Starting /dee2/code/volunteer_pipeline.sh SRR1772234 current disk space = 1552298889216 free memory = 1605423696 SRR1772234 SRAfilesize b1f1d09fb5e23bbb17610d709e9ecbf3 SRR1772234.sra SRR1772234.sra file validated SRR1772234 is single end SRR1772234 is conventional basespace SRR1772234 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772234_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.9105 34.0 31.0 34.0 31.0 34.0 2 33.04525 34.0 31.0 34.0 31.0 34.0 3 32.74575 34.0 31.0 34.0 31.0 34.0 4 36.2465 37.0 37.0 37.0 35.0 37.0 5 36.304 37.0 37.0 37.0 35.0 37.0 6 36.2075 37.0 37.0 37.0 35.0 37.0 7 36.26575 37.0 37.0 37.0 35.0 37.0 8 36.24975 37.0 37.0 37.0 35.0 37.0 9 37.9675 39.0 38.0 39.0 35.0 39.0 10 37.85825 39.0 38.0 39.0 35.0 39.0 11 37.9275 39.0 38.0 39.0 35.0 39.0 12 37.953 39.0 38.0 39.0 35.0 39.0 13 37.9165 39.0 38.0 39.0 35.0 39.0 14 39.23025 41.0 39.0 41.0 36.0 41.0 15 39.3515 41.0 39.0 41.0 36.0 41.0 16 39.1655 41.0 39.0 41.0 36.0 41.0 17 39.3485 41.0 39.0 41.0 36.0 41.0 18 39.35275 41.0 39.0 41.0 36.0 41.0 19 39.17275 41.0 39.0 41.0 36.0 41.0 20 39.27125 41.0 39.0 41.0 36.0 41.0 21 39.15075 41.0 39.0 41.0 36.0 41.0 22 39.156 40.0 39.0 41.0 36.0 41.0 23 38.85975 40.0 39.0 41.0 35.0 41.0 24 38.99825 41.0 39.0 41.0 35.0 41.0 25 39.101 40.0 39.0 41.0 36.0 41.0 26 38.53175 40.0 38.0 41.0 34.0 41.0 27 38.67175 40.0 38.0 41.0 34.0 41.0 28 38.7235 40.0 38.0 41.0 35.0 41.0 29 38.612 40.0 38.0 41.0 35.0 41.0 30 38.504 40.0 38.0 41.0 34.0 41.0 31 38.36875 40.0 38.0 41.0 34.0 41.0 32 38.33875 40.0 38.0 41.0 34.0 41.0 33 38.35675 40.0 38.0 41.0 34.0 41.0 34 38.5085 40.0 38.0 41.0 35.0 41.0 35 38.6035 40.0 38.0 41.0 35.0 41.0 36 38.51075 40.0 38.0 41.0 35.0 41.0 37 38.24475 40.0 38.0 41.0 34.0 41.0 38 37.98375 40.0 38.0 41.0 33.0 41.0 39 38.127 40.0 38.0 41.0 34.0 41.0 40 38.0815 40.0 38.0 41.0 34.0 41.0 41 37.91425 40.0 38.0 41.0 33.0 41.0 42 37.99875 40.0 38.0 41.0 33.0 41.0 43 37.76875 40.0 38.0 41.0 33.0 41.0 44 37.76275 40.0 38.0 41.0 33.0 41.0 45 37.4805 40.0 38.0 41.0 33.0 41.0 46 37.536 40.0 38.0 41.0 33.0 41.0 47 37.11725 40.0 37.0 41.0 32.0 41.0 48 36.993 40.0 37.0 41.0 31.0 41.0 49 37.10925 40.0 37.0 41.0 32.0 41.0 50 36.77275 40.0 37.0 41.0 31.0 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 12 1.0 13 0.0 14 2.0 15 0.0 16 5.0 17 1.0 18 4.0 19 2.0 20 5.0 21 8.0 22 5.0 23 13.0 24 7.0 25 10.0 26 9.0 27 22.0 28 19.0 29 24.0 30 57.0 31 61.0 32 65.0 33 98.0 34 104.0 35 145.0 36 193.0 37 352.0 38 616.0 39 2172.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.11955977988995 12.581290645322662 13.1815907953977 35.1175587793897 2 31.025000000000002 12.075 28.125 28.775000000000002 3 36.6658272475447 19.84386804331403 18.131453034500126 25.358851674641148 4 31.874999999999996 27.725 16.025 24.375 5 33.35 30.599999999999998 19.625 16.425 6 24.15 34.375 16.975 24.5 7 11.700000000000001 38.2 34.949999999999996 15.15 8 20.925 27.725 30.049999999999997 21.3 9 22.175 20.8 32.525 24.5 10 15.65 45.275 24.125 14.95 11 26.375 31.5 19.45 22.675 12 26.224999999999998 28.95 20.775 24.05 13 17.349999999999998 39.300000000000004 24.3 19.05 14 24.725 31.525 26.0 17.75 15 20.424999999999997 36.7 20.925 21.95 16 21.5 34.925 23.150000000000002 20.424999999999997 17 23.65 35.025 21.95 19.375 18 18.3 35.625 23.599999999999998 22.475 19 19.55 34.075 26.25 20.125 20 17.224999999999998 33.800000000000004 27.775 21.2 21 18.099999999999998 30.85 26.150000000000002 24.9 22 14.674999999999999 42.225 23.05 20.05 23 19.35 36.0 25.224999999999998 19.425 24 19.650000000000002 33.5 21.425 25.424999999999997 25 16.725 34.75 27.450000000000003 21.075 26 18.25 36.025 22.925 22.8 27 23.75 30.275000000000002 25.8 20.175 28 23.0 40.075 21.15 15.775 29 26.825 33.125 22.35 17.7 30 25.124999999999996 30.475 25.374999999999996 19.025 31 28.225 27.625 22.625 21.525 32 23.225 32.35 24.775 19.650000000000002 33 26.6 33.525 18.875 21.0 34 22.45 35.4 20.075000000000003 22.075 35 21.525 34.375 22.375 21.725 36 20.775 28.799999999999997 30.775000000000002 19.650000000000002 37 22.664663160530928 28.750313047833707 28.07412972702229 20.510894064613073 38 20.7 27.0 31.674999999999997 20.625 39 23.200000000000003 26.25 28.499999999999996 22.05 40 18.85 34.625 27.800000000000004 18.725 41 25.025 26.650000000000002 27.975 20.349999999999998 42 21.224999999999998 33.074999999999996 22.425 23.275000000000002 43 19.35 34.1 24.975 21.575 44 20.175 29.275000000000002 28.175 22.375 45 20.035061357375408 28.249436513899322 33.007763586275985 18.707738542449288 46 17.792792792792792 30.38038038038038 33.433433433433436 18.393393393393392 47 21.096096096096094 34.55955955955956 26.05105105105105 18.293293293293296 48 22.692019014260694 32.94971228421316 25.268951713785338 19.089316987740805 49 22.6976976976977 32.55755755755756 24.94994994994995 19.794794794794797 50 25.237618809404704 26.563281640820406 27.43871935967984 20.76038019009505 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 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 0.5 16 0.0 17 0.5 18 1.0 19 3.5 20 6.0 21 7.0 22 8.0 23 11.0 24 14.0 25 26.0 26 38.0 27 31.0 28 24.0 29 37.5 30 51.0 31 64.0 32 77.0 33 129.0 34 181.0 35 261.5 36 342.0 37 436.0 38 530.0 39 462.5 40 395.0 41 373.5 42 352.0 43 406.0 44 460.0 45 442.5 46 425.0 47 328.0 48 231.0 49 246.5 50 262.0 51 223.0 52 184.0 53 138.5 54 93.0 55 70.0 56 47.0 57 51.0 58 55.0 59 44.5 60 34.0 61 35.0 62 36.0 63 28.5 64 21.0 65 21.5 66 22.0 67 24.5 68 27.0 69 23.5 70 20.0 71 22.5 72 25.0 73 18.5 74 12.0 75 9.0 76 6.0 77 5.0 78 4.0 79 5.5 80 7.0 81 5.0 82 3.0 83 2.5 84 2.0 85 2.0 86 2.0 87 1.0 88 0.0 89 0.5 90 1.0 91 0.5 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 0.05 2 0.0 3 0.7250000000000001 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 0.17500000000000002 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.17500000000000002 46 0.1 47 0.1 48 0.075 49 0.1 50 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 50.24999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 84.72636815920399 42.575 2 6.5174129353233825 6.550000000000001 3 2.3880597014925375 3.5999999999999996 4 1.5422885572139304 3.1 5 1.0447761194029852 2.625 6 0.3482587064676617 1.05 7 0.24875621890547264 0.8750000000000001 8 0.3482587064676617 1.4000000000000001 9 0.1990049751243781 0.8999999999999999 >10 2.288557213930348 23.025000000000002 >50 0.1990049751243781 6.2 >100 0.1492537313432836 8.1 >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 115 2.875 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 106 2.65 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 103 2.5749999999999997 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCTCTCTGATCTCGTAT 83 2.075 TruSeq Adapter, Index 23 (97% over 40bp) GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 55 1.375 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 55 1.375 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 55 1.375 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 45 1.125 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 42 1.05 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 41 1.0250000000000001 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 40 1.0 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 37 0.9249999999999999 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 32 0.8 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 30 0.75 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 29 0.7250000000000001 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 29 0.7250000000000001 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 29 0.7250000000000001 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 28 0.7000000000000001 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 27 0.675 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 26 0.65 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 25 0.625 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 23 0.575 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 21 0.525 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 21 0.525 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 21 0.525 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 19 0.475 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 18 0.44999999999999996 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 17 0.42500000000000004 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 16 0.4 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 16 0.4 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 16 0.4 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 16 0.4 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 15 0.375 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 15 0.375 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 14 0.35000000000000003 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 13 0.325 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 13 0.325 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 13 0.325 No Hit GGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTC 13 0.325 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 13 0.325 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 12 0.3 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 12 0.3 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 12 0.3 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 12 0.3 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 12 0.3 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 12 0.3 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 11 0.27499999999999997 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit ATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTT 11 0.27499999999999997 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 11 0.27499999999999997 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 10 0.25 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 10 0.25 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 9 0.22499999999999998 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 9 0.22499999999999998 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 9 0.22499999999999998 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 9 0.22499999999999998 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 8 0.2 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 8 0.2 No Hit CTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTTGAAC 8 0.2 No Hit TTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAG 8 0.2 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 8 0.2 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 8 0.2 No Hit CACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCA 8 0.2 No Hit CGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCC 7 0.17500000000000002 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 7 0.17500000000000002 No Hit TCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGA 7 0.17500000000000002 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 7 0.17500000000000002 No Hit GCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTC 7 0.17500000000000002 No Hit GGGCGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACA 6 0.15 No Hit CGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGTT 6 0.15 No Hit GGCGCATACCCAAACGGAAACTAAGTTCCCACTCACGACCCATATAACAA 6 0.15 No Hit ATAATTAACTGCATTGATCTCGGTAGCTACGCCACCCACGGAATTTAAAG 6 0.15 No Hit CCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGT 6 0.15 No Hit TCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGT 6 0.15 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 6 0.15 No Hit AGAGAAGCTTCCTTGACCAATAGGGTAAATCAAGAAAACAGCAGTCGCAG 5 0.125 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 5 0.125 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 5 0.125 No Hit GGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACT 5 0.125 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 5 0.125 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 5 0.125 No Hit ACCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGG 5 0.125 No Hit TAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAAC 5 0.125 No Hit CTCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAG 5 0.125 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 5 0.125 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 5 0.125 No Hit CCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAAAA 5 0.125 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 5 0.125 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 5 0.125 No Hit GAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTAG 5 0.125 No Hit GCTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCA 5 0.125 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 5 0.125 No Hit AGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTACCAAGG 5 0.125 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 5 0.125 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 5 0.125 No Hit GCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAA 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 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018966 spots for SRR1772234.sra Written 1018966 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra Read 1018953 spots for SRR1772234.sra Written 1018953 spots for SRR1772234.sra SRR ids: ['SRR1772234.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xmf9lhvo SRR1772234.sra spots: 20379073 blocks: [[1, 1018953], [1018954, 2037906], [2037907, 3056859], [3056860, 4075812], [4075813, 5094765], [5094766, 6113718], [6113719, 7132671], [7132672, 8151624], [8151625, 9170577], [9170578, 10189530], [10189531, 11208483], [11208484, 12227436], [12227437, 13246389], [13246390, 14265342], [14265343, 15284295], [15284296, 16303248], [16303249, 17322201], [17322202, 18341154], [18341155, 19360107], [19360108, 20379073]] SRR1772234 file size 3521203 SRR1772234 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 SRR1772234 SRR1772234_1.fastq Input file: SRR1772234_1.fastq trimmed: SRR1772234-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 09:49:40 2024 >> started Fri Dec 6 09:49:53 2024 >> done (12.607s) 20379073 reads processed; of these: 2385 ( 0.01%) short reads filtered out after trimming by size control 414733 ( 2.04%) empty reads filtered out after trimming by size control 19961955 (97.95%) reads available; of these: 849572 ( 4.26%) trimmed reads available after processing 19112383 (95.74%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1104 0.01% 19 1637 0.01% 20 3615 0.02% 21 4161 0.02% 22 4863 0.02% 23 4660 0.02% 24 6756 0.03% 25 7545 0.04% 26 6640 0.03% 27 8728 0.04% 28 9415 0.05% 29 14124 0.07% 30 12909 0.06% 31 14069 0.07% 32 16002 0.08% 33 11742 0.06% 34 12792 0.06% 35 15924 0.08% 36 15559 0.08% 37 20635 0.10% 38 16982 0.09% 39 19823 0.10% 40 30009 0.15% 41 27834 0.14% 42 48132 0.24% 43 45934 0.23% 44 60029 0.30% 45 58737 0.29% 46 70577 0.35% 47 88014 0.44% 48 100406 0.50% 49 90215 0.45% 50 19112383 95.74% 19961955 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=17 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=36.67 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=4.8 sequence=AAAAAGAATAGAGGTATGACAGGCATAAAATCCACGATTGGGTTGAAAATAGCATAAGCTTCGGGTAGTTTAGCAAAGAAAAAACTAGTCGGATAAAGAACACAATTAAAACAGATACAGGTTAAACTAAGTATATTAGGCATAACAAG Started job on | Dec 06 09:51:00 Started mapping on | Dec 06 09:51:00 Finished on | Dec 06 09:51:14 Mapping speed, Million of reads per hour | 5133.07 Number of input reads | 19961955 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4594477 Uniquely mapped reads % | 23.02% Average mapped length | 49.38 Number of splices: Total | 303935 Number of splices: Annotated (sjdb) | 288411 Number of splices: GT/AG | 298125 Number of splices: GC/AG | 3803 Number of splices: AT/AC | 145 Number of splices: Non-canonical | 1862 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 1.43 Insertion rate per base | 0.01% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 15041114 % of reads mapped to multiple loci | 75.35% Number of reads mapped to too many loci | 56400 % of reads mapped to too many loci | 0.28% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.34% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 326364 326364 326364 N_multimapping 15041114 15041114 15041114 N_noFeature 1093886 4474120 1152419 N_ambiguous 90724 855 28787 UnstrandedReadsAssigned:3409867 PositiveStrandReadsAssigned:119502 NegativeStrandReadsAssigned:3413271 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772234 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: SRR1772234-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,961,955 reads, 17,019,747 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,338 rounds 52973 SRR1772234.ke.tsv 35125 SRR1772234.se.tsv 88098 total ==> SRR1772234.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.957686 0.0671513 PNS24249 1928 1829 24.1269 0.874081 PNS24246 1044 945 0.957686 0.0671513 PNS24248 1044 945 0.957686 0.0671513 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 90.6684 3.99458 KQK14071 474 375 55.9573 9.88754 ==> SRR1772234.se.tsv <== BRADI_1g14170v3 243 BRADI_1g53295v3 2 BRADI_1g59795v3 45 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 14 BRADI_1g74790v3 13 BRADI_1g09890v3 0 BRADI_1g77505v3 43 BRADI_1g48960v3 0 SRR1772234 completed mapping pipeline successfully