Starting /dee2/code/volunteer_pipeline.sh ERR6133369 current disk space = 1548025241600 free memory = 1603204428 ERR6133369 SRAfilesize b6ea9ac5b4bfa2acf009fdd474ed5c94 ERR6133369.sra ERR6133369.sra file validated ERR6133369 is single end ERR6133369 is conventional basespace ERR6133369 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133369_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.89125 37.0 37.0 37.0 37.0 37.0 2 36.7775 37.0 37.0 37.0 37.0 37.0 3 36.60825 37.0 37.0 37.0 37.0 37.0 4 36.0865 37.0 37.0 37.0 33.0 37.0 5 36.125 37.0 37.0 37.0 33.0 37.0 6 36.29875 37.0 37.0 37.0 33.0 37.0 7 38.29225 40.0 37.0 40.0 37.0 40.0 8 38.30675 40.0 37.0 40.0 37.0 40.0 9 38.281 40.0 37.0 40.0 37.0 40.0 10-11 38.2375 40.0 37.0 40.0 37.0 40.0 12-13 38.283500000000004 40.0 37.0 40.0 37.0 40.0 14-15 38.18875 40.0 37.0 40.0 37.0 40.0 16-17 38.108374999999995 40.0 37.0 40.0 35.0 40.0 18-19 38.090875 40.0 37.0 40.0 35.0 40.0 20-21 38.00575 40.0 37.0 40.0 35.0 40.0 22-23 37.971375 40.0 37.0 40.0 33.0 40.0 24-25 37.775375 40.0 37.0 40.0 33.0 40.0 26-27 37.678375 40.0 37.0 40.0 33.0 40.0 28-29 37.593 40.0 37.0 40.0 33.0 40.0 30-31 37.542 38.5 37.0 40.0 33.0 40.0 32-33 37.211749999999995 37.0 37.0 40.0 33.0 40.0 34-35 37.046499999999995 37.0 37.0 40.0 33.0 40.0 36-37 37.091125 37.0 37.0 40.0 33.0 40.0 38-39 37.189625 37.0 37.0 40.0 33.0 40.0 40-41 37.40875 37.0 37.0 40.0 33.0 40.0 42-43 37.228125000000006 37.0 37.0 40.0 33.0 40.0 44-45 37.216125 37.0 37.0 40.0 33.0 40.0 46-47 36.941375 37.0 37.0 40.0 33.0 40.0 48-49 36.842375000000004 37.0 37.0 40.0 33.0 40.0 50-51 36.79275 37.0 37.0 40.0 33.0 40.0 52-53 36.63475 37.0 37.0 38.5 33.0 40.0 54-55 36.401125 37.0 37.0 37.0 33.0 40.0 56-57 36.152875 37.0 37.0 37.0 33.0 40.0 58-59 36.035624999999996 37.0 37.0 37.0 33.0 40.0 60-61 35.920625 37.0 37.0 37.0 33.0 38.5 62-63 35.588625 37.0 35.0 37.0 33.0 37.0 64-65 35.304 37.0 33.0 37.0 33.0 37.0 66-67 35.358000000000004 37.0 33.0 37.0 33.0 37.0 68-69 34.406875 35.0 33.0 37.0 30.0 37.0 70-71 34.63567352241422 37.0 33.0 37.0 33.0 37.0 72-73 35.07314127519159 37.0 33.0 37.0 33.0 37.0 74-75 35.09363445886403 37.0 33.0 37.0 33.0 37.0 76-77 34.91416336615434 37.0 33.0 37.0 33.0 37.0 78-79 35.08457230994054 37.0 33.0 37.0 33.0 37.0 80-81 34.88675356539454 37.0 33.0 37.0 33.0 37.0 82-83 34.545480705056676 37.0 33.0 37.0 33.0 37.0 84-85 34.61288728974293 37.0 33.0 37.0 33.0 37.0 86-87 34.59320512820513 37.0 33.0 37.0 33.0 37.0 88-89 34.57076923076923 37.0 33.0 37.0 33.0 37.0 90-91 34.203974358974364 37.0 33.0 37.0 33.0 37.0 92-93 34.01102564102564 37.0 33.0 37.0 30.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 5.0 21 8.0 22 10.0 23 5.0 24 13.0 25 15.0 26 20.0 27 16.0 28 26.0 29 41.0 30 54.0 31 48.0 32 99.0 33 123.0 34 167.0 35 352.0 36 834.0 37 1102.0 38 1029.0 39 33.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 78.975 4.75 5.425 10.85 2 55.1 26.674999999999997 11.825 6.4 3 31.474999999999998 37.85 16.75 13.925 4 33.625 25.124999999999996 20.05 21.2 5 22.275 30.0 27.425 20.3 6 19.2 39.025 26.3 15.475 7 33.650000000000006 29.525000000000002 22.0 14.825 8 30.3 28.225 24.75 16.725 9 26.3 25.424999999999997 29.349999999999998 18.925 10-11 22.9875 28.3875 28.487499999999997 20.1375 12-13 27.037499999999998 24.3 29.2875 19.375 14-15 21.85 26.487500000000004 31.75 19.9125 16-17 25.525 30.0 26.8375 17.6375 18-19 22.8375 26.637499999999996 27.9125 22.6125 20-21 26.150000000000002 26.424999999999997 27.8625 19.5625 22-23 25.912499999999998 25.15 27.675 21.2625 24-25 24.85 24.925 29.1375 21.087500000000002 26-27 26.3625 25.362499999999997 29.4 18.875 28-29 24.425 26.387500000000003 28.325 20.8625 30-31 26.150000000000002 24.5625 28.249999999999996 21.0375 32-33 23.5 27.9375 28.6625 19.900000000000002 34-35 25.525 25.337500000000002 28.5875 20.549999999999997 36-37 24.85 24.587500000000002 28.075 22.4875 38-39 25.4625 24.425 30.9375 19.175 40-41 26.174999999999997 25.275 27.750000000000004 20.8 42-43 24.15 27.6625 27.6375 20.549999999999997 44-45 23.549999999999997 26.900000000000002 29.525000000000002 20.025000000000002 46-47 23.200000000000003 23.6125 30.362499999999997 22.825 48-49 23.962500000000002 25.924999999999997 29.6875 20.424999999999997 50-51 24.212500000000002 24.675 29.625 21.4875 52-53 25.4625 26.075 28.050000000000004 20.4125 54-55 24.7875 27.474999999999998 27.975 19.7625 56-57 24.9 25.6125 29.799999999999997 19.6875 58-59 22.9875 25.0125 30.887500000000003 21.1125 60-61 24.625 25.624999999999996 29.862499999999997 19.8875 62-63 21.7 28.375 30.612499999999997 19.3125 64-65 23.575 26.474999999999998 29.612500000000004 20.3375 66-67 24.5625 28.475 27.9375 19.025 68-69 23.775 27.125 29.4 19.7 70-71 25.29713499311898 24.82171900412861 29.5258351057175 20.355310897034904 72-73 25.71213452126992 24.808633454636716 29.213201154473584 20.266030869619776 74-75 22.61964735516373 26.574307304785894 29.798488664987406 21.007556675062972 76-77 21.858407079646017 27.079646017699115 30.809102402022752 20.25284450063211 78-79 23.5226984529546 26.46462084707076 30.776058838447884 19.236621861526757 80-81 24.172606924643585 26.883910386965375 30.180753564154788 18.76272912423625 82-83 23.500127648710748 25.79780444217513 30.30380393158029 20.398263977533826 84-85 24.055334955808892 24.298706289227617 32.08658895862687 19.55936979633662 86-87 23.038461538461537 25.82051282051282 31.602564102564102 19.538461538461537 88-89 22.038461538461537 29.435897435897434 30.602564102564102 17.923076923076923 90-91 24.55128205128205 26.179487179487182 30.166666666666668 19.102564102564102 92-93 22.153846153846153 28.192307692307693 30.69230769230769 18.96153846153846 >>END_MODULE >>Per sequence GC content warn #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 1.0 16 1.0 17 11.5 18 12.5 19 1.0 20 0.5 21 2.0 22 2.0 23 4.0 24 5.5 25 5.0 26 8.5 27 14.0 28 21.5 29 26.0 30 31.0 31 40.0 32 60.0 33 76.5 34 87.0 35 106.5 36 112.5 37 135.0 38 159.0 39 174.0 40 185.5 41 189.0 42 210.0 43 224.0 44 209.5 45 181.0 46 191.0 47 206.5 48 192.5 49 187.0 50 191.5 51 171.5 52 130.5 53 137.5 54 129.0 55 80.5 56 62.0 57 58.5 58 47.0 59 38.0 60 42.0 61 35.5 62 26.0 63 27.0 64 21.5 65 13.5 66 13.5 67 13.5 68 9.5 69 4.0 70 2.0 71 1.0 72 1.0 73 1.0 74 0.5 75 0.5 76 1.0 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 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 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 7.0 71 6.0 72 5.0 73 9.0 74 6.0 75 9.0 76 6.0 77 6.0 78 6.0 79 6.0 80 12.0 81 2.0 82 6.0 83 7.0 84 7.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3900.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.1 #Duplication Level Percentage of deduplicated Percentage of total 1 93.62214199759326 77.8 2 3.7605294825511435 6.25 3 0.9326113116726835 2.325 4 0.5114320096269556 1.7000000000000002 5 0.24067388688327318 1.0 6 0.15042117930204574 0.75 7 0.030084235860409148 0.17500000000000002 8 0.15042117930204574 1.0 9 0.060168471720818295 0.44999999999999996 >10 0.5114320096269556 6.775 >50 0.030084235860409148 1.775 >100 0.0 0.0 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 71 1.775 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 36 0.8999999999999999 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 23 0.575 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 20 0.5 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 17 0.42500000000000004 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 17 0.42500000000000004 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 17 0.42500000000000004 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 15 0.375 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 13 0.325 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 13 0.325 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 13 0.325 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 12 0.3 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 11 0.27499999999999997 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 11 0.27499999999999997 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 10 0.25 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 9 0.22499999999999998 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 8 0.2 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 8 0.2 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 8 0.2 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 8 0.2 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 6 0.15 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 5 0.125 No Hit TAGTTTCCACCGCCTGTCCAGGGTTGAGCCCTGGGATTTGACGGCGGACT 5 0.125 No Hit GGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTT 5 0.125 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 5 0.125 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 5 0.125 No Hit AACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGC 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 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 GTATCCT 15 8.853982E-4 86.65 4 CCTTGAT 15 8.853982E-4 86.65 8 AGTATCC 15 8.853982E-4 86.65 3 GAGTATC 15 8.853982E-4 86.65 2 GGAGTAT 15 8.853982E-4 86.65 1 TCCTTGA 20 0.0027738798 64.9875 7 TATCCTT 20 0.0027738798 64.9875 5 CTTGATA 20 0.0027738798 64.9875 9 ATCCTTG 25 0.0067130965 51.989998 6 TTAGAAG 20 7.98181E-4 43.325 38-39 AACGAAG 20 7.98181E-4 43.325 62-63 CGAAGGG 20 7.98181E-4 43.325 64-65 GTACAAG 20 7.98181E-4 43.325 50-51 GCTCGTA 20 7.98181E-4 43.325 56-57 TCGTAAC 20 7.98181E-4 43.325 58-59 AAGCCTG 20 7.98181E-4 43.325 42-43 GTAACGA 20 7.98181E-4 43.325 60-61 AAGCTCG 20 7.98181E-4 43.325 54-55 GCGCGAT 30 1.2546351E-4 36.331234 70-71 TCGTGAA 25 0.0021082864 35.548717 82-83 >>END_MODULE Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215811 READS because READLEN < 1 Read 215811 spots for ERR6133369.sra Written 215811 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra Rejected 215794 READS because READLEN < 1 Read 215794 spots for ERR6133369.sra Written 215794 spots for ERR6133369.sra SRR ids: ['ERR6133369.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_utyz58gr ERR6133369.sra spots: 4315897 blocks: [[1, 215794], [215795, 431588], [431589, 647382], [647383, 863176], [863177, 1078970], [1078971, 1294764], [1294765, 1510558], [1510559, 1726352], [1726353, 1942146], [1942147, 2157940], [2157941, 2373734], [2373735, 2589528], [2589529, 2805322], [2805323, 3021116], [3021117, 3236910], [3236911, 3452704], [3452705, 3668498], [3668499, 3884292], [3884293, 4100086], [4100087, 4315897]] ERR6133369 file size 954612 ERR6133369 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 ERR6133369 ERR6133369_1.fastq Input file: ERR6133369_1.fastq trimmed: ERR6133369-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 01:51:29 2024 >> started Sat Dec 7 01:51:31 2024 >> done (2.273s) 4315897 reads processed; of these: 106 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 4315788 (100.00%) reads available; of these: 166228 ( 3.85%) trimmed reads available after processing 4149560 (96.15%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 18 0.00% 20 7 0.00% 21 5 0.00% 22 3 0.00% 23 5 0.00% 24 6 0.00% 25 2 0.00% 26 4 0.00% 27 2 0.00% 28 3 0.00% 29 60 0.00% 30 5 0.00% 31 3 0.00% 32 14 0.00% 33 4 0.00% 34 7 0.00% 35 4 0.00% 36 3 0.00% 37 9 0.00% 38 13 0.00% 39 28 0.00% 40 26 0.00% 41 29 0.00% 42 22 0.00% 43 25 0.00% 44 25 0.00% 45 42 0.00% 46 79 0.00% 47 108 0.00% 48 212 0.00% 49 1514 0.04% 50 352 0.01% 51 351 0.01% 52 404 0.01% 53 496 0.01% 54 522 0.01% 55 604 0.01% 56 654 0.02% 57 763 0.02% 58 813 0.02% 59 945 0.02% 60 1130 0.03% 61 985 0.02% 62 1042 0.02% 63 1393 0.03% 64 1225 0.03% 65 1387 0.03% 66 1472 0.03% 67 1591 0.04% 68 2015 0.05% 69 935 0.02% 70 8765 0.20% 71 8766 0.20% 72 10898 0.25% 73 10016 0.23% 74 10290 0.24% 75 11122 0.26% 76 10033 0.23% 77 10484 0.24% 78 12514 0.29% 79 13160 0.30% 80 12694 0.29% 81 12583 0.29% 82 15271 0.35% 83 19103 0.44% 84 15764 0.37% 85 6847 0.16% 86 7656 0.18% 87 9008 0.21% 88 11155 0.26% 89 11055 0.26% 90 15376 0.36% 91 17671 0.41% 92 18977 0.44% 93 4015202 93.04% 4315788 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.94 fanout-score-rank=29 prefix-density=0.49 prefix-fanout=2.4 sequence=TGTACATTTGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=71.02 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=5.6 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 01:51:44 Started mapping on | Dec 07 01:51:45 Finished on | Dec 07 01:51:51 Mapping speed, Million of reads per hour | 2589.47 Number of input reads | 4315788 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3132437 Uniquely mapped reads % | 72.58% Average mapped length | 91.72 Number of splices: Total | 117000 Number of splices: Annotated (sjdb) | 93637 Number of splices: GT/AG | 108571 Number of splices: GC/AG | 2917 Number of splices: AT/AC | 38 Number of splices: Non-canonical | 5474 Mismatch rate per base, % | 0.48% Deletion rate per base | 0.03% Deletion average length | 1.75 Insertion rate per base | 0.02% Insertion average length | 1.99 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1046173 % of reads mapped to multiple loci | 24.24% Number of reads mapped to too many loci | 38758 % of reads mapped to too many loci | 0.90% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.16% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 137178 137178 137178 N_multimapping 1046173 1046173 1046173 N_noFeature 162424 201491 2977100 N_ambiguous 127681 11444 401 UnstrandedReadsAssigned:2842332 PositiveStrandReadsAssigned:2919502 NegativeStrandReadsAssigned:154936 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133369 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: ERR6133369-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,315,788 reads, 3,605,880 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 989 rounds 52973 ERR6133369.ke.tsv 35125 ERR6133369.se.tsv 88098 total ==> ERR6133369.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 92 25.8494 PNS24243 293 194 0 0 KQK14069 1603 1504 81 20.7613 KQK14071 474 375 0 0 ==> ERR6133369.se.tsv <== BRADI_1g14170v3 81 BRADI_1g53295v3 50 BRADI_1g59795v3 18 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 29 BRADI_1g74790v3 43 BRADI_1g09890v3 0 BRADI_1g77505v3 84 BRADI_1g48960v3 0 ERR6133369 completed mapping pipeline successfully