Starting /dee2/code/volunteer_pipeline.sh SRR1850587 current disk space = 1545967202304 free memory = 1594932288 SRR1850587 SRAfilesize 23021c9ecbaa7862c38b2d6ebeadcf3a SRR1850587.sra SRR1850587.sra file validated SRR1850587 is single end SRR1850587 is conventional basespace SRR1850587 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1850587_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 32.8365 34.0 31.0 34.0 31.0 34.0 2 33.1345 34.0 33.0 34.0 31.0 34.0 3 33.09825 34.0 33.0 34.0 31.0 34.0 4 36.49525 37.0 37.0 37.0 35.0 37.0 5 36.46075 37.0 37.0 37.0 35.0 37.0 6 36.3765 37.0 37.0 37.0 35.0 37.0 7 36.3875 37.0 37.0 37.0 35.0 37.0 8 36.4075 37.0 37.0 37.0 35.0 37.0 9 38.2175 39.0 39.0 39.0 37.0 39.0 10 38.25825 39.0 39.0 39.0 37.0 39.0 11 38.23125 39.0 39.0 39.0 37.0 39.0 12 38.17325 39.0 39.0 39.0 37.0 39.0 13 38.13 39.0 39.0 39.0 37.0 39.0 14 39.65 41.0 40.0 41.0 37.0 41.0 15 39.58125 41.0 40.0 41.0 37.0 41.0 16 39.614 41.0 40.0 41.0 37.0 41.0 17 39.577 41.0 40.0 41.0 37.0 41.0 18 39.62525 41.0 40.0 41.0 37.0 41.0 19 39.5045 41.0 40.0 41.0 37.0 41.0 20 39.44075 41.0 40.0 41.0 37.0 41.0 21 39.4195 41.0 39.0 41.0 36.0 41.0 22 39.468 41.0 39.0 41.0 37.0 41.0 23 39.51175 41.0 40.0 41.0 37.0 41.0 24 39.488 41.0 39.0 41.0 37.0 41.0 25 39.335 41.0 39.0 41.0 36.0 41.0 26 39.23325 41.0 39.0 41.0 36.0 41.0 27 39.0545 41.0 39.0 41.0 35.0 41.0 28 38.84925 40.0 39.0 41.0 35.0 41.0 29 38.88525 40.0 39.0 41.0 35.0 41.0 30 38.7535 40.0 39.0 41.0 35.0 41.0 31 38.704 40.0 38.0 41.0 35.0 41.0 32 38.47225 40.0 38.0 41.0 35.0 41.0 33 38.486 40.0 38.0 41.0 34.0 41.0 34 38.4825 40.0 38.0 41.0 34.0 41.0 35 38.655 40.0 38.0 41.0 35.0 41.0 36 38.624 40.0 38.0 41.0 35.0 41.0 37 38.583 40.0 38.0 41.0 35.0 41.0 38 38.5275 40.0 38.0 41.0 35.0 41.0 39 38.31775 40.0 38.0 41.0 34.0 41.0 40 38.2545 40.0 38.0 41.0 34.0 41.0 41 38.33975 40.0 38.0 41.0 34.0 41.0 42 38.25625 40.0 38.0 41.0 34.0 41.0 43 38.0405 40.0 38.0 41.0 33.0 41.0 44 37.8975 40.0 38.0 41.0 33.0 41.0 45 37.69725 40.0 38.0 41.0 33.0 41.0 46 37.7485 40.0 38.0 41.0 33.0 41.0 47 37.60025 40.0 38.0 41.0 33.0 41.0 48 37.49325 40.0 38.0 41.0 33.0 41.0 49 37.36675 40.0 38.0 41.0 33.0 41.0 50 36.985 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 14 1.0 15 2.0 16 2.0 17 3.0 18 2.0 19 4.0 20 3.0 21 6.0 22 9.0 23 7.0 24 4.0 25 10.0 26 12.0 27 19.0 28 16.0 29 18.0 30 40.0 31 50.0 32 54.0 33 73.0 34 106.0 35 133.0 36 178.0 37 290.0 38 563.0 39 2395.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.1 14.575 13.225000000000001 33.1 2 28.225 14.075 29.599999999999998 28.1 3 36.90267700775582 19.389542156617463 19.16437327995997 24.54340755566675 4 32.0 28.000000000000004 16.925 23.075000000000003 5 31.25 32.35 19.625 16.775000000000002 6 24.5 35.65 17.45 22.400000000000002 7 11.600000000000001 36.199999999999996 35.85 16.35 8 21.75 28.299999999999997 28.975 20.974999999999998 9 23.025000000000002 19.225 33.625 24.125 10 16.950000000000003 43.675000000000004 22.900000000000002 16.475 11 26.05 31.324999999999996 18.7 23.925 12 25.374999999999996 27.200000000000003 22.925 24.5 13 18.775 37.375 24.375 19.475 14 24.375 31.025000000000002 25.85 18.75 15 20.4 35.099999999999994 22.45 22.05 16 21.675 34.225 23.025000000000002 21.075 17 23.799999999999997 33.050000000000004 23.075000000000003 20.075000000000003 18 19.325 34.5 23.9 22.275 19 20.65 32.475 26.400000000000002 20.474999999999998 20 18.05 33.225 27.474999999999998 21.25 21 19.650000000000002 28.025 27.250000000000004 25.074999999999996 22 16.625 39.425 23.95 20.0 23 19.225 34.75 25.85 20.175 24 19.15 32.975 22.025 25.85 25 18.875 33.225 27.6 20.3 26 20.1 33.95 22.45 23.5 27 23.875 31.25 26.325 18.55 28 24.925 37.45 20.775 16.85 29 25.924999999999997 31.275 23.549999999999997 19.25 30 24.425 31.474999999999998 25.0 19.1 31 28.275 26.474999999999998 22.775000000000002 22.475 32 25.900000000000002 30.475 24.675 18.95 33 25.8 32.574999999999996 20.349999999999998 21.275 34 24.425 34.35 20.825 20.4 35 21.75 32.775 25.8 19.675 36 21.65 29.799999999999997 28.125 20.424999999999997 37 25.075075075075077 28.37837837837838 27.902902902902905 18.643643643643642 38 20.275000000000002 29.549999999999997 29.625 20.549999999999997 39 26.775 25.900000000000002 27.325 20.0 40 18.025 34.25 26.424999999999997 21.3 41 23.875 26.55 27.175 22.400000000000002 42 21.19089316987741 31.248436327245432 24.293219914936202 23.267450587940957 43 20.075000000000003 31.924999999999997 25.174999999999997 22.825 44 21.349999999999998 27.775 27.224999999999998 23.65 45 20.766533066132265 29.63426853707415 30.561122244488974 19.03807615230461 46 19.389542156617463 28.271203402551915 32.24918689016762 20.090067550662997 47 21.77177177177177 33.00800800800801 25.475475475475474 19.744744744744743 48 22.455613903475868 31.557889472368096 25.906476619154787 20.080020005001252 49 22.175 31.6 25.8 20.424999999999997 50 25.431357839459867 26.481620405101275 25.731432858214554 22.355588897224308 >>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 0.5 14 1.0 15 1.5 16 2.0 17 3.0 18 4.0 19 2.5 20 1.0 21 6.0 22 11.0 23 13.0 24 15.0 25 32.5 26 50.0 27 51.5 28 53.0 29 52.0 30 51.0 31 70.5 32 90.0 33 138.0 34 186.0 35 260.0 36 334.0 37 405.5 38 477.0 39 411.5 40 346.0 41 341.0 42 336.0 43 376.5 44 417.0 45 401.5 46 386.0 47 290.0 48 194.0 49 269.0 50 344.0 51 232.0 52 120.0 53 111.0 54 102.0 55 91.5 56 81.0 57 73.0 58 65.0 59 54.0 60 43.0 61 48.5 62 54.0 63 47.5 64 41.0 65 37.5 66 34.0 67 37.5 68 41.0 69 41.5 70 42.0 71 35.5 72 29.0 73 23.5 74 18.0 75 16.0 76 14.0 77 12.0 78 10.0 79 6.0 80 2.0 81 1.0 82 0.0 83 2.0 84 4.0 85 2.5 86 1.0 87 0.5 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.5 94 1.0 95 0.5 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 0.075 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 0.1 38 0.0 39 0.0 40 0.0 41 0.0 42 0.075 43 0.0 44 0.0 45 0.2 46 0.075 47 0.1 48 0.025 49 0.0 50 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 57.099999999999994 #Duplication Level Percentage of deduplicated Percentage of total 1 88.66024518388792 50.625 2 5.472854640980736 6.25 3 1.3134851138353765 2.25 4 0.7443082311733801 1.7000000000000002 5 0.6567425569176882 1.875 6 0.43782837127845886 1.5 7 0.2626970227670753 1.05 8 0.17513134851138354 0.8 9 0.21891418563922943 1.125 >10 1.7950963222416811 21.075 >50 0.21891418563922943 8.9 >100 0.043782837127845885 2.85 >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 114 2.85 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 82 2.0500000000000003 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 77 1.925 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGAGATCTCGTAT 74 1.8499999999999999 TruSeq Adapter, Index 3 (97% over 37bp) GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 71 1.775 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 52 1.3 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 46 1.15 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 42 1.05 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 36 0.8999999999999999 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 36 0.8999999999999999 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 36 0.8999999999999999 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 35 0.8750000000000001 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 34 0.8500000000000001 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 31 0.775 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 30 0.75 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 29 0.7250000000000001 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 29 0.7250000000000001 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 27 0.675 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 26 0.65 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 25 0.625 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 23 0.575 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 23 0.575 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 22 0.5499999999999999 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 21 0.525 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 19 0.475 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 17 0.42500000000000004 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 16 0.4 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 16 0.4 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 15 0.375 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 15 0.375 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 14 0.35000000000000003 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 13 0.325 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 13 0.325 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 13 0.325 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 12 0.3 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 12 0.3 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 12 0.3 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 11 0.27499999999999997 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 11 0.27499999999999997 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 11 0.27499999999999997 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 11 0.27499999999999997 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 10 0.25 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 10 0.25 No Hit CTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAC 10 0.25 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 10 0.25 No Hit GCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATAA 10 0.25 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 9 0.22499999999999998 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 9 0.22499999999999998 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 9 0.22499999999999998 No Hit ATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTT 9 0.22499999999999998 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 9 0.22499999999999998 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 8 0.2 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 8 0.2 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 8 0.2 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 8 0.2 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 7 0.17500000000000002 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 7 0.17500000000000002 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 7 0.17500000000000002 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 7 0.17500000000000002 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 7 0.17500000000000002 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 7 0.17500000000000002 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 6 0.15 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 6 0.15 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 6 0.15 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 6 0.15 No Hit GCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTA 6 0.15 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 6 0.15 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 6 0.15 No Hit GTGAAATGGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAA 6 0.15 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 6 0.15 No Hit ATAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATAAGGAC 6 0.15 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 5 0.125 No Hit AGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTT 5 0.125 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 5 0.125 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 5 0.125 No Hit ATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAA 5 0.125 No Hit TGGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATA 5 0.125 No Hit CACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTAG 5 0.125 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGGCTC 5 0.125 No Hit GCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATT 5 0.125 No Hit AACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTA 5 0.125 No Hit GTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCA 5 0.125 No Hit CCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATA 5 0.125 No Hit GCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTACTTCCAT 5 0.125 No Hit CGCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCC 5 0.125 No Hit CCAGATATTCCTAAAGGCATACCATCAGAGAAGCTTCCTTGACCAATAGG 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 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra Read 838958 spots for SRR1850587.sra Written 838958 spots for SRR1850587.sra Read 838951 spots for SRR1850587.sra Written 838951 spots for SRR1850587.sra SRR ids: ['SRR1850587.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hjvzs9ye SRR1850587.sra spots: 16779027 blocks: [[1, 838951], [838952, 1677902], [1677903, 2516853], [2516854, 3355804], [3355805, 4194755], [4194756, 5033706], [5033707, 5872657], [5872658, 6711608], [6711609, 7550559], [7550560, 8389510], [8389511, 9228461], [9228462, 10067412], [10067413, 10906363], [10906364, 11745314], [11745315, 12584265], [12584266, 13423216], [13423217, 14262167], [14262168, 15101118], [15101119, 15940069], [15940070, 16779027]] SRR1850587 file size 2897259 SRR1850587 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 SRR1850587 SRR1850587_1.fastq Input file: SRR1850587_1.fastq trimmed: SRR1850587-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 Sat Dec 7 05:43:31 2024 >> started Sat Dec 7 05:43:42 2024 >> done (10.512s) 16779027 reads processed; of these: 2594 ( 0.02%) short reads filtered out after trimming by size control 353379 ( 2.11%) empty reads filtered out after trimming by size control 16423054 (97.88%) reads available; of these: 713410 ( 4.34%) trimmed reads available after processing 15709644 (95.66%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1156 0.01% 19 1640 0.01% 20 3413 0.02% 21 3361 0.02% 22 4163 0.03% 23 4539 0.03% 24 5574 0.03% 25 6879 0.04% 26 7540 0.05% 27 9080 0.06% 28 8567 0.05% 29 14505 0.09% 30 12637 0.08% 31 10728 0.07% 32 17163 0.10% 33 11187 0.07% 34 11723 0.07% 35 12706 0.08% 36 12893 0.08% 37 18737 0.11% 38 14659 0.09% 39 17236 0.10% 40 22542 0.14% 41 22394 0.14% 42 35086 0.21% 43 37374 0.23% 44 54721 0.33% 45 50679 0.31% 46 61623 0.38% 47 70163 0.43% 48 79016 0.48% 49 69726 0.42% 50 15709644 95.66% 16423054 reads passed initial QC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=18 prefix-density=0.00 prefix-fanout=1.0 sequence=GCGCGACCTTGA criterion=fanout-score sequence-density=0.06 sequence-density-rank=6 fanout-score=21.87 fanout-score-rank=1 prefix-density=1.28 prefix-fanout=1.0 sequence=TCTCTAAAATTTCAGTCATGGTA Started job on | Dec 07 05:43:52 Started mapping on | Dec 07 05:43:52 Finished on | Dec 07 05:44:07 Mapping speed, Million of reads per hour | 3941.53 Number of input reads | 16423054 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 5528607 Uniquely mapped reads % | 33.66% Average mapped length | 49.43 Number of splices: Total | 230423 Number of splices: Annotated (sjdb) | 215259 Number of splices: GT/AG | 224775 Number of splices: GC/AG | 3018 Number of splices: AT/AC | 115 Number of splices: Non-canonical | 2515 Mismatch rate per base, % | 0.29% Deletion rate per base | 0.01% Deletion average length | 1.49 Insertion rate per base | 0.01% Insertion average length | 1.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 10484649 % of reads mapped to multiple loci | 63.84% Number of reads mapped to too many loci | 98389 % of reads mapped to too many loci | 0.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.77% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 409798 409798 409798 N_multimapping 10484649 10484649 10484649 N_noFeature 2033882 5063705 2432339 N_ambiguous 94168 3373 25233 UnstrandedReadsAssigned:3400557 PositiveStrandReadsAssigned:461529 NegativeStrandReadsAssigned:3071035 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1850587 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: SRR1850587-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,423,054 reads, 12,218,648 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 968 rounds 52973 SRR1850587.ke.tsv 35125 SRR1850587.se.tsv 88098 total ==> SRR1850587.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 27 1.35837 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 83.9344 5.13522 KQK14071 474 375 22.0026 5.39896 ==> SRR1850587.se.tsv <== BRADI_1g14170v3 173 BRADI_1g53295v3 22 BRADI_1g59795v3 26 BRADI_1g07683v3 1 BRADI_1g00485v3 2 BRADI_1g20270v3 30 BRADI_1g74790v3 17 BRADI_1g09890v3 5 BRADI_1g77505v3 20 BRADI_1g48960v3 0 SRR1850587 completed mapping pipeline successfully