Starting /dee2/code/volunteer_pipeline.sh SRR1797574 current disk space = 1525775224832 free memory = 1576228268 SRR1797574 SRAfilesize 01d69671d3cdd0f8535e3eb31c76b631 SRR1797574.sra SRR1797574.sra file validated SRR1797574 is paired end SRR1797574 is conventional basespace SRR1797574 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797574_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 55 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.909 34.0 34.0 34.0 31.0 34.0 2 32.77425 34.0 34.0 34.0 31.0 34.0 3 33.34125 34.0 34.0 34.0 31.0 34.0 4 36.70125 37.0 37.0 37.0 35.0 37.0 5 36.7395 37.0 37.0 37.0 37.0 37.0 6 36.75925 37.0 37.0 37.0 37.0 37.0 7 36.7235 37.0 37.0 37.0 37.0 37.0 8 36.766 37.0 37.0 37.0 37.0 37.0 9 38.7225 39.0 39.0 39.0 39.0 39.0 10-14 38.98135 39.4 39.2 39.4 38.4 39.4 15-19 40.2529 41.0 40.0 41.0 38.8 41.0 20-24 40.122249999999994 41.0 40.0 41.0 38.4 41.0 25-29 39.69635000000001 41.0 39.8 41.0 37.4 41.0 30-34 39.53195 41.0 39.8 41.0 36.0 41.0 35-39 39.117149999999995 41.0 39.0 41.0 35.0 41.0 40-44 38.72455 40.8 37.8 41.0 35.0 41.0 45-49 38.08615 40.0 35.4 41.0 34.0 41.0 50-54 37.42455 39.2 35.0 41.0 33.2 41.0 55-59 36.62349999999999 37.6 35.0 40.8 32.8 41.0 60-64 35.9973 36.2 35.0 39.8 32.0 41.0 65-69 35.45735 35.0 35.0 38.8 32.2 41.0 70-74 34.8668 35.0 35.0 36.8 32.2 39.6 75-79 33.89585 35.0 34.0 35.6 30.6 37.6 80-84 33.67035 35.0 34.0 35.0 31.0 36.6 85-89 33.32075 35.0 34.0 35.0 30.6 35.8 90-94 32.92335 35.0 34.0 35.0 29.4 35.0 95-99 32.64125 35.0 33.0 35.0 28.6 35.0 100-104 31.990600000000008 35.0 33.0 35.0 25.8 35.0 105-109 31.7692 35.0 33.0 35.0 25.0 35.0 110-114 31.271500000000003 35.0 32.0 35.0 24.0 35.0 115-119 30.6504 34.0 31.2 35.0 21.2 35.0 120-124 29.719450000000002 34.0 29.6 35.0 15.8 35.0 125-129 29.1295 34.0 29.0 35.0 6.8 35.0 130-134 28.0591 33.4 27.0 35.0 2.0 35.0 135-139 27.05205 33.0 25.0 35.0 2.0 35.0 140-144 26.234550000000002 33.0 23.8 35.0 2.0 35.0 145-149 24.5036 32.0 11.4 34.8 2.0 35.0 150 17.296 20.0 2.0 29.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 1.0 7 0.0 8 6.0 9 5.0 10 9.0 11 6.0 12 4.0 13 6.0 14 1.0 15 10.0 16 8.0 17 12.0 18 10.0 19 16.0 20 14.0 21 21.0 22 19.0 23 32.0 24 34.0 25 44.0 26 54.0 27 61.0 28 64.0 29 116.0 30 110.0 31 127.0 32 196.0 33 261.0 34 370.0 35 644.0 36 1020.0 37 716.0 38 2.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 32.35682238057535 10.662443916600687 13.064133016627078 43.91660068619689 2 30.575000000000003 10.2 22.8 36.425000000000004 3 26.8 11.325000000000001 16.7 45.175 4 28.849999999999998 14.825 16.0 40.325 5 30.349999999999998 21.525 20.65 27.474999999999998 6 32.5 20.9 20.95 25.650000000000002 7 20.200000000000003 29.299999999999997 30.2 20.3 8 24.8 22.525000000000002 27.400000000000002 25.275 9 25.3 19.825 28.050000000000004 26.825 10-14 24.68 24.315 24.15 26.855 15-19 25.45 23.21 23.544999999999998 27.794999999999998 20-24 26.181309065453274 23.631181559077955 22.57612880644032 27.611380569028455 25-29 25.665 22.395 23.49 28.449999999999996 30-34 25.374999999999996 22.555 23.64 28.43 35-39 26.115 22.81 23.0 28.075 40-44 26.355 22.81 22.865 27.97 45-49 25.795 23.26 22.61 28.335 50-54 26.174999999999997 22.68 22.62 28.525 55-59 26.745 22.35 22.75 28.155 60-64 25.779999999999998 22.955000000000002 23.18 28.084999999999997 65-69 25.665 22.305 23.255 28.775000000000002 70-74 26.119999999999997 22.415 22.985 28.48 75-79 26.305 22.095000000000002 22.475 29.125 80-84 26.205000000000002 22.74 22.445 28.610000000000003 85-89 25.805 22.365 21.995 29.835 90-94 26.884999999999998 21.92 22.495 28.7 95-99 26.6 22.015 22.58 28.804999999999996 100-104 26.545 22.085 22.225 29.145 105-109 26.83 21.605 22.770000000000003 28.794999999999998 110-114 26.46 21.92 22.88 28.74 115-119 27.015 21.535 22.650000000000002 28.799999999999997 120-124 27.095000000000002 21.654999999999998 21.905 29.345 125-129 27.235 21.505 22.345000000000002 28.915000000000003 130-134 27.24 21.675 21.834999999999997 29.25 135-139 27.515 21.27 22.195 29.020000000000003 140-144 27.58 21.215 22.515 28.689999999999998 145-149 27.905 21.98 21.255 28.860000000000003 150 29.125 20.5 18.425 31.95 >>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 0.5 13 0.5 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 0.5 23 0.5 24 0.5 25 0.5 26 0.5 27 1.0 28 0.5 29 0.0 30 0.5 31 2.0 32 6.0 33 10.0 34 14.0 35 17.0 36 22.5 37 35.0 38 51.5 39 64.5 40 70.5 41 93.0 42 110.0 43 106.0 44 127.0 45 143.0 46 153.0 47 155.0 48 137.5 49 128.5 50 132.5 51 147.5 52 139.5 53 131.5 54 110.5 55 98.5 56 113.0 57 98.0 58 82.5 59 82.5 60 95.0 61 89.0 62 71.0 63 74.5 64 76.0 65 81.0 66 88.0 67 80.0 68 86.0 69 88.5 70 75.0 71 72.5 72 71.0 73 71.5 74 64.0 75 53.5 76 43.5 77 29.0 78 25.5 79 21.5 80 13.5 81 11.0 82 9.0 83 8.5 84 6.0 85 3.0 86 2.5 87 1.5 88 0.5 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 warn #Base N-Count 1 5.2749999999999995 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 0.005 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 99.67385850476668 99.325 2 0.3010536879076769 0.6 3 0.025087807325639738 0.075 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 0.0 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 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0125 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 0.025 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 0.11249999999999999 0.0 0.0 0.0 0.0 118-119 0.15 0.0 0.0 0.0 0.0 120-121 0.15 0.0 0.0 0.0 0.0 122-123 0.1875 0.0 0.0 0.0 0.0 124-125 0.3 0.0 0.0 0.0 0.0 126-127 0.375 0.0 0.0 0.0 0.0 128-129 0.425 0.0 0.0 0.0 0.0 130-131 0.725 0.0 0.0 0.0 0.0 132-133 1.0125 0.0 0.0 0.0 0.0 134-135 1.3125 0.0 0.0 0.0 0.0 136-137 1.7000000000000002 0.0 0.0 0.0 0.0 138 2.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAACAG 10 0.0069827023 143.9375 5 GGCAGAA 10 0.0069827023 143.9375 2 >>END_MODULE SRR1797574 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797574_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 55 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.09 34.0 33.0 34.0 31.0 34.0 2 33.24625 34.0 34.0 34.0 31.0 34.0 3 33.2 34.0 33.0 34.0 31.0 34.0 4 36.598 37.0 37.0 37.0 35.0 37.0 5 36.68525 37.0 37.0 37.0 37.0 37.0 6 36.60375 37.0 37.0 37.0 35.0 37.0 7 36.5245 37.0 37.0 37.0 35.0 37.0 8 36.587 37.0 37.0 37.0 35.0 37.0 9 38.541 39.0 39.0 39.0 38.0 39.0 10-14 38.842000000000006 39.4 39.2 39.4 38.0 39.4 15-19 39.85975 41.0 40.0 41.0 38.2 41.0 20-24 39.7842 41.0 40.0 41.0 38.0 41.0 25-29 39.416999999999994 41.0 39.8 41.0 36.4 41.0 30-34 38.8403 40.4 38.6 41.0 35.0 41.0 35-39 38.76065 41.0 38.4 41.0 35.0 41.0 40-44 38.11045 40.0 36.2 41.0 34.8 41.0 45-49 37.5175 39.6 35.0 41.0 33.2 41.0 50-54 36.5231 38.2 34.8 40.4 32.0 41.0 55-59 36.2641 36.6 35.0 40.8 32.4 41.0 60-64 35.982499999999995 35.4 35.0 39.8 33.0 41.0 65-69 35.25285 35.0 35.0 38.4 33.0 40.8 70-74 34.520799999999994 35.0 35.0 36.6 31.4 39.2 75-79 33.7548 35.0 34.6 35.4 30.6 37.4 80-84 33.16375000000001 35.0 34.0 35.0 29.4 36.0 85-89 32.84505 35.0 34.0 35.0 29.2 35.2 90-94 32.48094999999999 35.0 33.2 35.0 27.4 35.0 95-99 32.1013 35.0 33.0 35.0 26.6 35.0 100-104 31.7796 35.0 33.0 35.0 25.4 35.0 105-109 31.309949999999997 35.0 32.6 35.0 23.8 35.0 110-114 30.48245 34.2 31.0 35.0 20.0 35.0 115-119 30.112949999999994 34.0 30.6 35.0 17.6 35.0 120-124 29.425399999999996 34.0 29.4 35.0 10.4 35.0 125-129 28.7023 33.8 29.0 35.0 2.6 35.0 130-134 28.132749999999998 33.8 27.8 35.0 2.0 35.0 135-139 26.788099999999996 33.0 24.8 35.0 2.0 35.0 140-144 25.837849999999996 32.4 22.2 35.0 2.0 35.0 145-149 23.9049 31.6 8.0 34.0 2.0 35.0 150 17.87925 23.0 2.0 30.0 2.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 7.0 3 0.0 4 3.0 5 3.0 6 2.0 7 7.0 8 7.0 9 5.0 10 4.0 11 4.0 12 6.0 13 7.0 14 8.0 15 9.0 16 16.0 17 9.0 18 12.0 19 17.0 20 17.0 21 30.0 22 28.0 23 41.0 24 38.0 25 45.0 26 48.0 27 66.0 28 76.0 29 74.0 30 108.0 31 129.0 32 189.0 33 281.0 34 421.0 35 693.0 36 1027.0 37 561.0 38 2.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.375 17.925 10.125 42.575 2 34.57686529794692 23.86079118678017 17.376064096144216 24.18627941912869 3 24.925 25.7 21.85 27.525 4 28.549999999999997 25.224999999999998 19.2 27.025 5 30.9 26.575 19.2 23.325000000000003 6 26.325 31.8 17.925 23.95 7 24.7 18.0 31.474999999999998 25.825 8 27.750000000000004 19.975 21.95 30.325000000000003 9 27.450000000000003 20.625 23.575 28.349999999999998 10-14 28.865000000000002 24.12 19.935 27.08 15-19 28.134999999999998 23.41 21.645 26.810000000000002 20-24 28.785 23.189999999999998 21.224999999999998 26.8 25-29 28.54 22.98 21.335 27.145000000000003 30-34 28.77 22.545 21.425 27.26 35-39 28.59 22.6 21.77 27.04 40-44 29.09 22.38 21.34 27.189999999999998 45-49 28.67 22.384999999999998 21.66 27.284999999999997 50-54 29.025000000000002 22.165000000000003 21.404999999999998 27.405 55-59 29.095 22.41 21.355 27.139999999999997 60-64 28.68 22.79 21.425 27.105 65-69 29.14 22.869999999999997 20.979999999999997 27.01 70-74 29.225 22.439999999999998 21.44 26.895000000000003 75-79 28.904999999999998 22.915 21.39 26.790000000000003 80-84 29.32 22.705000000000002 21.395 26.58 85-89 29.054999999999996 22.455 21.759999999999998 26.729999999999997 90-94 28.88 22.814999999999998 21.525 26.779999999999998 95-99 29.42 22.745 21.265 26.57 100-104 29.635 22.545 21.615000000000002 26.205000000000002 105-109 29.294999999999998 22.705000000000002 21.715 26.284999999999997 110-114 29.354999999999997 22.975 21.62 26.05 115-119 29.84 22.41 21.825 25.924999999999997 120-124 29.060000000000002 22.395 22.18 26.365 125-129 29.78 22.145 21.805 26.27 130-134 29.406470323516174 22.87614380719036 21.326066303315166 26.3913195659783 135-139 29.78 22.685 21.37 26.165 140-144 30.17 23.200000000000003 20.580000000000002 26.05 145-149 30.514999999999997 22.305 21.27 25.91 150 29.975 21.95 19.45 28.625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 0.5 25 0.0 26 0.0 27 0.5 28 1.5 29 2.0 30 2.0 31 3.5 32 5.0 33 4.5 34 7.0 35 10.0 36 20.5 37 34.0 38 49.0 39 57.5 40 61.5 41 77.0 42 94.0 43 108.5 44 119.0 45 134.0 46 149.0 47 145.5 48 129.0 49 130.0 50 132.5 51 121.5 52 129.0 53 125.5 54 98.5 55 92.5 56 95.0 57 88.5 58 86.0 59 92.5 60 86.0 61 84.5 62 89.5 63 89.0 64 95.0 65 96.0 66 103.5 67 102.0 68 88.0 69 95.0 70 96.0 71 88.5 72 78.5 73 66.5 74 68.5 75 56.5 76 41.0 77 37.0 78 36.5 79 28.5 80 16.0 81 11.0 82 10.5 83 7.0 84 4.5 85 4.5 86 3.0 87 1.5 88 0.5 89 2.0 90 2.0 91 0.5 92 0.5 93 1.0 94 0.5 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 0.15 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 0.005 135-139 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 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.69909729187563 99.4 2 0.3009027081243731 0.6 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 0.0 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 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0125 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 0.025 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 0.11249999999999999 0.0 0.0 0.0 0.0 118-119 0.15 0.0 0.0 0.0 0.0 120-121 0.15 0.0 0.0 0.0 0.0 122-123 0.175 0.0 0.0 0.0 0.0 124-125 0.275 0.0 0.0 0.0 0.0 126-127 0.35 0.0 0.0 0.0 0.0 128-129 0.4125 0.0 0.0 0.0 0.0 130-131 0.7 0.0 0.0 0.0 0.0 132-133 0.9874999999999999 0.0 0.0 0.0 0.0 134-135 1.2875 0.0 0.0 0.0 0.0 136-137 1.6749999999999998 0.0 0.0 0.0 0.0 138 2.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTCTAA 10 0.006973645 144.0 5 >>END_MODULE Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218452 spots for SRR1797574.sra Written 1218452 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra Read 1218445 spots for SRR1797574.sra Written 1218445 spots for SRR1797574.sra SRR ids: ['SRR1797574.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_uur75g27 SRR1797574.sra spots: 24368907 blocks: [[1, 1218445], [1218446, 2436890], [2436891, 3655335], [3655336, 4873780], [4873781, 6092225], [6092226, 7310670], [7310671, 8529115], [8529116, 9747560], [9747561, 10966005], [10966006, 12184450], [12184451, 13402895], [13402896, 14621340], [14621341, 15839785], [15839786, 17058230], [17058231, 18276675], [18276676, 19495120], [19495121, 20713565], [20713566, 21932010], [21932011, 23150455], [23150456, 24368907]] SRR1797574 file size 8188527 SRR1797574 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 SRR1797574 SRR1797574_1.fastq SRR1797574_2.fastq Input file: SRR1797574_1.fastq Paired file: SRR1797574_2.fastq trimmed: SRR1797574-trimmed-pair1.fastq, SRR1797574-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 12:52:57 2024 >> started Mon Dec 9 12:53:41 2024 >> done (43.724s) 24368907 read pairs processed; of these: 52549 ( 0.22%) short read pairs filtered out after trimming by size control 35751 ( 0.15%) empty read pairs filtered out after trimming by size control 24280607 (99.64%) read pairs available; of these: 17638455 (72.64%) trimmed read pairs available after processing 6642152 (27.36%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 19 0.00% 19 43 0.00% 20 58 0.00% 21 84 0.00% 22 169 0.00% 23 206 0.00% 24 242 0.00% 25 309 0.00% 26 437 0.00% 27 506 0.00% 28 639 0.00% 29 767 0.00% 30 828 0.00% 31 1012 0.00% 32 1078 0.00% 33 1253 0.01% 34 1294 0.01% 35 1507 0.01% 36 1627 0.01% 37 1710 0.01% 38 1922 0.01% 39 2045 0.01% 40 2202 0.01% 41 2286 0.01% 42 2482 0.01% 43 2559 0.01% 44 2761 0.01% 45 2922 0.01% 46 3112 0.01% 47 3153 0.01% 48 3284 0.01% 49 3646 0.02% 50 3720 0.02% 51 3962 0.02% 52 4173 0.02% 53 4368 0.02% 54 4627 0.02% 55 4846 0.02% 56 5069 0.02% 57 5320 0.02% 58 5563 0.02% 59 5841 0.02% 60 6256 0.03% 61 6478 0.03% 62 6768 0.03% 63 7073 0.03% 64 7602 0.03% 65 7897 0.03% 66 8242 0.03% 67 8726 0.04% 68 9017 0.04% 69 9718 0.04% 70 10210 0.04% 71 10678 0.04% 72 11354 0.05% 73 11916 0.05% 74 12688 0.05% 75 13370 0.06% 76 14220 0.06% 77 15052 0.06% 78 16029 0.07% 79 16682 0.07% 80 18083 0.07% 81 19331 0.08% 82 20537 0.08% 83 22372 0.09% 84 26530 0.11% 85 28050 0.12% 86 29607 0.12% 87 31347 0.13% 88 33304 0.14% 89 34545 0.14% 90 35741 0.15% 91 37830 0.16% 92 38942 0.16% 93 40217 0.17% 94 42122 0.17% 95 43524 0.18% 96 45574 0.19% 97 46855 0.19% 98 49469 0.20% 99 51418 0.21% 100 52427 0.22% 101 54398 0.22% 102 56687 0.23% 103 59561 0.25% 104 62407 0.26% 105 66241 0.27% 106 69882 0.29% 107 73980 0.30% 108 77869 0.32% 109 81987 0.34% 110 86993 0.36% 111 92022 0.38% 112 96488 0.40% 113 100913 0.42% 114 107140 0.44% 115 115265 0.47% 116 120680 0.50% 117 125354 0.52% 118 131566 0.54% 119 136660 0.56% 120 143145 0.59% 121 155148 0.64% 122 163944 0.68% 123 177862 0.73% 124 183196 0.75% 125 191562 0.79% 126 199465 0.82% 127 211540 0.87% 128 226307 0.93% 129 243440 1.00% 130 257399 1.06% 131 269266 1.11% 132 287399 1.18% 133 303302 1.25% 134 315073 1.30% 135 330008 1.36% 136 347065 1.43% 137 366061 1.51% 138 384439 1.58% 139 409375 1.69% 140 438040 1.80% 141 469564 1.93% 142 505243 2.08% 143 544126 2.24% 144 603225 2.48% 145 694184 2.86% 146 822872 3.39% 147 1034397 4.26% 148 1443300 5.94% 149 3150963 12.98% 150 6642152 27.36% 24280607 reads passed initial QC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=3.78 fanout-score-rank=32 prefix-density=0.33 prefix-fanout=3.5 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCTTCGGTCGAGTGCTCGAACTTGCTTAGGAAGAAGATTAAGCTGAAGGCTTCTAGGCTTGTGTGTGC criterion=fanout-score sequence-density=0.04 sequence-density-rank=34 fanout-score=486.39 fanout-score-rank=1 prefix-density=1.00 prefix-fanout=20.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=5.95 fanout-score-rank=21 prefix-density=0.61 prefix-fanout=2.3 sequence=CAAGTGCGGCAGCGGCTGCAACGGCTGCAACATGTACCCTGAAGCCGAGGTCCAGACCTCCAGCCTCCTCGTCGTCGCCACCGCCGCCCACAAGGCGAGCTCCGGCGGGATGGAGATGGCCGCGGAGAACGGCGGCTGCGGCTGC criterion=fanout-score sequence-density=0.11 sequence-density-rank=27 fanout-score=329.62 fanout-score-rank=1 prefix-density=1.45 prefix-fanout=25.1 sequence=CGGCGGCGGCAG SRR1797574 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 12:55:30 Started mapping on | Dec 09 12:55:35 Finished on | Dec 09 12:58:00 Mapping speed, Million of reads per hour | 602.83 Number of input reads | 24280607 Average input read length | 278 UNIQUE READS: Uniquely mapped reads number | 23053627 Uniquely mapped reads % | 94.95% Average mapped length | 277.61 Number of splices: Total | 18284088 Number of splices: Annotated (sjdb) | 17326619 Number of splices: GT/AG | 18047327 Number of splices: GC/AG | 196226 Number of splices: AT/AC | 11289 Number of splices: Non-canonical | 29246 Mismatch rate per base, % | 0.27% Deletion rate per base | 0.02% Deletion average length | 2.38 Insertion rate per base | 0.01% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 318789 % of reads mapped to multiple loci | 1.31% Number of reads mapped to too many loci | 82592 % of reads mapped to too many loci | 0.34% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.84% % of reads unmapped: other | 2.56% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 932807 932807 932807 N_multimapping 318789 318789 318789 N_noFeature 512577 22322159 907066 N_ambiguous 390618 2771 56779 UnstrandedReadsAssigned:22150432 PositiveStrandReadsAssigned:728697 NegativeStrandReadsAssigned:22089782 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=142 echo kmer=137 SRR1797574 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: SRR1797574-trimmed-pair1.fastq SRR1797574-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,280,607 reads, 22,250,149 reads pseudoaligned [quant] estimated average fragment length: 210.22 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,182 rounds 52973 SRR1797574.ke.tsv 35125 SRR1797574.se.tsv 88098 total ==> SRR1797574.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 726.953 0 0 PNS24247 1044 834.78 35.4912 2.6957 PNS24249 1928 1718.78 468.758 17.2923 PNS24246 1044 834.78 35.4912 2.6957 PNS24248 1044 834.78 35.4912 2.6957 PNS24244 1471 1261.78 59.7684 3.00339 PNS24243 293 92.9243 0 0 KQK14069 1603 1393.78 8620.05 392.138 KQK14071 474 266.286 456.454 108.686 ==> SRR1797574.se.tsv <== BRADI_1g14170v3 9267 BRADI_1g53295v3 252 BRADI_1g59795v3 221 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 497 BRADI_1g74790v3 426 BRADI_1g09890v3 0 BRADI_1g77505v3 198 BRADI_1g48960v3 0 SRR1797574 completed mapping pipeline successfully