Starting /dee2/code/volunteer_pipeline.sh SRR1850716 current disk space = 1515674832896 free memory = 1607689172 SRR1850716 SRAfilesize 262adf4fa08270f97353b35c3fde87d9 SRR1850716.sra SRR1850716.sra file validated SRR1850716 is single end SRR1850716 is conventional basespace SRR1850716 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1850716_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 32.69475 34.0 31.0 34.0 31.0 34.0 2 33.0315 34.0 31.0 34.0 31.0 34.0 3 32.99875 34.0 31.0 34.0 31.0 34.0 4 36.41 37.0 37.0 37.0 35.0 37.0 5 36.37925 37.0 37.0 37.0 35.0 37.0 6 36.22825 37.0 37.0 37.0 35.0 37.0 7 36.28125 37.0 37.0 37.0 35.0 37.0 8 36.33475 37.0 37.0 37.0 35.0 37.0 9 38.09425 39.0 39.0 39.0 37.0 39.0 10 38.10325 39.0 39.0 39.0 35.0 39.0 11 38.0565 39.0 38.0 39.0 35.0 39.0 12 38.01025 39.0 38.0 39.0 35.0 39.0 13 37.996 39.0 38.0 39.0 35.0 39.0 14 39.48275 41.0 39.0 41.0 36.0 41.0 15 39.395 41.0 39.0 41.0 36.0 41.0 16 39.3995 41.0 39.0 41.0 36.0 41.0 17 39.36975 41.0 39.0 41.0 36.0 41.0 18 39.4155 41.0 39.0 41.0 36.0 41.0 19 39.312 41.0 39.0 41.0 36.0 41.0 20 39.25175 41.0 39.0 41.0 36.0 41.0 21 39.10825 41.0 39.0 41.0 36.0 41.0 22 39.0865 41.0 39.0 41.0 36.0 41.0 23 39.04325 41.0 39.0 41.0 36.0 41.0 24 39.03 41.0 39.0 41.0 36.0 41.0 25 38.89525 41.0 39.0 41.0 35.0 41.0 26 38.6835 40.0 38.0 41.0 35.0 41.0 27 38.66525 40.0 38.0 41.0 35.0 41.0 28 38.524 40.0 38.0 41.0 34.0 41.0 29 38.55325 40.0 38.0 41.0 35.0 41.0 30 38.34 40.0 38.0 41.0 34.0 41.0 31 38.26525 40.0 38.0 41.0 34.0 41.0 32 38.01125 40.0 38.0 41.0 33.0 41.0 33 37.9205 40.0 38.0 41.0 33.0 41.0 34 37.76925 40.0 38.0 41.0 33.0 41.0 35 38.108 40.0 38.0 41.0 34.0 41.0 36 38.06225 40.0 38.0 41.0 34.0 41.0 37 38.012 40.0 38.0 41.0 34.0 41.0 38 37.90575 40.0 38.0 41.0 33.0 41.0 39 37.7035 40.0 38.0 41.0 33.0 41.0 40 37.646 40.0 38.0 41.0 33.0 41.0 41 37.68475 40.0 38.0 41.0 33.0 41.0 42 37.66125 40.0 38.0 41.0 33.0 41.0 43 37.50925 40.0 38.0 41.0 33.0 41.0 44 37.37975 40.0 38.0 41.0 32.0 41.0 45 37.09025 40.0 37.0 41.0 31.0 41.0 46 37.1505 40.0 38.0 41.0 32.0 41.0 47 36.98325 40.0 38.0 41.0 31.0 41.0 48 36.6995 40.0 37.0 41.0 30.0 41.0 49 36.6445 40.0 37.0 41.0 31.0 41.0 50 36.322 40.0 37.0 41.0 30.0 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 11 1.0 12 2.0 13 3.0 14 4.0 15 6.0 16 6.0 17 2.0 18 5.0 19 7.0 20 11.0 21 9.0 22 6.0 23 12.0 24 10.0 25 14.0 26 19.0 27 17.0 28 23.0 29 25.0 30 36.0 31 54.0 32 69.0 33 88.0 34 123.0 35 143.0 36 230.0 37 259.0 38 547.0 39 2269.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.074999999999996 11.275 14.35 36.3 2 29.225 9.625 29.5 31.65 3 37.90947736934234 15.228807201800452 18.72968242060515 28.132033008252062 4 34.300000000000004 22.375 16.8 26.525 5 33.25 27.900000000000002 20.525 18.325 6 22.85 35.575 17.5 24.075 7 12.025 34.1 35.949999999999996 17.925 8 21.8 27.325 26.8 24.075 9 22.400000000000002 19.15 35.699999999999996 22.75 10 17.4 42.449999999999996 23.5 16.650000000000002 11 25.15 31.3 18.75 24.8 12 26.424999999999997 29.725 22.475 21.375 13 20.3 36.95 22.400000000000002 20.349999999999998 14 24.8 32.025 25.924999999999997 17.25 15 20.225 37.225 19.875 22.675 16 23.125 34.849999999999994 23.375 18.65 17 21.375 34.175 23.325000000000003 21.125 18 18.45 37.3 22.375 21.875 19 21.775 34.775 23.825 19.625 20 16.950000000000003 34.075 25.6 23.375 21 17.724999999999998 29.5 29.525000000000002 23.25 22 14.000000000000002 41.3 24.25 20.45 23 19.05 35.25 24.75 20.95 24 20.125 35.4 21.375 23.1 25 19.6 34.2 25.674999999999997 20.525 26 18.45 37.175000000000004 23.0 21.375 27 22.15 32.625 26.450000000000003 18.775 28 26.05 36.199999999999996 20.825 16.925 29 26.275 31.974999999999998 22.85 18.9 30 25.224999999999998 33.525 22.650000000000002 18.6 31 29.599999999999998 26.575 22.775000000000002 21.05 32 25.974999999999998 29.5 23.35 21.175 33 28.632158039509875 33.633408352088026 18.779694923730933 18.95473868467117 34 23.305826456614152 35.108777194298575 19.829957489372344 21.75543885971493 35 22.325 36.35 20.925 20.4 36 23.48087021755439 28.75718929732433 27.581895473868467 20.180045011252815 37 22.3973973973974 27.87787787787788 29.27927927927928 20.445445445445447 38 20.225 25.974999999999998 30.475 23.325000000000003 39 23.225 26.724999999999998 29.049999999999997 21.0 40 18.375 33.975 25.8 21.85 41 22.875 28.075 27.125 21.925 42 20.630946419629446 32.048072108162245 27.065598397596396 20.255383074611917 43 20.674999999999997 32.05 24.675 22.6 44 20.38009502375594 29.557389347336834 25.95648912228057 24.10602650662666 45 21.30696044066099 30.67100650976465 29.14371557336004 18.87831747621432 46 19.989992494370778 27.420565424068048 33.75031273455092 18.839129347010257 47 20.31523642732049 33.37503127345509 27.070302727045288 19.239429572179134 48 21.580395098774694 32.53313328332083 25.906476619154787 19.979994998749685 49 23.9 32.6 22.775000000000002 20.724999999999998 50 29.307326831707925 25.681420355088775 23.730932733183295 21.280320080020005 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 1.0 17 0.5 18 0.0 19 3.0 20 6.0 21 7.5 22 9.0 23 9.5 24 10.0 25 20.0 26 30.0 27 31.5 28 33.0 29 36.0 30 39.0 31 55.5 32 72.0 33 121.0 34 170.0 35 291.5 36 413.0 37 476.5 38 540.0 39 419.0 40 298.0 41 301.5 42 305.0 43 382.5 44 460.0 45 411.5 46 363.0 47 289.0 48 215.0 49 254.5 50 294.0 51 209.0 52 124.0 53 132.5 54 141.0 55 108.5 56 76.0 57 71.5 58 67.0 59 54.0 60 41.0 61 42.0 62 43.0 63 42.5 64 42.0 65 41.0 66 40.0 67 34.0 68 28.0 69 30.5 70 33.0 71 28.5 72 24.0 73 26.0 74 28.0 75 23.5 76 19.0 77 17.5 78 16.0 79 11.0 80 6.0 81 5.0 82 4.0 83 4.0 84 4.0 85 4.0 86 4.0 87 2.5 88 1.0 89 1.0 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 0.0 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 0.025 34 0.025 35 0.0 36 0.025 37 0.1 38 0.0 39 0.0 40 0.0 41 0.0 42 0.15 43 0.0 44 0.025 45 0.15 46 0.075 47 0.075 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 53.05 #Duplication Level Percentage of deduplicated Percentage of total 1 87.51178133836004 46.425 2 5.136663524976438 5.45 3 2.3091423185673894 3.675 4 0.6597549481621112 1.4000000000000001 5 0.5655042412818096 1.5 6 0.6597549481621112 2.1 7 0.23562676720075398 0.8750000000000001 8 0.3298774740810556 1.4000000000000001 9 0.23562676720075398 1.125 >10 1.9792648444863337 20.825 >50 0.3298774740810556 11.85 >100 0.0471253534401508 3.375 >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 135 3.375 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 92 2.3 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 82 2.0500000000000003 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 71 1.775 No Hit TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 63 1.575 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 58 1.4500000000000002 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 57 1.425 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 51 1.275 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 47 1.175 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 39 0.975 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 39 0.975 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGCCTCGATCTCGTAT 34 0.8500000000000001 TruSeq Adapter, Index 10 (97% over 37bp) CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 32 0.8 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 30 0.75 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 30 0.75 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 30 0.75 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 29 0.7250000000000001 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 27 0.675 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 25 0.625 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 25 0.625 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 25 0.625 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 25 0.625 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 22 0.5499999999999999 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 21 0.525 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 20 0.5 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 20 0.5 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 19 0.475 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 19 0.475 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 18 0.44999999999999996 No Hit TGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAA 15 0.375 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 15 0.375 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 15 0.375 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 15 0.375 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 14 0.35000000000000003 No Hit CGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATTGC 14 0.35000000000000003 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 13 0.325 No Hit CTTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCAT 13 0.325 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 12 0.3 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 12 0.3 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 12 0.3 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 12 0.3 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 11 0.27499999999999997 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 11 0.27499999999999997 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 11 0.27499999999999997 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 11 0.27499999999999997 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 11 0.27499999999999997 No Hit CGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 10 0.25 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 10 0.25 No Hit GTTGAAACTAGCATATTGGAAGATTAATCGGCCAAAATAACCATGAGCAG 10 0.25 No Hit TAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTCTC 10 0.25 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 9 0.22499999999999998 No Hit CGCGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTTTATTCAAATT 9 0.22499999999999998 No Hit TGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 9 0.22499999999999998 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 9 0.22499999999999998 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 9 0.22499999999999998 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 8 0.2 No Hit CCGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGT 8 0.2 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 8 0.2 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 8 0.2 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 8 0.2 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 8 0.2 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 8 0.2 No Hit GCACGGTTGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATC 7 0.17500000000000002 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 7 0.17500000000000002 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 7 0.17500000000000002 No Hit CGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAA 7 0.17500000000000002 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 7 0.17500000000000002 No Hit CTTGTACTTTCGCGTCTCTCTAAAATTGCAGTCATGGTAAGATCTTGGTT 6 0.15 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 6 0.15 No Hit CGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 6 0.15 No Hit TGATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACA 6 0.15 No Hit CCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 6 0.15 No Hit CGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACA 6 0.15 No Hit ATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCAT 6 0.15 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 6 0.15 No Hit CTCATAAGGACCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCC 6 0.15 No Hit GTGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCG 6 0.15 No Hit TTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAA 6 0.15 No Hit TGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGG 6 0.15 No Hit GCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTC 6 0.15 No Hit GCCAAGAAGAAGTGTAAAGAACGAGAGTTGTTGAAACTAGCATATTGGAA 6 0.15 No Hit CGCCATAGTACTAATACCTAAAGCAGTGAACCAGATTCCTACTACAGGCC 5 0.125 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 5 0.125 No Hit CAGTGCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCG 5 0.125 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGGC 5 0.125 No Hit TAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCG 5 0.125 No Hit GCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGAT 5 0.125 No Hit GGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTA 5 0.125 No Hit CGCAGCTGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGGCGCATAC 5 0.125 No Hit ATGATATCAGCCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGA 5 0.125 No Hit ATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACC 5 0.125 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 5 0.125 No Hit AGCAGCCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCT 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 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956441 spots for SRR1850716.sra Written 956441 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra Read 956425 spots for SRR1850716.sra Written 956425 spots for SRR1850716.sra SRR ids: ['SRR1850716.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0ioy6_29 SRR1850716.sra spots: 19128516 blocks: [[1, 956425], [956426, 1912850], [1912851, 2869275], [2869276, 3825700], [3825701, 4782125], [4782126, 5738550], [5738551, 6694975], [6694976, 7651400], [7651401, 8607825], [8607826, 9564250], [9564251, 10520675], [10520676, 11477100], [11477101, 12433525], [12433526, 13389950], [13389951, 14346375], [14346376, 15302800], [15302801, 16259225], [16259226, 17215650], [17215651, 18172075], [18172076, 19128516]] SRR1850716 file size 3304465 SRR1850716 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 SRR1850716 SRR1850716_1.fastq Input file: SRR1850716_1.fastq trimmed: SRR1850716-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 Thu Dec 12 02:38:19 2024 >> started Thu Dec 12 02:38:33 2024 >> done (14.029s) 19128516 reads processed; of these: 3230 ( 0.02%) short reads filtered out after trimming by size control 172594 ( 0.90%) empty reads filtered out after trimming by size control 18952692 (99.08%) reads available; of these: 942461 ( 4.97%) trimmed reads available after processing 18010231 (95.03%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1736 0.01% 19 2534 0.01% 20 6035 0.03% 21 5716 0.03% 22 6016 0.03% 23 6427 0.03% 24 7819 0.04% 25 8753 0.05% 26 9014 0.05% 27 10220 0.05% 28 10218 0.05% 29 17692 0.09% 30 17786 0.09% 31 14192 0.07% 32 22829 0.12% 33 15556 0.08% 34 16999 0.09% 35 17164 0.09% 36 17829 0.09% 37 26329 0.14% 38 19379 0.10% 39 22108 0.12% 40 28951 0.15% 41 27257 0.14% 42 45656 0.24% 43 47641 0.25% 44 72080 0.38% 45 68014 0.36% 46 82325 0.43% 47 94585 0.50% 48 105651 0.56% 49 87950 0.46% 50 18010231 95.03% 18952692 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.11 sequence-density-rank=6 fanout-score=20.53 fanout-score-rank=1 prefix-density=2.24 prefix-fanout=1.0 sequence=TCTCTAAAATTTCAGTCATGGTA Started job on | Dec 12 02:38:44 Started mapping on | Dec 12 02:38:45 Finished on | Dec 12 02:38:58 Mapping speed, Million of reads per hour | 5248.44 Number of input reads | 18952692 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 5134879 Uniquely mapped reads % | 27.09% Average mapped length | 49.36 Number of splices: Total | 285027 Number of splices: Annotated (sjdb) | 268262 Number of splices: GT/AG | 279034 Number of splices: GC/AG | 3602 Number of splices: AT/AC | 155 Number of splices: Non-canonical | 2236 Mismatch rate per base, % | 0.29% Deletion rate per base | 0.01% Deletion average length | 1.47 Insertion rate per base | 0.01% Insertion average length | 1.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 13446604 % of reads mapped to multiple loci | 70.95% Number of reads mapped to too many loci | 73700 % of reads mapped to too many loci | 0.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.52% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 371209 371209 371209 N_multimapping 13446604 13446604 13446604 N_noFeature 1477759 4816861 1727118 N_ambiguous 103213 1913 33883 UnstrandedReadsAssigned:3553907 PositiveStrandReadsAssigned:316105 NegativeStrandReadsAssigned:3373878 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1850716 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: SRR1850716-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,952,692 reads, 15,414,519 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 960 rounds 52973 SRR1850716.ke.tsv 35125 SRR1850716.se.tsv 88098 total ==> SRR1850716.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 41 1.64857 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 24.7709 1.21125 KQK14071 474 375 19.2362 3.77248 ==> SRR1850716.se.tsv <== BRADI_1g14170v3 166 BRADI_1g53295v3 16 BRADI_1g59795v3 15 BRADI_1g07683v3 2 BRADI_1g00485v3 3 BRADI_1g20270v3 23 BRADI_1g74790v3 17 BRADI_1g09890v3 4 BRADI_1g77505v3 44 BRADI_1g48960v3 3 SRR1850716 completed mapping pipeline successfully