Starting /dee2/code/volunteer_pipeline.sh SRR1772225 current disk space = 1515868549120 free memory = 1607717264 SRR1772225 SRAfilesize 56ca252a3a242493b82501da044b67f0 SRR1772225.sra SRR1772225.sra file validated SRR1772225 is single end SRR1772225 is conventional basespace SRR1772225 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1772225_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.93125 34.0 31.0 34.0 31.0 34.0 2 33.06625 34.0 33.0 34.0 31.0 34.0 3 32.79475 34.0 31.0 34.0 31.0 34.0 4 36.247 37.0 37.0 37.0 35.0 37.0 5 36.29775 37.0 37.0 37.0 35.0 37.0 6 36.2555 37.0 37.0 37.0 35.0 37.0 7 36.2595 37.0 37.0 37.0 35.0 37.0 8 36.261 37.0 37.0 37.0 35.0 37.0 9 38.0525 39.0 38.0 39.0 35.0 39.0 10 37.83375 39.0 38.0 39.0 35.0 39.0 11 37.90775 39.0 38.0 39.0 35.0 39.0 12 37.89425 39.0 38.0 39.0 35.0 39.0 13 37.92375 39.0 38.0 39.0 35.0 39.0 14 39.14575 41.0 39.0 41.0 36.0 41.0 15 39.2705 41.0 39.0 41.0 36.0 41.0 16 39.05875 41.0 39.0 41.0 36.0 41.0 17 39.30275 41.0 39.0 41.0 36.0 41.0 18 39.384 41.0 39.0 41.0 36.0 41.0 19 39.231 41.0 39.0 41.0 36.0 41.0 20 39.26525 41.0 39.0 41.0 36.0 41.0 21 39.0895 41.0 39.0 41.0 36.0 41.0 22 39.1435 40.0 39.0 41.0 36.0 41.0 23 38.9175 40.0 39.0 41.0 35.0 41.0 24 38.934 40.0 39.0 41.0 35.0 41.0 25 38.93825 40.0 39.0 41.0 36.0 41.0 26 38.41525 40.0 38.0 41.0 34.0 41.0 27 38.481 40.0 38.0 41.0 34.0 41.0 28 38.5695 40.0 38.0 41.0 34.0 41.0 29 38.45225 40.0 38.0 41.0 35.0 41.0 30 38.37025 40.0 38.0 41.0 34.0 41.0 31 38.23025 40.0 38.0 41.0 34.0 41.0 32 38.16625 40.0 38.0 41.0 34.0 41.0 33 38.04475 40.0 38.0 41.0 33.0 41.0 34 38.47675 40.0 38.0 41.0 35.0 41.0 35 38.44475 40.0 38.0 41.0 35.0 41.0 36 38.4045 40.0 38.0 41.0 34.0 41.0 37 38.08725 40.0 38.0 41.0 34.0 41.0 38 37.81075 40.0 38.0 41.0 33.0 41.0 39 37.96675 40.0 38.0 41.0 33.0 41.0 40 37.8875 40.0 38.0 41.0 33.0 41.0 41 37.69375 40.0 38.0 41.0 33.0 41.0 42 37.7385 40.0 38.0 41.0 33.0 41.0 43 37.55575 40.0 38.0 41.0 33.0 41.0 44 37.4005 40.0 38.0 41.0 33.0 41.0 45 37.17275 40.0 37.0 41.0 32.0 41.0 46 37.20125 40.0 37.0 41.0 33.0 41.0 47 36.8625 40.0 37.0 41.0 31.0 41.0 48 36.717 40.0 37.0 41.0 31.0 41.0 49 36.8185 40.0 37.0 41.0 31.0 41.0 50 36.41175 40.0 36.0 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 10 1.0 11 1.0 12 0.0 13 1.0 14 3.0 15 1.0 16 1.0 17 5.0 18 6.0 19 6.0 20 9.0 21 12.0 22 4.0 23 5.0 24 7.0 25 15.0 26 19.0 27 27.0 28 21.0 29 29.0 30 34.0 31 57.0 32 74.0 33 74.0 34 121.0 35 156.0 36 223.0 37 328.0 38 643.0 39 2117.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.65966491622906 12.578144536134033 12.77819454863716 35.98399599899975 2 31.0 10.525 29.5 28.975 3 37.858942065491185 17.858942065491185 17.732997481108313 26.54911838790932 4 32.875 25.7 15.625 25.8 5 32.574999999999996 29.049999999999997 20.625 17.75 6 23.9 33.4 18.5 24.2 7 11.55 35.825 37.475 15.15 8 21.224999999999998 25.275 30.425 23.075000000000003 9 20.599999999999998 19.825 33.525 26.05 10 17.05 41.55 24.525 16.875 11 26.75 30.4 20.025000000000002 22.825 12 27.35 27.35 23.674999999999997 21.625 13 19.875 36.625 23.925 19.575 14 24.4 30.275000000000002 27.650000000000002 17.675 15 21.25 34.575 22.225 21.95 16 22.225 33.625 23.875 20.275000000000002 17 23.025000000000002 34.075 23.075000000000003 19.825 18 18.224999999999998 34.275 24.224999999999998 23.275000000000002 19 21.575 31.5 25.825 21.099999999999998 20 17.925 32.125 26.075 23.875 21 19.225 28.825 28.4 23.549999999999997 22 16.775000000000002 38.625 23.674999999999997 20.925 23 20.025000000000002 33.475 25.874999999999996 20.625 24 20.075000000000003 33.925 21.7 24.3 25 18.675 33.900000000000006 26.025 21.4 26 19.05 34.725 23.375 22.85 27 25.35 28.4 25.0 21.25 28 24.224999999999998 37.075 21.375 17.325 29 25.6 30.825000000000003 23.799999999999997 19.775000000000002 30 26.174999999999997 29.849999999999998 24.175 19.8 31 27.875 27.35 21.45 23.325000000000003 32 23.45 31.35 24.6 20.599999999999998 33 26.35 33.525 21.099999999999998 19.025 34 23.799999999999997 33.725 21.65 20.825 35 23.45 33.125 23.25 20.175 36 22.425 28.725 27.825 21.025 37 23.89069942341439 28.72900476309852 27.275006267234897 20.105289546252195 38 19.900000000000002 28.275 30.099999999999998 21.725 39 25.2 25.85 27.05 21.9 40 19.075 33.675 24.625 22.625 41 23.674999999999997 28.249999999999996 26.275 21.8 42 22.2 30.925000000000004 23.95 22.925 43 21.075 32.225 24.425 22.275 44 20.8 28.675 27.650000000000002 22.875 45 21.459012283780396 29.355728252694913 28.6287290047631 20.556530458761593 46 19.459053343350863 29.07588279489106 30.728775356874532 20.736288504883547 47 20.52565707133917 33.01627033792241 25.15644555694618 21.30162703379224 48 24.212106053026513 31.390695347673837 24.81240620310155 19.5847923961981 49 22.57822277847309 31.038798498122656 24.90613266583229 21.476846057571965 50 24.55613903475869 27.206801700425103 26.881720430107524 21.355338834708675 >>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 1.5 18 2.0 19 3.0 20 4.0 21 4.5 22 5.0 23 10.5 24 16.0 25 27.5 26 39.0 27 42.5 28 46.0 29 43.5 30 41.0 31 62.0 32 83.0 33 125.5 34 168.0 35 234.5 36 301.0 37 382.0 38 463.0 39 387.5 40 312.0 41 331.5 42 351.0 43 401.0 44 451.0 45 434.0 46 417.0 47 328.0 48 239.0 49 268.5 50 298.0 51 212.5 52 127.0 53 114.0 54 101.0 55 94.5 56 88.0 57 79.0 58 70.0 59 67.0 60 64.0 61 57.0 62 50.0 63 41.0 64 32.0 65 37.5 66 43.0 67 41.0 68 39.0 69 44.5 70 50.0 71 47.0 72 44.0 73 30.5 74 17.0 75 14.0 76 11.0 77 11.5 78 12.0 79 8.0 80 4.0 81 5.0 82 6.0 83 3.5 84 1.0 85 2.0 86 3.0 87 2.0 88 1.0 89 0.5 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 0.025 2 0.0 3 0.75 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 0.27499999999999997 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.27499999999999997 46 0.17500000000000002 47 0.125 48 0.05 49 0.125 50 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 61.824999999999996 #Duplication Level Percentage of deduplicated Percentage of total 1 88.43509906995553 54.675 2 5.37808329963607 6.65 3 2.0218358269308534 3.75 4 0.8491710473109584 2.1 5 0.646987464617873 2.0 6 0.4852405984634048 1.7999999999999998 7 0.20218358269308534 0.8750000000000001 8 0.16174686615446826 0.8 9 0.16174686615446826 0.8999999999999999 >10 1.4961585119288312 18.375 >50 0.1213101496158512 5.55 >100 0.040436716538617065 2.5250000000000004 >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 101 2.5250000000000004 No Hit GGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTT 86 2.15 No Hit CTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGG 80 2.0 No Hit GTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTA 56 1.4000000000000001 No Hit GCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAG 47 1.175 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGGCAGAAATCTCGTAT 37 0.9249999999999999 TruSeq Adapter, Index 13 (97% over 38bp) TCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGG 35 0.8750000000000001 No Hit GCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGAT 33 0.8250000000000001 No Hit CGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGA 31 0.775 No Hit GTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTC 29 0.7250000000000001 No Hit CGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGT 27 0.675 No Hit CTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATAC 27 0.675 No Hit ACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 26 0.65 No Hit GCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 24 0.6 No Hit GCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCAT 24 0.6 No Hit CGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGT 22 0.5499999999999999 No Hit CGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATC 22 0.5499999999999999 No Hit CGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCT 21 0.525 No Hit CAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGAT 20 0.5 No Hit GGAGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAA 20 0.5 No Hit GGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGAC 20 0.5 No Hit GTCAATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACG 19 0.475 No Hit ATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACC 18 0.44999999999999996 No Hit CCACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTA 17 0.42500000000000004 No Hit CGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGG 16 0.4 No Hit GCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAA 16 0.4 No Hit CGCAGAAGTAGGAATAATAGCACCAGAGATAATATTGTTTCCATAAAGTA 15 0.375 No Hit TTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCC 15 0.375 No Hit GGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAA 14 0.35000000000000003 No Hit GTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCC 14 0.35000000000000003 No Hit GCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGAC 14 0.35000000000000003 No Hit TTTCTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATT 13 0.325 No Hit CTCGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAA 13 0.325 No Hit CTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGTTA 12 0.3 No Hit AGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 12 0.3 No Hit GCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAAC 11 0.27499999999999997 No Hit CTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAG 11 0.27499999999999997 No Hit CGCGAATACCATCAATATCTACTGGAGGGGCTGCGATGAAGGCGATAATA 10 0.25 No Hit CCGGGGTGTAGTAAGTCAATCTATAATCTTTAACACCAGCTTTAAATCCA 10 0.25 No Hit CCCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAA 10 0.25 No Hit GCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAGG 10 0.25 No Hit GCTAGTTATCCAGTTGCAGAAGCGACCCCACAGGCTTGTACTTTCGCGTC 9 0.22499999999999998 No Hit CCACAATATTATAAGTCTCTTCCTCTTGACCAAATTTGTAACCCTCATTA 9 0.22499999999999998 No Hit CCAAGTATTAATAACGCGACCTTGACTATCAACTACAGATTGGTTGAAAT 9 0.22499999999999998 No Hit AATAAATACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGA 9 0.22499999999999998 No Hit GGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATCTA 8 0.2 No Hit CTGTGCCTGCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTC 8 0.2 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 8 0.2 No Hit CCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGCATA 8 0.2 No Hit CTTTTCTTCAAAAATTCTTATATGTTAGCGGAAAAACCTTATCCATTAAT 7 0.17500000000000002 No Hit TTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCA 7 0.17500000000000002 No Hit GGCCAAAATAACCATGAGCAGCCACAATATTATAAGTCTCTTCCTCTTGA 7 0.17500000000000002 No Hit GCGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAG 7 0.17500000000000002 No Hit GCGGAAAAACCTTATCCATTAATAGCGGGAACTTCAAGAGCAGCTAGATC 7 0.17500000000000002 No Hit AATAAGGTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATT 6 0.15 No Hit CTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTA 6 0.15 No Hit ATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGATGATAT 6 0.15 No Hit TGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 6 0.15 No Hit GTGAGCATTACGTTCGTGCATTACTTCCATACCAAGATTAGCACGGTTGA 6 0.15 No Hit GGATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAA 6 0.15 No Hit CCCTCATTAGCAGATTCATTTTCAGTAGTTTCCCTGATCAAACTAGAGGT 6 0.15 No Hit TCTTCCTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGT 6 0.15 No Hit AAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTACGTTCGTGCATTA 6 0.15 No Hit AGCGGGAACTTCAAGAGCAGCTAGATCTAGAGGGAAGTTGTGAGCATTAC 6 0.15 No Hit CTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCTAAAGGC 6 0.15 No Hit GGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGT 6 0.15 No Hit GCCGAAAACACCAGCTACACCTAACATGTGAAATGGATGCATAAGGATGT 5 0.125 No Hit CTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCGGCCCGTTA 5 0.125 No Hit ATGCATAAGGATGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAG 5 0.125 No Hit ACCAGATATTCCTAAAGGCATACCATCAGAGAAGCTTCCTTGACCAATAG 5 0.125 No Hit TGTTGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATT 5 0.125 No Hit GTAGGGATCATCAAAACACCGAACCATCCGATGTAAAGACGATTTTCAGT 5 0.125 No Hit GGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGGTAG 5 0.125 No Hit GTGGTTCGCTGGAGTAGGCTGCGAGGCCCAAGCGGCCAAGGAGTGCAGCG 5 0.125 No Hit TGTGCTCTGCCTGGAATACAATCATAAAGTTGAAAGTACCAGATATTCCT 5 0.125 No Hit AACGCGACCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTA 5 0.125 No Hit GCGGCCTTGACTATCAACTACAGATTGGTTGAAATTGAATCCATTTAGGT 5 0.125 No Hit GCCAACATTATGGGCCGCGAAGCCTAGCTTTCGCTTAAGCTCCAACGGCC 5 0.125 No Hit ACAGAAGTTGCGGTCAATAAGGTAGGGATCATCAAAACACCGAACCATCC 5 0.125 No Hit CTCTTGACCAAATTTGTAACCCTCATTAGCAGATTCATTTTCAGTAGTTT 5 0.125 No Hit CACCATTGTATAACCATTCATCAACGGATGCAGCTTCCCAAATTGGGTAA 5 0.125 No Hit GGGGGCTGCGATGAAGGCGATAATAAATACAGAAGTTGCGGTCAATAAGG 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACCGAA 25 0.0020930516 35.17 24 ACACCGA 25 0.0020930516 35.17 23 GGATCAT 25 0.0020930516 35.17 12 CATCAAA 25 0.0020930516 35.17 16 AGGGATC 25 0.0020930516 35.17 10 ACCGAAC 25 0.0020930516 35.17 25 TCAAAAC 25 0.0020930516 35.17 18 AAGACGA 25 0.0020930516 35.17 43 AGACGAT 25 0.0020930516 35.17 44 GATCATC 25 0.0020930516 35.17 13 GGGATCA 25 0.0020930516 35.17 11 ATCATCA 25 0.0020930516 35.17 14 ATCAAAA 25 0.0020930516 35.17 17 TCATCAA 25 0.0020930516 35.17 15 TAAAGAC 25 0.0020930516 35.17 41 AAAGACG 25 0.0020930516 35.17 42 AACACCG 25 0.0020930516 35.17 22 ATCCGAT 35 2.6978442E-4 31.401783 33 AAACACC 30 0.005116581 29.308332 21 ACCATCC 30 0.005116581 29.308332 30 >>END_MODULE Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786241 spots for SRR1772225.sra Written 786241 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra Read 786233 spots for SRR1772225.sra Written 786233 spots for SRR1772225.sra SRR ids: ['SRR1772225.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jx0_r9di SRR1772225.sra spots: 15724668 blocks: [[1, 786233], [786234, 1572466], [1572467, 2358699], [2358700, 3144932], [3144933, 3931165], [3931166, 4717398], [4717399, 5503631], [5503632, 6289864], [6289865, 7076097], [7076098, 7862330], [7862331, 8648563], [8648564, 9434796], [9434797, 10221029], [10221030, 11007262], [11007263, 11793495], [11793496, 12579728], [12579729, 13365961], [13365962, 14152194], [14152195, 14938427], [14938428, 15724668]] SRR1772225 file size 2714506 SRR1772225 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 SRR1772225 SRR1772225_1.fastq Input file: SRR1772225_1.fastq trimmed: SRR1772225-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 02:29:26 2024 >> started Thu Dec 12 02:29:34 2024 >> done (8.503s) 15724668 reads processed; of these: 2249 ( 0.01%) short reads filtered out after trimming by size control 113088 ( 0.72%) empty reads filtered out after trimming by size control 15609331 (99.27%) reads available; of these: 680404 ( 4.36%) trimmed reads available after processing 14928927 (95.64%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1051 0.01% 19 1413 0.01% 20 2690 0.02% 21 3280 0.02% 22 4138 0.03% 23 4331 0.03% 24 6151 0.04% 25 6668 0.04% 26 6351 0.04% 27 7440 0.05% 28 7622 0.05% 29 10744 0.07% 30 9604 0.06% 31 10854 0.07% 32 12345 0.08% 33 9764 0.06% 34 10784 0.07% 35 13160 0.08% 36 13698 0.09% 37 16689 0.11% 38 14704 0.09% 39 16828 0.11% 40 23534 0.15% 41 22662 0.15% 42 34149 0.22% 43 35819 0.23% 44 47592 0.30% 45 45087 0.29% 46 56280 0.36% 47 70442 0.45% 48 80094 0.51% 49 74436 0.48% 50 14928927 95.64% 15609331 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=22 prefix-density=0.00 prefix-fanout=1.0 sequence=TGCGGGAACTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=24 fanout-score=10.05 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=1.5 sequence=AAAAGTAACCCCTCTTTTCCCATTTGCTCTCTATTGCATGGGTGGAAGAACAAAAATGGAGGATTCTTAAAAAAAAAGA Started job on | Dec 12 02:29:43 Started mapping on | Dec 12 02:29:43 Finished on | Dec 12 02:29:59 Mapping speed, Million of reads per hour | 3512.10 Number of input reads | 15609331 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 4935943 Uniquely mapped reads % | 31.62% Average mapped length | 49.29 Number of splices: Total | 344885 Number of splices: Annotated (sjdb) | 326579 Number of splices: GT/AG | 338573 Number of splices: GC/AG | 4016 Number of splices: AT/AC | 197 Number of splices: Non-canonical | 2099 Mismatch rate per base, % | 0.32% Deletion rate per base | 0.01% Deletion average length | 1.53 Insertion rate per base | 0.01% Insertion average length | 1.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 10234332 % of reads mapped to multiple loci | 65.57% Number of reads mapped to too many loci | 84752 % of reads mapped to too many loci | 0.54% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.19% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 439056 439056 439056 N_multimapping 10234332 10234332 10234332 N_noFeature 976497 4781084 1055473 N_ambiguous 118472 848 42669 UnstrandedReadsAssigned:3840974 PositiveStrandReadsAssigned:154011 NegativeStrandReadsAssigned:3837801 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR1772225 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: SRR1772225-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,609,331 reads, 12,615,107 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 966 rounds 52973 SRR1772225.ke.tsv 35125 SRR1772225.se.tsv 88098 total ==> SRR1772225.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 1.98309 0.189442 PNS24249 1928 1829 38.0507 1.87808 PNS24246 1044 945 1.98309 0.189442 PNS24248 1044 945 1.98309 0.189442 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 25.1804 1.5114 KQK14071 474 375 33.559 8.07872 ==> SRR1772225.se.tsv <== BRADI_1g14170v3 108 BRADI_1g53295v3 5 BRADI_1g59795v3 45 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 43 BRADI_1g74790v3 21 BRADI_1g09890v3 2 BRADI_1g77505v3 27 BRADI_1g48960v3 0 SRR1772225 completed mapping pipeline successfully