Starting /dee2/code/volunteer_pipeline.sh SRR1797580 current disk space = 1524887949312 free memory = 1386518252 SRR1797580 SRAfilesize 5c1569204bbbb9f806e494e056aabf85 SRR1797580.sra SRR1797580.sra file validated SRR1797580 is paired end SRR1797580 is conventional basespace SRR1797580 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797580_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 53 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.2295 34.0 34.0 34.0 31.0 34.0 2 32.922 34.0 34.0 34.0 31.0 34.0 3 33.4235 34.0 34.0 34.0 31.0 34.0 4 36.7465 37.0 37.0 37.0 37.0 37.0 5 36.7605 37.0 37.0 37.0 37.0 37.0 6 36.78375 37.0 37.0 37.0 37.0 37.0 7 36.77825 37.0 37.0 37.0 37.0 37.0 8 36.77475 37.0 37.0 37.0 37.0 37.0 9 38.63875 39.0 39.0 39.0 38.0 39.0 10-14 39.0058 39.4 39.4 39.4 38.4 39.4 15-19 40.29935 41.0 40.6 41.0 39.0 41.0 20-24 40.09415 41.0 40.0 41.0 38.4 41.0 25-29 39.864250000000006 41.0 40.0 41.0 37.8 41.0 30-34 39.75885 41.0 40.0 41.0 37.0 41.0 35-39 39.44885000000001 41.0 39.4 41.0 35.2 41.0 40-44 38.93605 41.0 38.4 41.0 35.0 41.0 45-49 38.51455 40.2 37.2 41.0 35.0 41.0 50-54 37.966899999999995 40.0 35.4 41.0 34.2 41.0 55-59 37.2192 38.8 35.0 41.0 33.0 41.0 60-64 36.65865 37.4 35.0 40.2 33.0 41.0 65-69 36.03245 36.2 35.0 39.2 33.0 41.0 70-74 35.16695 35.0 35.0 37.6 32.6 39.8 75-79 34.0977 35.0 34.0 36.2 31.0 38.0 80-84 33.73285 35.0 34.0 35.0 31.0 36.6 85-89 33.01365 35.0 33.6 35.0 29.6 35.8 90-94 32.6837 35.0 33.0 35.0 29.0 35.0 95-99 32.294349999999994 35.0 33.0 35.0 27.4 35.0 100-104 31.982799999999997 35.0 32.6 35.0 26.2 35.0 105-109 31.4775 34.6 32.2 35.0 24.4 35.0 110-114 30.927100000000003 34.0 31.2 35.0 23.4 35.0 115-119 30.3587 34.0 30.6 35.0 20.6 35.0 120-124 29.192 33.8 29.0 35.0 13.0 35.0 125-129 28.245549999999998 33.0 27.0 35.0 3.2 35.0 130-134 27.247249999999998 33.0 25.0 35.0 2.0 35.0 135-139 26.23295 32.2 23.8 34.8 2.0 35.0 140-144 25.190800000000003 31.6 20.4 34.0 2.0 35.0 145-149 22.86145 30.6 4.6 34.0 2.0 35.0 150 14.982 18.0 2.0 27.0 2.0 32.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 2.0 7 4.0 8 2.0 9 1.0 10 5.0 11 7.0 12 9.0 13 8.0 14 3.0 15 1.0 16 5.0 17 11.0 18 16.0 19 22.0 20 14.0 21 15.0 22 15.0 23 34.0 24 32.0 25 41.0 26 65.0 27 66.0 28 78.0 29 91.0 30 135.0 31 143.0 32 205.0 33 291.0 34 405.0 35 636.0 36 1005.0 37 629.0 38 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.28098095486564 12.470649621706235 12.966344899556484 43.28202452387164 2 29.225 11.200000000000001 23.95 35.625 3 23.425 12.825000000000001 17.724999999999998 46.025 4 28.025 15.950000000000001 17.575 38.45 5 27.950000000000003 22.0 21.925 28.125 6 31.900000000000002 22.400000000000002 20.474999999999998 25.224999999999998 7 19.3 30.575000000000003 29.45 20.674999999999997 8 22.0 24.775 28.849999999999998 24.375 9 22.1 20.875 29.45 27.575 10-14 23.369999999999997 25.91 24.985 25.735000000000003 15-19 24.364237084501404 23.93372046455747 24.364237084501404 27.337805366439728 20-24 24.21 23.79 24.83 27.169999999999998 25-29 24.01 24.66 23.775 27.555000000000003 30-34 24.62 24.365000000000002 23.82 27.195000000000004 35-39 25.080000000000002 23.965 23.51 27.445000000000004 40-44 24.779999999999998 24.404999999999998 23.715 27.1 45-49 24.03 24.2 23.599999999999998 28.17 50-54 25.124999999999996 23.97 23.655 27.250000000000004 55-59 24.795 24.525 23.21 27.47 60-64 24.635 23.935000000000002 23.835 27.595 65-69 25.16 23.79 23.72 27.33 70-74 25.009999999999998 23.615 23.385 27.99 75-79 26.07 23.535 22.64 27.755000000000003 80-84 25.490000000000002 23.445 23.16 27.905 85-89 25.105 24.075 22.93 27.889999999999997 90-94 25.64 23.965 22.884999999999998 27.51 95-99 25.145 22.685 23.61 28.560000000000002 100-104 26.040000000000003 22.86 22.86 28.24 105-109 26.165 22.795 23.26 27.779999999999998 110-114 25.985000000000003 22.89 23.22 27.905 115-119 26.290000000000003 22.63 22.97 28.110000000000003 120-124 26.985 22.395 22.325 28.294999999999998 125-129 26.265 22.439999999999998 22.8 28.494999999999997 130-134 26.534999999999997 22.88 22.259999999999998 28.325 135-139 26.700000000000003 22.35 22.75 28.199999999999996 140-144 26.515 22.255 22.58 28.65 145-149 27.189999999999998 22.97 21.23 28.610000000000003 150 26.8 22.575 20.0 30.625000000000004 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 1.0 5 1.0 6 0.0 7 0.5 8 0.5 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 0.5 21 0.5 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 1.0 28 1.0 29 0.5 30 1.0 31 4.5 32 10.0 33 10.0 34 14.5 35 24.0 36 33.5 37 51.0 38 65.0 39 79.0 40 99.5 41 122.5 42 131.5 43 136.5 44 155.5 45 166.0 46 158.0 47 146.0 48 152.0 49 160.5 50 156.0 51 150.0 52 137.5 53 131.5 54 121.5 55 108.5 56 106.0 57 92.5 58 82.0 59 85.0 60 79.0 61 71.0 62 71.0 63 66.0 64 67.0 65 70.5 66 65.0 67 60.5 68 62.0 69 68.0 70 58.0 71 45.0 72 44.0 73 40.5 74 40.0 75 33.5 76 26.0 77 28.0 78 24.5 79 19.0 80 19.0 81 15.0 82 9.0 83 7.0 84 5.0 85 2.5 86 2.0 87 1.0 88 1.0 89 1.0 90 0.5 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 4.175 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 0.12 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.725 #Duplication Level Percentage of deduplicated Percentage of total 1 99.72424166457759 99.45 2 0.2757583354224116 0.5499999999999999 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >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 pass >>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 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.025 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 90-91 0.025 0.0 0.0 0.0 0.0 92-93 0.025 0.0 0.0 0.0 0.0 94-95 0.025 0.0 0.0 0.0 0.0 96-97 0.025 0.0 0.0 0.0 0.0 98-99 0.025 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.025 0.0 0.0 0.0 0.0 104-105 0.025 0.0 0.0 0.0 0.0 106-107 0.025 0.0 0.0 0.0 0.0 108-109 0.025 0.0 0.0 0.0 0.0 110-111 0.075 0.0 0.0 0.0 0.0 112-113 0.075 0.0 0.0 0.0 0.0 114-115 0.075 0.0 0.0 0.0 0.0 116-117 0.1125 0.0 0.0 0.0 0.0 118-119 0.125 0.0 0.0 0.0 0.0 120-121 0.125 0.0 0.0 0.0 0.0 122-123 0.1875 0.0 0.0 0.0 0.0 124-125 0.25 0.0 0.0 0.0 0.0 126-127 0.275 0.0 0.0 0.0 0.0 128-129 0.32499999999999996 0.0 0.0 0.0 0.0 130-131 0.47500000000000003 0.0 0.0 0.0 0.0 132-133 0.6625 0.0 0.0 0.0 0.0 134-135 0.9750000000000001 0.0 0.0 0.0 0.0 136-137 1.5125 0.0 0.0 0.0 0.0 138 1.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGGGTCA 10 0.0069772652 143.975 4 >>END_MODULE SRR1797580 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797580_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 54 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.88175 34.0 33.0 34.0 31.0 34.0 2 33.20025 34.0 33.0 34.0 31.0 34.0 3 33.2985 34.0 34.0 34.0 31.0 34.0 4 36.5065 37.0 37.0 37.0 35.0 37.0 5 36.65225 37.0 37.0 37.0 35.0 37.0 6 36.67925 37.0 37.0 37.0 37.0 37.0 7 36.72125 37.0 37.0 37.0 37.0 37.0 8 36.67125 37.0 37.0 37.0 37.0 37.0 9 38.57275 39.0 39.0 39.0 38.0 39.0 10-14 38.828250000000004 39.4 39.2 39.4 37.8 39.4 15-19 40.084849999999996 41.0 40.0 41.0 38.4 41.0 20-24 39.886250000000004 41.0 40.0 41.0 38.0 41.0 25-29 39.608 41.0 40.0 41.0 37.6 41.0 30-34 38.96875 40.2 38.6 41.0 35.4 41.0 35-39 38.8577 40.8 38.6 41.0 35.0 41.0 40-44 38.383449999999996 40.2 37.4 41.0 35.0 41.0 45-49 37.722950000000004 40.0 35.2 41.0 33.6 41.0 50-54 36.82955 38.8 35.0 40.4 32.8 41.0 55-59 36.324 37.4 35.0 40.4 32.6 41.0 60-64 36.02865 36.2 35.0 39.8 33.0 41.0 65-69 35.3898 35.0 35.0 38.8 33.0 41.0 70-74 34.53425 35.0 34.8 36.8 31.2 39.2 75-79 33.798649999999995 35.0 34.0 35.6 30.8 37.6 80-84 32.986900000000006 35.0 33.6 35.0 29.2 36.2 85-89 32.57135000000001 35.0 33.0 35.0 28.2 35.4 90-94 31.963149999999995 35.0 33.0 35.0 26.2 35.0 95-99 31.753499999999995 35.0 32.8 35.0 25.8 35.0 100-104 31.267899999999997 34.6 31.6 35.0 24.2 35.0 105-109 30.743150000000004 34.0 31.0 35.0 22.2 35.0 110-114 29.805149999999998 34.0 29.8 35.0 17.0 35.0 115-119 29.415750000000003 34.0 29.2 35.0 13.4 35.0 120-124 28.933300000000003 34.0 29.0 35.0 5.0 35.0 125-129 27.8308 33.0 26.6 35.0 2.0 35.0 130-134 27.0353 32.8 24.8 35.0 2.0 35.0 135-139 25.54965 31.6 21.2 34.0 2.0 35.0 140-144 24.1147 31.0 13.6 34.0 2.0 35.0 145-149 22.2923 30.2 2.0 34.0 2.0 35.0 150 16.079 18.0 2.0 29.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 3 1.0 4 2.0 5 8.0 6 4.0 7 5.0 8 9.0 9 5.0 10 4.0 11 8.0 12 6.0 13 5.0 14 10.0 15 7.0 16 14.0 17 14.0 18 11.0 19 21.0 20 31.0 21 25.0 22 23.0 23 36.0 24 44.0 25 47.0 26 54.0 27 60.0 28 85.0 29 107.0 30 126.0 31 161.0 32 243.0 33 296.0 34 420.0 35 694.0 36 949.0 37 456.0 38 7.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 28.187751004016064 17.796184738955823 11.295180722891567 42.72088353413655 2 36.525 24.075 18.525 20.875 3 23.599999999999998 26.575 22.175 27.650000000000002 4 27.450000000000003 25.650000000000002 20.625 26.275 5 31.15 27.55 18.825 22.475 6 24.349999999999998 32.6 18.525 24.525 7 25.324999999999996 17.325 31.175000000000004 26.174999999999997 8 27.1 22.1 23.200000000000003 27.6 9 25.874999999999996 21.8 24.325 28.000000000000004 10-14 27.46 24.565 21.185000000000002 26.790000000000003 15-19 28.065 23.724999999999998 21.95 26.26 20-24 27.755000000000003 24.32 21.36 26.565 25-29 28.139999999999997 23.385 22.155 26.32 30-34 27.339999999999996 24.005000000000003 22.470000000000002 26.185000000000002 35-39 28.115000000000002 23.39 22.025 26.47 40-44 28.470000000000002 22.825 22.305 26.400000000000002 45-49 27.794999999999998 23.599999999999998 22.2 26.405 50-54 28.99 23.115 22.25 25.645 55-59 28.244999999999997 23.04 22.215 26.5 60-64 28.215 23.05 22.48 26.255 65-69 28.58 22.915 22.5 26.005 70-74 28.449999999999996 23.035 22.145 26.369999999999997 75-79 27.955000000000002 22.900000000000002 22.82 26.325 80-84 28.575 24.205 22.185 25.035 85-89 29.315 22.58 22.085 26.02 90-94 28.189999999999998 23.635 22.71 25.465 95-99 28.38 23.549999999999997 22.36 25.71 100-104 27.860000000000003 22.985 22.61 26.545 105-109 28.599999999999998 23.015 22.685 25.7 110-114 28.860000000000003 23.28 22.509999999999998 25.35 115-119 28.71 22.555 23.01 25.724999999999998 120-124 28.775000000000002 23.715 22.535 24.975 125-129 28.310000000000002 23.595 22.63 25.465 130-134 29.080000000000002 22.765 22.66 25.495 135-139 28.675 23.599999999999998 22.86 24.865000000000002 140-144 28.825 23.35 22.62 25.205 145-149 29.775000000000002 23.52 21.695 25.009999999999998 150 31.424999999999997 24.375 19.900000000000002 24.3 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 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 0.5 26 0.5 27 0.0 28 0.5 29 1.0 30 2.5 31 7.0 32 6.0 33 9.0 34 15.5 35 16.5 36 24.5 37 35.5 38 45.5 39 62.5 40 82.5 41 92.5 42 110.0 43 130.0 44 143.0 45 148.5 46 143.0 47 147.5 48 164.5 49 167.5 50 148.5 51 127.0 52 125.0 53 117.5 54 109.0 55 102.0 56 88.0 57 90.0 58 93.0 59 92.0 60 91.0 61 87.5 62 83.0 63 76.5 64 72.0 65 77.0 66 84.0 67 86.5 68 80.5 69 75.5 70 62.0 71 60.0 72 63.0 73 57.5 74 54.0 75 45.0 76 42.0 77 36.0 78 28.5 79 24.5 80 17.0 81 13.5 82 10.0 83 4.0 84 3.5 85 4.5 86 4.5 87 2.0 88 0.5 89 1.5 90 1.5 91 0.5 92 0.5 93 0.5 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 0.4 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 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.65 #Duplication Level Percentage of deduplicated Percentage of total 1 99.64877069744105 99.3 2 0.35122930255895635 0.7000000000000001 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >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 pass >>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 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.025 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 90-91 0.025 0.0 0.0 0.0 0.0 92-93 0.025 0.0 0.0 0.0 0.0 94-95 0.025 0.0 0.0 0.0 0.0 96-97 0.025 0.0 0.0 0.0 0.0 98-99 0.025 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.025 0.0 0.0 0.0 0.0 104-105 0.025 0.0 0.0 0.0 0.0 106-107 0.025 0.0 0.0 0.0 0.0 108-109 0.025 0.0 0.0 0.0 0.0 110-111 0.075 0.0 0.0 0.0 0.0 112-113 0.075 0.0 0.0 0.0 0.0 114-115 0.075 0.0 0.0 0.0 0.0 116-117 0.1125 0.0 0.0 0.0 0.0 118-119 0.125 0.0 0.0 0.0 0.0 120-121 0.1375 0.0 0.0 0.0 0.0 122-123 0.21250000000000002 0.0 0.0 0.0 0.0 124-125 0.275 0.0 0.0 0.0 0.0 126-127 0.3 0.0 0.0 0.0 0.0 128-129 0.35 0.0 0.0 0.0 0.0 130-131 0.5 0.0 0.0 0.0 0.0 132-133 0.7 0.0 0.0 0.0 0.0 134-135 1.0375 0.0 0.0 0.0 0.0 136-137 1.5625 0.0 0.0 0.0 0.0 138 1.925 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCCATC 10 0.006973645 144.0 7 AGCTGCT 10 0.006973645 144.0 4 CCCCCCC 55 0.0026350126 15.709091 115-119 >>END_MODULE Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206921 spots for SRR1797580.sra Written 1206921 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra Read 1206906 spots for SRR1797580.sra Written 1206906 spots for SRR1797580.sra SRR ids: ['SRR1797580.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lz_sr8z_ SRR1797580.sra spots: 24138135 blocks: [[1, 1206906], [1206907, 2413812], [2413813, 3620718], [3620719, 4827624], [4827625, 6034530], [6034531, 7241436], [7241437, 8448342], [8448343, 9655248], [9655249, 10862154], [10862155, 12069060], [12069061, 13275966], [13275967, 14482872], [14482873, 15689778], [15689779, 16896684], [16896685, 18103590], [18103591, 19310496], [19310497, 20517402], [20517403, 21724308], [21724309, 22931214], [22931215, 24138135]] SRR1797580 file size 8110776 SRR1797580 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 SRR1797580 SRR1797580_1.fastq SRR1797580_2.fastq Input file: SRR1797580_1.fastq Paired file: SRR1797580_2.fastq trimmed: SRR1797580-trimmed-pair1.fastq, SRR1797580-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 13:34:08 2024 >> started Mon Dec 9 13:36:23 2024 >> done (135.383s) 24138135 read pairs processed; of these: 45041 ( 0.19%) short read pairs filtered out after trimming by size control 33165 ( 0.14%) empty read pairs filtered out after trimming by size control 24059929 (99.68%) read pairs available; of these: 18405326 (76.50%) trimmed read pairs available after processing 5654603 (23.50%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 27 0.00% 20 55 0.00% 21 71 0.00% 22 111 0.00% 23 185 0.00% 24 180 0.00% 25 245 0.00% 26 293 0.00% 27 333 0.00% 28 469 0.00% 29 529 0.00% 30 637 0.00% 31 710 0.00% 32 802 0.00% 33 888 0.00% 34 982 0.00% 35 1140 0.00% 36 1197 0.00% 37 1282 0.01% 38 1451 0.01% 39 1590 0.01% 40 1649 0.01% 41 1673 0.01% 42 1874 0.01% 43 2000 0.01% 44 2204 0.01% 45 2287 0.01% 46 2431 0.01% 47 2591 0.01% 48 2575 0.01% 49 2747 0.01% 50 2841 0.01% 51 3050 0.01% 52 3170 0.01% 53 3454 0.01% 54 3627 0.02% 55 3794 0.02% 56 4038 0.02% 57 4290 0.02% 58 4424 0.02% 59 4665 0.02% 60 4814 0.02% 61 5168 0.02% 62 5285 0.02% 63 5680 0.02% 64 5835 0.02% 65 6216 0.03% 66 6519 0.03% 67 6996 0.03% 68 7299 0.03% 69 7778 0.03% 70 8187 0.03% 71 8483 0.04% 72 8979 0.04% 73 9481 0.04% 74 10031 0.04% 75 10486 0.04% 76 11368 0.05% 77 11824 0.05% 78 12628 0.05% 79 13331 0.06% 80 14456 0.06% 81 15469 0.06% 82 16427 0.07% 83 17746 0.07% 84 21699 0.09% 85 22960 0.10% 86 23914 0.10% 87 25261 0.10% 88 26179 0.11% 89 27624 0.11% 90 28410 0.12% 91 29713 0.12% 92 30394 0.13% 93 31567 0.13% 94 33406 0.14% 95 34266 0.14% 96 35363 0.15% 97 36676 0.15% 98 38279 0.16% 99 39969 0.17% 100 40729 0.17% 101 42206 0.18% 102 44281 0.18% 103 45870 0.19% 104 47694 0.20% 105 51453 0.21% 106 54848 0.23% 107 58810 0.24% 108 61781 0.26% 109 65613 0.27% 110 69003 0.29% 111 73772 0.31% 112 77884 0.32% 113 80473 0.33% 114 85664 0.36% 115 95155 0.40% 116 100802 0.42% 117 104371 0.43% 118 111464 0.46% 119 117058 0.49% 120 122346 0.51% 121 130729 0.54% 122 141064 0.59% 123 158549 0.66% 124 166007 0.69% 125 177590 0.74% 126 187160 0.78% 127 196639 0.82% 128 215342 0.90% 129 235651 0.98% 130 252192 1.05% 131 267364 1.11% 132 297542 1.24% 133 318579 1.32% 134 334363 1.39% 135 352409 1.46% 136 374987 1.56% 137 400014 1.66% 138 426436 1.77% 139 458049 1.90% 140 492755 2.05% 141 531127 2.21% 142 574655 2.39% 143 625186 2.60% 144 703078 2.92% 145 805332 3.35% 146 959796 3.99% 147 1214327 5.05% 148 1659350 6.90% 149 3409035 14.17% 150 5654603 23.50% 24059929 reads passed initial QC criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=3.62 fanout-score-rank=36 prefix-density=0.18 prefix-fanout=2.8 sequence=GCCCAGGCGAGGCCGCCCACGAAGCA criterion=fanout-score sequence-density=0.03 sequence-density-rank=34 fanout-score=623.67 fanout-score-rank=1 prefix-density=0.82 prefix-fanout=23.0 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=10.35 fanout-score-rank=29 prefix-density=0.46 prefix-fanout=6.8 sequence=AAGGAGCTGGAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=38 fanout-score=1347.54 fanout-score-rank=1 prefix-density=1.11 prefix-fanout=20.8 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGA SRR1797580 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 13:40:55 Started mapping on | Dec 09 13:40:55 Finished on | Dec 09 13:48:16 Mapping speed, Million of reads per hour | 196.41 Number of input reads | 24059929 Average input read length | 280 UNIQUE READS: Uniquely mapped reads number | 22977135 Uniquely mapped reads % | 95.50% Average mapped length | 279.45 Number of splices: Total | 20192012 Number of splices: Annotated (sjdb) | 19097085 Number of splices: GT/AG | 19905342 Number of splices: GC/AG | 237186 Number of splices: AT/AC | 17679 Number of splices: Non-canonical | 31805 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.02% Deletion average length | 2.29 Insertion rate per base | 0.01% Insertion average length | 2.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 398593 % of reads mapped to multiple loci | 1.66% Number of reads mapped to too many loci | 61445 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.96% % of reads unmapped: other | 1.63% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 708169 708169 708169 N_multimapping 398593 398593 398593 N_noFeature 545864 22318097 875023 N_ambiguous 396470 3310 71268 UnstrandedReadsAssigned:22034801 PositiveStrandReadsAssigned:655728 NegativeStrandReadsAssigned:22030844 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=138 echo kmer=133 SRR1797580 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: SRR1797580-trimmed-pair1.fastq SRR1797580-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,059,929 reads, 22,242,086 reads pseudoaligned [quant] estimated average fragment length: 208.814 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,153 rounds 52973 SRR1797580.ke.tsv 35125 SRR1797580.se.tsv 88098 total ==> SRR1797580.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 728.297 52.2169 4.2932 PNS24247 1044 836.186 32.1885 2.30503 PNS24249 1928 1720.19 543.365 18.9145 PNS24246 1044 836.186 32.1885 2.30503 PNS24248 1044 836.186 32.1885 2.30503 PNS24244 1471 1263.19 54.853 2.60023 PNS24243 293 94.4756 0 0 KQK14069 1603 1395.19 75.4759 3.23933 KQK14071 474 267.903 0.507138 0.113351 ==> SRR1797580.se.tsv <== BRADI_1g14170v3 77 BRADI_1g53295v3 20 BRADI_1g59795v3 385 BRADI_1g07683v3 0 BRADI_1g00485v3 42 BRADI_1g20270v3 1753 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 520 BRADI_1g48960v3 0 SRR1797580 completed mapping pipeline successfully