Starting /dee2/code/volunteer_pipeline.sh SRR5578474 current disk space = 1522330963968 free memory = 1572857420 SRR5578474 SRAfilesize 6ed8b59645b125760be7ebee50610686 SRR5578474.sra SRR5578474.sra file validated SRR5578474 is paired end SRR5578474 is conventional basespace SRR5578474 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578474_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.57325 34.0 34.0 34.0 33.0 34.0 2 33.40875 34.0 34.0 34.0 33.0 34.0 3 33.51325 34.0 34.0 34.0 33.0 34.0 4 33.52775 34.0 34.0 34.0 33.0 34.0 5 33.59325 34.0 34.0 34.0 33.0 34.0 6 37.22225 38.0 38.0 38.0 36.0 38.0 7 37.4915 38.0 38.0 38.0 37.0 38.0 8 37.5695 38.0 38.0 38.0 38.0 38.0 9 37.65325 38.0 38.0 38.0 38.0 38.0 10-14 37.604499999999994 38.0 38.0 38.0 38.0 38.0 15-19 37.60275 38.0 38.0 38.0 38.0 38.0 20-24 37.601099999999995 38.0 38.0 38.0 38.0 38.0 25-29 37.528499999999994 38.0 38.0 38.0 38.0 38.0 30-34 37.47755 38.0 38.0 38.0 38.0 38.0 35-39 37.43345000000001 38.0 38.0 38.0 38.0 38.0 40-44 37.28775 38.0 38.0 38.0 37.2 38.0 45-49 37.35185 38.0 38.0 38.0 37.2 38.0 50-54 37.2727 38.0 38.0 38.0 37.0 38.0 55-59 37.19070000000001 38.0 38.0 38.0 37.0 38.0 60-64 37.187799999999996 38.0 38.0 38.0 37.0 38.0 65-69 37.07770000000001 38.0 38.0 38.0 36.2 38.0 70-74 36.9365 38.0 38.0 38.0 36.0 38.0 75-79 36.50790000000001 38.0 38.0 38.0 35.0 38.0 80-84 36.42265 38.0 38.0 38.0 35.2 38.0 85-89 36.2648 38.0 38.0 38.0 35.0 38.0 90-94 36.12185000000001 38.0 38.0 38.0 34.2 38.0 95-99 36.0439 38.0 38.0 38.0 34.0 38.0 100-104 35.8322 38.0 38.0 38.0 33.4 38.0 105-109 35.7247 38.0 38.0 38.0 33.0 38.0 110-114 35.54110000000001 38.0 37.6 38.0 32.4 38.0 115-119 35.385749999999994 38.0 37.0 38.0 31.6 38.0 120-124 35.206450000000004 38.0 36.4 38.0 31.0 38.0 125-129 35.0315 38.0 36.0 38.0 30.2 38.0 130-134 34.72525 38.0 36.0 38.0 28.2 38.0 135-139 34.38405 38.0 35.4 38.0 26.0 38.0 140-144 33.788650000000004 38.0 35.0 38.0 21.8 38.0 145-149 33.24395 38.0 34.6 38.0 16.0 38.0 150-151 29.233999999999998 36.0 24.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 0.0 5 2.0 6 0.0 7 2.0 8 2.0 9 2.0 10 1.0 11 2.0 12 3.0 13 2.0 14 5.0 15 2.0 16 10.0 17 6.0 18 17.0 19 39.0 20 6.0 21 6.0 22 7.0 23 8.0 24 11.0 25 11.0 26 13.0 27 11.0 28 22.0 29 24.0 30 41.0 31 31.0 32 49.0 33 61.0 34 112.0 35 210.0 36 634.0 37 2647.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.332644628099175 11.363636363636363 8.212809917355372 34.090909090909086 2 25.15 13.375 31.1 30.375000000000004 3 23.34834834834835 17.46746746746747 25.775775775775777 33.408408408408405 4 28.025 23.35 21.575 27.05 5 28.225 26.900000000000002 24.625 20.25 6 23.200000000000003 29.825000000000003 24.975 22.0 7 19.475 24.7 37.175000000000004 18.65 8 20.575 24.45 30.275000000000002 24.7 9 20.625 20.25 34.375 24.75 10-14 24.45244524452445 25.492549254925496 24.927492749274926 25.127512751275127 15-19 23.405 25.055 26.305 25.235000000000003 20-24 23.865 24.945 26.235000000000003 24.955 25-29 23.405 25.145 26.655 24.795 30-34 23.549999999999997 25.34 25.5 25.61 35-39 23.325000000000003 25.39 25.785000000000004 25.5 40-44 24.3 25.105 25.03 25.564999999999998 45-49 24.555 25.430000000000003 25.6 24.415 50-54 24.7 25.080000000000002 24.425 25.795 55-59 24.125 24.695 25.82 25.36 60-64 23.13 25.515 25.19 26.165 65-69 23.445 25.89 25.16 25.505 70-74 24.965 25.990000000000002 24.555 24.490000000000002 75-79 23.955000000000002 25.885 24.65 25.509999999999998 80-84 24.98 25.575 24.245 25.2 85-89 24.965 24.715 25.085 25.235000000000003 90-94 25.235000000000003 24.9 24.895 24.97 95-99 23.830000000000002 24.505 26.13 25.535000000000004 100-104 25.009999999999998 25.365 24.39 25.235000000000003 105-109 25.21 25.97 24.41 24.41 110-114 24.2 25.480000000000004 24.265 26.055 115-119 23.945 25.729999999999997 24.495 25.83 120-124 25.085 25.89 23.24 25.785000000000004 125-129 24.2 25.905 24.05 25.845000000000002 130-134 25.35 25.485000000000003 23.615 25.55 135-139 24.385 26.61 23.9 25.105 140-144 23.885 26.540000000000003 23.635 25.94 145-149 23.555 26.729999999999997 23.325000000000003 26.39 150-151 24.0125 25.1 24.212500000000002 26.674999999999997 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 2.0 1 1.5 2 1.0 3 1.0 4 1.5 5 1.5 6 1.0 7 1.0 8 0.5 9 1.0 10 1.0 11 0.0 12 0.0 13 0.0 14 0.5 15 1.0 16 0.5 17 0.0 18 0.0 19 0.0 20 0.0 21 1.0 22 1.5 23 0.5 24 1.0 25 2.5 26 3.0 27 3.0 28 3.0 29 8.0 30 22.5 31 33.5 32 36.5 33 32.0 34 41.5 35 64.0 36 95.0 37 119.0 38 122.5 39 124.0 40 125.5 41 119.0 42 115.0 43 112.5 44 126.0 45 134.5 46 126.5 47 148.0 48 159.0 49 150.0 50 136.0 51 136.0 52 130.0 53 123.5 54 116.5 55 100.0 56 98.5 57 93.5 58 88.0 59 87.5 60 78.0 61 69.5 62 69.5 63 68.5 64 66.0 65 67.5 66 62.0 67 60.5 68 56.5 69 43.0 70 42.5 71 36.5 72 29.0 73 27.5 74 22.0 75 15.0 76 12.5 77 9.5 78 5.0 79 2.5 80 2.0 81 1.0 82 0.5 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 3.2 2 0.0 3 0.1 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.01 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.025 #Duplication Level Percentage of deduplicated Percentage of total 1 94.2431901151362 83.89999999999999 2 3.7349059253018817 6.65 3 1.1794439764111204 3.15 4 0.2527379949452401 0.8999999999999999 5 0.02808199943836001 0.125 6 0.19657399606852008 1.05 7 0.11232799775344005 0.7000000000000001 8 0.05616399887672002 0.4 9 0.08424599831508003 0.675 >10 0.08424599831508003 1.075 >50 0.02808199943836001 1.375 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTCAGAATCTCGTATGC 55 1.375 TruSeq Adapter, Index 1 (97% over 37bp) GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 18 0.44999999999999996 No Hit GCCTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAG 14 0.35000000000000003 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 11 0.27499999999999997 No Hit GCAGTAGTTTATAAGGAATATATCCCATTTTTAGTTATAATGATGCCTTA 9 0.22499999999999998 No Hit GTGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGA 9 0.22499999999999998 No Hit GGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATGG 9 0.22499999999999998 No Hit GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 8 0.2 No Hit GGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGG 8 0.2 No Hit GCCCATAACAATAGGAAATATCAGAAATCCAATAAGAATCAGCAATTCAG 7 0.17500000000000002 No Hit GGGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATT 7 0.17500000000000002 No Hit CTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATGGTGATTGT 7 0.17500000000000002 No Hit GCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAGAG 7 0.17500000000000002 No Hit CCCATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAAAAT 6 0.15 No Hit CTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGT 6 0.15 No Hit GCCAGCTAACGGAACAAGCTTTGTGCCATTCGGACCTACCGTAAGCCTAT 6 0.15 No Hit GGCAGTTTCCAGAAACGTGTATCACATCTAGGCATGGAATCTTATGCCAG 6 0.15 No Hit GGATAATTGGGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATA 6 0.15 No Hit GCCATTCGGACCTACCGTAAGCCTATATTTCGTTTTTCTGAGACCTATCC 6 0.15 No Hit GCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAA 6 0.15 No Hit GTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0125 16-17 0.025 0.0 0.0 0.0 0.025 18-19 0.025 0.0 0.0 0.0 0.025 20-21 0.025 0.0 0.0 0.0 0.025 22-23 0.025 0.0 0.0 0.0 0.025 24-25 0.025 0.0 0.0 0.0 0.025 26-27 0.025 0.0 0.0 0.0 0.025 28-29 0.025 0.0 0.0 0.0 0.025 30-31 0.025 0.0 0.0 0.0 0.025 32-33 0.025 0.0 0.0 0.0 0.025 34-35 0.025 0.0 0.0 0.0 0.025 36-37 0.025 0.0 0.0 0.0 0.025 38-39 0.025 0.0 0.0 0.0 0.025 40-41 0.025 0.0 0.0 0.0 0.025 42-43 0.025 0.0 0.0 0.0 0.025 44-45 0.025 0.0 0.0 0.0 0.025 46-47 0.025 0.0 0.0 0.0 0.025 48-49 0.025 0.0 0.0 0.0 0.025 50-51 0.025 0.0 0.0 0.0 0.025 52-53 0.025 0.0 0.0 0.0 0.025 54-55 0.037500000000000006 0.0 0.0 0.0 0.025 56-57 0.05 0.0 0.0 0.0 0.025 58-59 0.05 0.0 0.0 0.0 0.025 60-61 0.075 0.0 0.0 0.0 0.025 62-63 0.075 0.0 0.0 0.0 0.025 64-65 0.1 0.0 0.0 0.0 0.025 66-67 0.125 0.0 0.0 0.0 0.025 68-69 0.125 0.0 0.0 0.0 0.025 70-71 0.16249999999999998 0.0 0.0 0.0 0.025 72-73 0.175 0.0 0.0 0.0 0.025 74-75 0.1875 0.0 0.0 0.0 0.025 76-77 0.30000000000000004 0.0 0.0 0.0 0.025 78-79 0.38749999999999996 0.0 0.0 0.0 0.025 80-81 0.45 0.0 0.0 0.0 0.025 82-83 0.5375000000000001 0.0 0.0 0.0 0.025 84-85 0.7125 0.0 0.0 0.0 0.025 86-87 0.975 0.0 0.0 0.0 0.025 88-89 1.1875 0.0 0.0 0.0 0.025 90-91 1.3375 0.0 0.0 0.0 0.025 92-93 1.525 0.0 0.0 0.0 0.025 94-95 1.7625 0.0 0.0 0.0 0.025 96-97 2.05 0.0 0.0 0.0 0.025 98-99 2.4 0.0 0.0 0.0 0.025 100-101 2.9375 0.0 0.0 0.0 0.025 102-103 3.2125 0.0 0.0 0.0 0.025 104-105 3.6875 0.0 0.0 0.0 0.025 106-107 4.2125 0.0 0.0 0.0 0.025 108-109 4.8375 0.0 0.0 0.0 0.025 110-111 5.4375 0.0 0.0 0.0 0.025 112-113 6.1375 0.0 0.0 0.0 0.025 114-115 6.925000000000001 0.0 0.0 0.0 0.025 116-117 7.7 0.0 0.0 0.0 0.025 118-119 8.25 0.0 0.0 0.0 0.025 120-121 9.1375 0.0 0.0 0.0 0.025 122-123 9.825 0.0 0.0 0.0 0.025 124-125 10.575 0.0 0.0 0.0 0.025 126-127 11.287500000000001 0.0 0.0 0.0 0.025 128-129 12.1375 0.0 0.0 0.0 0.025 130-131 12.9375 0.0 0.0 0.0 0.025 132-133 13.95 0.0 0.0 0.0 0.025 134-135 14.7125 0.0 0.0 0.0 0.025 136-137 15.537500000000001 0.0 0.0 0.0 0.025 138-139 16.450000000000003 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGACCCC 10 0.006832588 144.9875 5 CTGACCC 10 0.006832588 144.9875 4 ACCCCGG 10 0.006832588 144.9875 7 CCCTGAC 10 0.006832588 144.9875 2 GACCCCG 10 0.006832588 144.9875 6 >>END_MODULE SRR5578474 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578474_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.93675 33.0 33.0 34.0 32.0 34.0 2 33.09125 34.0 33.0 34.0 33.0 34.0 3 33.0295 34.0 33.0 34.0 33.0 34.0 4 32.92275 34.0 33.0 34.0 33.0 34.0 5 32.99675 34.0 33.0 34.0 33.0 34.0 6 37.139 38.0 38.0 38.0 37.0 38.0 7 37.069 38.0 38.0 38.0 37.0 38.0 8 36.99475 38.0 38.0 38.0 37.0 38.0 9 37.03075 38.0 38.0 38.0 37.0 38.0 10-14 37.0359 38.0 38.0 38.0 37.0 38.0 15-19 36.9917 38.0 38.0 38.0 37.0 38.0 20-24 36.979350000000004 38.0 38.0 38.0 37.0 38.0 25-29 36.94805 38.0 38.0 38.0 37.0 38.0 30-34 36.938649999999996 38.0 38.0 38.0 37.0 38.0 35-39 36.866249999999994 38.0 38.0 38.0 37.0 38.0 40-44 36.8729 38.0 38.0 38.0 37.0 38.0 45-49 36.840199999999996 38.0 38.0 38.0 37.0 38.0 50-54 36.81285 38.0 38.0 38.0 37.0 38.0 55-59 36.77034999999999 38.0 38.0 38.0 36.4 38.0 60-64 36.738299999999995 38.0 38.0 38.0 36.4 38.0 65-69 36.4976 38.0 38.0 38.0 35.8 38.0 70-74 36.0599 38.0 38.0 38.0 35.0 38.0 75-79 36.05455 38.0 38.0 38.0 35.0 38.0 80-84 35.99305 38.0 38.0 38.0 34.8 38.0 85-89 35.8755 38.0 38.0 38.0 34.0 38.0 90-94 35.8267 38.0 38.0 38.0 34.0 38.0 95-99 35.6365 38.0 38.0 38.0 33.8 38.0 100-104 35.4793 38.0 38.0 38.0 33.0 38.0 105-109 35.35665 38.0 38.0 38.0 32.4 38.0 110-114 35.1955 38.0 38.0 38.0 31.4 38.0 115-119 34.90585 38.0 37.2 38.0 29.2 38.0 120-124 34.6494 38.0 36.0 38.0 27.6 38.0 125-129 34.431200000000004 38.0 35.8 38.0 26.2 38.0 130-134 33.81325 38.0 35.0 38.0 22.6 38.0 135-139 33.27759999999999 38.0 33.0 38.0 19.4 38.0 140-144 32.53145 38.0 33.0 38.0 12.8 38.0 145-149 31.39275 38.0 31.8 38.0 6.0 38.0 150-151 25.853749999999998 33.0 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 16.0 3 6.0 4 5.0 5 4.0 6 3.0 7 6.0 8 5.0 9 5.0 10 3.0 11 5.0 12 7.0 13 8.0 14 2.0 15 5.0 16 8.0 17 47.0 18 8.0 19 9.0 20 7.0 21 11.0 22 6.0 23 12.0 24 18.0 25 8.0 26 12.0 27 17.0 28 26.0 29 22.0 30 54.0 31 36.0 32 66.0 33 96.0 34 139.0 35 250.0 36 614.0 37 2454.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.325 17.9 11.774999999999999 30.0 2 27.224999999999998 25.224999999999998 24.85 22.7 3 24.275 24.775 27.525 23.425 4 28.325 28.975 19.025 23.674999999999997 5 27.625 31.874999999999996 19.075 21.425 6 24.525 33.275 20.349999999999998 21.85 7 22.85 22.225 31.6 23.325000000000003 8 23.65 24.85 23.25 28.249999999999996 9 24.425 23.0 25.825 26.75 10-14 26.295 25.75 21.709999999999997 26.245 15-19 26.734357024958737 25.10378632521382 23.048066823388186 25.113789826439252 20-24 26.864029604440663 25.59383907586138 22.828424263639548 24.71370705605841 25-29 27.293199219336433 24.966221288094882 22.919481559325426 24.82109793324326 30-34 27.2690843518333 24.604287717892205 23.3670607092767 24.7595672209978 35-39 26.085215040304412 23.53677464577179 23.94232213488209 26.435688179041705 40-44 27.60760760760761 24.394394394394396 23.58858858858859 24.40940940940941 45-49 26.242554682416536 24.060263276440264 23.815005756043846 25.882176285099355 50-54 25.825660528422738 23.383706965572458 25.155124099279426 25.635508406725382 55-59 25.60480841472577 25.179063360881543 24.74330077635863 24.47282744803406 60-64 25.663628167885406 25.212861865170787 24.271261143944706 24.852248822999098 65-69 25.157863085095723 26.06494938358224 23.95509672246166 24.822090808860377 70-74 24.69438877755511 25.59118236472946 24.70440881763527 25.01002004008016 75-79 24.735761158142562 26.233532034263384 23.668787256424384 25.361919551169663 80-84 24.898531843463445 25.97083730019542 23.951495715788944 25.17913514055219 85-89 24.85742871435718 25.87793896948474 24.58229114557279 24.682341170585293 90-94 26.023011505752873 25.65782891445723 23.761880940470235 24.55727863931966 95-99 25.631913509184646 26.4477701586666 23.875068822263376 24.045247509885378 100-104 25.75605848187462 26.106549168836366 23.74824754656519 24.389144802723813 105-109 25.888070544616465 27.536449721929955 22.87188736910667 23.70359236434691 110-114 26.066255700897106 26.913246128401745 23.14438931488999 23.876108855811157 115-119 26.57878909382518 27.21030473135525 23.125501202886927 23.08540497193264 120-124 26.07235919021848 27.0695530166366 23.02565644417719 23.832431348967727 125-129 27.157462162974845 26.470883030971233 23.027964317931243 23.343690488122682 130-134 27.197554375062644 26.871805151849255 22.937756840733687 22.992883632354417 135-139 27.55357500500701 26.857600640897257 23.272581614259963 22.316242739835772 140-144 28.69665397715889 26.74313764776598 23.17671809256662 21.383490282508514 145-149 27.914079711596234 26.622271179651513 23.17244141798518 22.291207690767074 150-151 28.785794673002375 25.034387895460796 24.346629986244842 21.833187445291983 >>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 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 1.0 17 1.5 18 1.0 19 2.0 20 4.0 21 2.0 22 1.0 23 2.0 24 1.0 25 0.0 26 1.5 27 5.5 28 7.0 29 6.5 30 8.5 31 21.5 32 28.0 33 21.0 34 27.5 35 36.0 36 53.0 37 92.0 38 110.5 39 117.5 40 158.5 41 144.0 42 97.0 43 105.5 44 111.5 45 115.0 46 126.0 47 136.5 48 141.0 49 131.0 50 120.0 51 122.0 52 126.0 53 124.5 54 135.0 55 141.0 56 126.5 57 108.0 58 99.0 59 92.5 60 87.5 61 84.5 62 84.0 63 86.5 64 79.0 65 73.0 66 73.0 67 71.5 68 69.0 69 58.5 70 52.5 71 44.0 72 32.5 73 27.5 74 18.5 75 16.0 76 12.0 77 7.0 78 6.0 79 2.0 80 0.5 81 0.5 82 0.5 83 0.5 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 10-14 0.0 15-19 0.034999999999999996 20-24 0.015 25-29 0.08499999999999999 30-34 0.18 35-39 0.135 40-44 0.1 45-49 0.105 50-54 0.08 55-59 0.17500000000000002 60-64 0.16999999999999998 65-69 0.22999999999999998 70-74 0.2 75-79 0.185 80-84 0.215 85-89 0.05 90-94 0.05 95-99 0.105 100-104 0.13999999999999999 105-109 0.20500000000000002 110-114 0.23500000000000001 115-119 0.24 120-124 0.22 125-129 0.22999999999999998 130-134 0.22999999999999998 135-139 0.13999999999999999 140-144 0.18 145-149 0.13999999999999999 150-151 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.775 #Duplication Level Percentage of deduplicated Percentage of total 1 94.12273120138289 81.675 2 3.543647363872083 6.15 3 1.0659752232785942 2.775 4 0.40334197637568425 1.4000000000000001 5 0.20167098818784213 0.8750000000000001 6 0.14405070584845864 0.75 7 0.17286084701815038 1.05 8 0.05762028233938346 0.4 9 0.02881014116969173 0.22499999999999998 >10 0.23048112935753384 3.4000000000000004 >50 0.02881014116969173 1.3 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 52 1.3 Illumina Single End PCR Primer 1 (100% over 50bp) CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 26 0.65 No Hit GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 22 0.5499999999999999 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 21 0.525 No Hit CCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGT 18 0.44999999999999996 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 16 0.4 No Hit CTTCAATATAAGCCTTGGTAGGGATAGATAGCCACCTATATAGTATAGCT 11 0.27499999999999997 No Hit AATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGA 11 0.27499999999999997 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 11 0.27499999999999997 No Hit ATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAG 9 0.22499999999999998 No Hit GCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGG 8 0.2 No Hit GGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGA 8 0.2 No Hit TGGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCC 7 0.17500000000000002 No Hit ATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATA 7 0.17500000000000002 No Hit CTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGA 7 0.17500000000000002 No Hit GCCACAGGCGTCATACTTCCCAAGAAGCGGCCATAGCCCAGATGCGAGGT 7 0.17500000000000002 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 7 0.17500000000000002 No Hit CTGGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATC 7 0.17500000000000002 No Hit CCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATTGGTTTAT 6 0.15 No Hit TAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGT 6 0.15 No Hit CGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGA 6 0.15 No Hit ACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATC 6 0.15 No Hit ACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTC 6 0.15 No Hit CTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTT 5 0.125 No Hit TTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAG 5 0.125 No Hit GGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTA 5 0.125 No Hit GCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGA 5 0.125 No Hit AGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTT 5 0.125 No Hit CCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCG 5 0.125 No Hit GCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.037500000000000006 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.0625 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.025 58-59 0.075 0.0 0.0 0.0 0.025 60-61 0.1 0.0 0.0 0.0 0.025 62-63 0.1 0.0 0.0 0.0 0.025 64-65 0.1375 0.0 0.0 0.0 0.025 66-67 0.175 0.0 0.0 0.0 0.025 68-69 0.175 0.0 0.0 0.0 0.025 70-71 0.21250000000000002 0.0 0.0 0.0 0.025 72-73 0.225 0.0 0.0 0.0 0.025 74-75 0.2375 0.0 0.0 0.0 0.025 76-77 0.35 0.0 0.0 0.0 0.025 78-79 0.4375 0.0 0.0 0.0 0.025 80-81 0.5 0.0 0.0 0.0 0.025 82-83 0.5874999999999999 0.0 0.0 0.0 0.025 84-85 0.7625 0.0 0.0 0.0 0.025 86-87 1.05 0.0 0.0 0.0 0.025 88-89 1.2625000000000002 0.0 0.0 0.0 0.025 90-91 1.3875 0.0 0.0 0.0 0.025 92-93 1.5625 0.0 0.0 0.0 0.025 94-95 1.8125 0.0 0.0 0.0 0.025 96-97 2.15 0.0 0.0 0.0 0.025 98-99 2.4875 0.0 0.0 0.0 0.025 100-101 3.025 0.0 0.0 0.0 0.025 102-103 3.2875 0.0 0.0 0.0 0.025 104-105 3.75 0.0 0.0 0.0 0.025 106-107 4.35 0.0 0.0 0.0 0.025 108-109 5.025 0.0 0.0 0.0 0.025 110-111 5.65 0.0 0.0 0.0 0.025 112-113 6.3125 0.0 0.0 0.0 0.025 114-115 7.1125 0.0 0.0 0.0 0.025 116-117 7.862500000000001 0.0 0.0 0.0 0.025 118-119 8.4 0.0 0.0 0.0 0.025 120-121 9.3 0.0 0.0 0.0 0.025 122-123 10.075 0.0 0.0 0.0 0.025 124-125 10.825 0.0 0.0 0.0 0.025 126-127 11.587499999999999 0.0 0.0 0.0 0.025 128-129 12.412500000000001 0.0 0.0 0.0 0.025 130-131 13.2125 0.0 0.0 0.0 0.025 132-133 14.225 0.0 0.0 0.0 0.025 134-135 14.9875 0.0 0.0 0.0 0.025 136-137 15.775 0.0 0.0 0.0 0.025 138-139 16.6875 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACGATA 10 0.006830828 145.0 2 ACGATAT 10 0.006830828 145.0 3 AGCAAGG 10 0.006830828 145.0 2 AAAAAAA 55 1.1668232E-4 26.363638 145 >>END_MODULE Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754401 spots for SRR5578474.sra Written 754401 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra Read 754395 spots for SRR5578474.sra Written 754395 spots for SRR5578474.sra SRR ids: ['SRR5578474.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ekbbpe1s SRR5578474.sra spots: 15087906 blocks: [[1, 754395], [754396, 1508790], [1508791, 2263185], [2263186, 3017580], [3017581, 3771975], [3771976, 4526370], [4526371, 5280765], [5280766, 6035160], [6035161, 6789555], [6789556, 7543950], [7543951, 8298345], [8298346, 9052740], [9052741, 9807135], [9807136, 10561530], [10561531, 11315925], [11315926, 12070320], [12070321, 12824715], [12824716, 13579110], [13579111, 14333505], [14333506, 15087906]] SRR5578474 file size 5091095 SRR5578474 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 SRR5578474 SRR5578474_1.fastq SRR5578474_2.fastq Input file: SRR5578474_1.fastq Paired file: SRR5578474_2.fastq trimmed: SRR5578474-trimmed-pair1.fastq, SRR5578474-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Mon Dec 9 19:33:53 2024 >> started Mon Dec 9 19:34:10 2024 >> done (16.647s) 15087906 read pairs processed; of these: 40465 ( 0.27%) short read pairs filtered out after trimming by size control 245494 ( 1.63%) empty read pairs filtered out after trimming by size control 14801947 (98.10%) read pairs available; of these: 8462026 (57.17%) trimmed read pairs available after processing 6339921 (42.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 17 0.00% 20 27 0.00% 21 20 0.00% 22 27 0.00% 23 19 0.00% 24 37 0.00% 25 32 0.00% 26 33 0.00% 27 28 0.00% 28 37 0.00% 29 37 0.00% 30 47 0.00% 31 45 0.00% 32 35 0.00% 33 33 0.00% 34 61 0.00% 35 57 0.00% 36 52 0.00% 37 77 0.00% 38 73 0.00% 39 80 0.00% 40 97 0.00% 41 123 0.00% 42 119 0.00% 43 157 0.00% 44 176 0.00% 45 237 0.00% 46 246 0.00% 47 305 0.00% 48 313 0.00% 49 388 0.00% 50 517 0.00% 51 631 0.00% 52 725 0.00% 53 601 0.00% 54 629 0.00% 55 769 0.01% 56 816 0.01% 57 915 0.01% 58 1055 0.01% 59 934 0.01% 60 1094 0.01% 61 1230 0.01% 62 1500 0.01% 63 1758 0.01% 64 1958 0.01% 65 2622 0.02% 66 3834 0.03% 67 6604 0.04% 68 8013 0.05% 69 13347 0.09% 70 18734 0.13% 71 13511 0.09% 72 8697 0.06% 73 7045 0.05% 74 6742 0.05% 75 7153 0.05% 76 7425 0.05% 77 8187 0.06% 78 8807 0.06% 79 9602 0.06% 80 10413 0.07% 81 11504 0.08% 82 13045 0.09% 83 14357 0.10% 84 17387 0.12% 85 18984 0.13% 86 20452 0.14% 87 22546 0.15% 88 23736 0.16% 89 24338 0.16% 90 25041 0.17% 91 26004 0.18% 92 27540 0.19% 93 28925 0.20% 94 30141 0.20% 95 31190 0.21% 96 32570 0.22% 97 33457 0.23% 98 34705 0.23% 99 35983 0.24% 100 37364 0.25% 101 38870 0.26% 102 40542 0.27% 103 42057 0.28% 104 44127 0.30% 105 45799 0.31% 106 48633 0.33% 107 49355 0.33% 108 50135 0.34% 109 50075 0.34% 110 51367 0.35% 111 53057 0.36% 112 55121 0.37% 113 58957 0.40% 114 62244 0.42% 115 63806 0.43% 116 64391 0.44% 117 64123 0.43% 118 63605 0.43% 119 63952 0.43% 120 66503 0.45% 121 65419 0.44% 122 69100 0.47% 123 70212 0.47% 124 71803 0.49% 125 72984 0.49% 126 75060 0.51% 127 74973 0.51% 128 74122 0.50% 129 78367 0.53% 130 77762 0.53% 131 77602 0.52% 132 80513 0.54% 133 82210 0.56% 134 84335 0.57% 135 84993 0.57% 136 86578 0.58% 137 88672 0.60% 138 92483 0.62% 139 96002 0.65% 140 99454 0.67% 141 101293 0.68% 142 112988 0.76% 143 118781 0.80% 144 127857 0.86% 145 147192 0.99% 146 173494 1.17% 147 217125 1.47% 148 316201 2.14% 149 620726 4.19% 150 3178823 21.48% 151 6339921 42.83% 14801947 reads passed initial QC criterion=sequence-density sequence-density=0.73 sequence-density-rank=1 fanout-score=3.05 fanout-score-rank=20 prefix-density=0.77 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.28 sequence-density-rank=22 fanout-score=8.70 fanout-score-rank=1 prefix-density=0.75 prefix-fanout=3.3 sequence=ACGCTGCCGAGGC criterion=sequence-density sequence-density=0.80 sequence-density-rank=1 fanout-score=2.30 fanout-score-rank=29 prefix-density=0.84 prefix-fanout=2.2 sequence=CTCAAGTCCACCGCCGGGCTCCCCATCGGCCGCCGCTCAGCCAGCGCTGGTCTCGGCAGCGTCTCCAACGGTGGAAGGATCAGGTGCATGCAGGTGTGGCCGATCGAGGGCATCAAGAAGTTCGAGACCCTCTCGTACCTGCCCCCTCTCTCCGTGGAGTCTCTCCTGAAGCAGATCGAGTACCTGATCCGCTCCAAGTGGGTTCCTTGCCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=42.43 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=4.6 sequence=GTGCTCATCATCTTGTTTAATACCAAAGCTCTTCATATTCTCCTCCTTGATTTCATCAGCTTGAGGTTAGAGAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGCCAGCACCACCAGCAGCACCCAGGCCCAGGTGCTGGTTCTCGGCATGGCGCCGGAGAAG SRR5578474 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 19:35:29 Started mapping on | Dec 09 19:35:29 Finished on | Dec 09 19:51:58 Mapping speed, Million of reads per hour | 53.88 Number of input reads | 14801947 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 9678935 Uniquely mapped reads % | 65.39% Average mapped length | 284.54 Number of splices: Total | 8141816 Number of splices: Annotated (sjdb) | 7671213 Number of splices: GT/AG | 8043621 Number of splices: GC/AG | 85387 Number of splices: AT/AC | 6888 Number of splices: Non-canonical | 5920 Mismatch rate per base, % | 0.09% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.20 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 84274 % of reads mapped to multiple loci | 0.57% Number of reads mapped to too many loci | 11662 % of reads mapped to too many loci | 0.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 33.62% % of reads unmapped: other | 0.34% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5051759 5051759 5051759 N_multimapping 84274 84274 84274 N_noFeature 207259 9363504 324841 N_ambiguous 239192 1055 41846 UnstrandedReadsAssigned:9232484 PositiveStrandReadsAssigned:314376 NegativeStrandReadsAssigned:9312248 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=138 echo kmer=133 SRR5578474 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: SRR5578474-trimmed-pair1.fastq SRR5578474-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,801,947 reads, 9,333,991 reads pseudoaligned [quant] estimated average fragment length: 210.178 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,054 rounds 52973 SRR5578474.ke.tsv 35125 SRR5578474.se.tsv 88098 total ==> SRR5578474.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 727 16.74 2.70276 PNS24247 1044 834.822 10.3235 1.4515 PNS24249 1928 1718.82 45.9279 3.13639 PNS24246 1044 834.822 10.3235 1.4515 PNS24248 1044 834.822 10.3235 1.4515 PNS24244 1471 1261.82 48.3616 4.4987 PNS24243 293 115.953 0 0 KQK14069 1603 1393.82 653.69 55.049 KQK14071 474 272.877 6.44312 2.7715 ==> SRR5578474.se.tsv <== BRADI_1g14170v3 665 BRADI_1g53295v3 452 BRADI_1g59795v3 224 BRADI_1g07683v3 0 BRADI_1g00485v3 7 BRADI_1g20270v3 364 BRADI_1g74790v3 71 BRADI_1g09890v3 2 BRADI_1g77505v3 81 BRADI_1g48960v3 0 SRR5578474 completed mapping pipeline successfully