATTGGCGTAACATGAAACCTATTAGTGCAAAAGCCCCGTGGAGAGCTACAAAAGTCCATAGGCCACCTAATTGACACCAACGAGTAAAATCTCCTTGTGCTTCCGGGCCCCATAGTAGCAACAAAGAGTGTGCTAAACTATTGGCAGGGGTAGAAACTGCTGCGGTTAAGAAATTACAACCTTCCAAATAGGAACTAGCCAATCCATGGGTATACCAAGAAGTTACAAAAGTTGTCCCTGTAAACCACCCTCCTAAAGCGAAATAAGCACAAGGAAAGAGCAATAAGCCGGACCATCCTACAAAAACGAAACGGTCCCTTCGTAACCAGTCGTCCACAGTATCAAATAGATCCTTTTCTTCTTTAGGAATTCT Started job on | Dec 06 09:50:23 Started mapping on | Dec 06 09:50:23 Finished on | Dec 06 09:50:36 Mapping speed, Million of reads per hour | 4361.33 Number of input reads | 15749260 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4084900 Uniquely mapped reads % | 25.94% Average mapped length | 49.39 Number of splices: Total | 279557 Number of splices: Annotated (sjdb) | 265348 Number of splices: GT/AG | 274091 Number of splices: GC/AG | 3633 Number of splices: AT/AC | 134 Number of splices: Non-canonical | 1699 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.01% Deletion average length | 1.61 Insertion rate per base | 0.00% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 11221011 % of reads mapped to multiple loci | 71.25% Number of reads mapped to too many loci | 196062 % of reads mapped to too many loci | 1.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.54% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 443349 443349 443349 N_multimapping 11221011 11221011 11221011 N_noFeature 909251 3967995 971164 N_ambiguous 81495 711 26351 UnstrandedReadsAssigned:3094154 PositiveStrandReadsAssigned:116194 NegativeStrandReadsAssigned:3087385 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772235 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR1772235-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,749,260 reads, 12,968,796 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,126 rounds 52973 SRR1772235.ke.tsv 35125 SRR1772235.se.tsv 88098 total ==> SRR1772235.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 11.8125 1.23323 PNS24247 1044 945 0 0 PNS24249 1928 1829 33.1875 1.58558 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 369.359 21.46 KQK14071 474 375 141.519 32.977 ==> SRR1772235.se.tsv <== BRADI_1g14170v3 682 BRADI_1g53295v3 8 BRADI_1g59795v3 36 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 18 BRADI_1g74790v3 13 BRADI_1g09890v3 0 BRADI_1g77505v3 34 BRADI_1g48960v3 0 SRR1772235 completed mapping pipeline successfully