Starting /dee2/code/volunteer_pipeline.sh SRR7166171 current disk space = 3109839613952 free memory = 1498300080 SRR7166171 SRAfilesize 73939ba2313b562760990c9b0a82455a SRR7166171.sra SRR7166171.sra file validated SRR7166171 is paired end SRR7166171 is conventional basespace SRR7166171 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166171_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.24425 33.0 33.0 34.0 32.0 34.0 2 32.87625 33.0 33.0 34.0 32.0 34.0 3 32.5425 33.0 33.0 34.0 31.0 34.0 4 32.75175 33.0 33.0 34.0 32.0 34.0 5 32.5295 33.0 33.0 33.0 32.0 34.0 6 36.41425 38.0 36.0 38.0 34.0 38.0 7 36.92925 38.0 37.0 38.0 35.0 38.0 8 37.251 38.0 38.0 38.0 36.0 38.0 9 37.465 38.0 38.0 38.0 37.0 38.0 10-14 37.50595 38.0 38.0 38.0 37.2 38.0 15-19 37.529199999999996 38.0 38.0 38.0 37.8 38.0 20-24 37.5106 38.0 38.0 38.0 37.8 38.0 25-29 37.50675 38.0 38.0 38.0 37.8 38.0 30-34 37.4483 38.0 38.0 38.0 37.4 38.0 35-39 37.427350000000004 38.0 38.0 38.0 37.2 38.0 40-44 37.429 38.0 38.0 38.0 37.0 38.0 45-49 37.427800000000005 38.0 38.0 38.0 37.0 38.0 50-54 37.292 38.0 38.0 38.0 37.0 38.0 55-59 36.91425 38.0 38.0 38.0 36.4 38.0 60-64 37.09125 38.0 38.0 38.0 36.0 38.0 65-69 37.23925 38.0 38.0 38.0 36.8 38.0 70-74 37.128 38.0 38.0 38.0 36.0 38.0 75-79 37.0889 38.0 38.0 38.0 36.0 38.0 80-84 36.934599999999996 38.0 38.0 38.0 36.0 38.0 85-89 36.909749999999995 38.0 38.0 38.0 35.8 38.0 90-94 36.80585000000001 38.0 38.0 38.0 35.0 38.0 95-99 36.707 38.0 38.0 38.0 34.8 38.0 100-104 36.675399999999996 38.0 38.0 38.0 34.8 38.0 105-109 36.450450000000004 38.0 38.0 38.0 34.0 38.0 110-114 36.44885 38.0 38.0 38.0 34.0 38.0 115-119 36.2565 38.0 37.8 38.0 33.6 38.0 120-124 36.08225 38.0 37.2 38.0 33.2 38.0 125-129 35.929950000000005 38.0 37.2 38.0 32.6 38.0 130-134 35.80115 38.0 36.8 38.0 32.8 38.0 135-139 35.51265 38.0 36.0 38.0 31.0 38.0 140-144 35.318349999999995 38.0 36.0 38.0 30.6 38.0 145-149 34.887449999999994 38.0 35.8 38.0 29.2 38.0 150-151 31.722375 36.5 31.5 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 0.0 15 1.0 16 3.0 17 2.0 18 3.0 19 1.0 20 6.0 21 4.0 22 5.0 23 5.0 24 3.0 25 13.0 26 11.0 27 14.0 28 28.0 29 16.0 30 35.0 31 48.0 32 64.0 33 105.0 34 112.0 35 229.0 36 580.0 37 2711.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.5366598778004 19.882892057026478 11.761710794297352 28.818737270875765 2 19.3 25.624999999999996 36.375 18.7 3 16.05 34.375 28.349999999999998 21.224999999999998 4 20.474999999999998 36.95 22.625 19.950000000000003 5 19.32899349023535 39.13370055082624 22.55883825738608 18.97846770155233 6 17.299999999999997 36.7 23.674999999999997 22.325 7 11.799999999999999 21.325 45.25 21.625 8 17.775 22.225 27.35 32.65 9 18.825 21.4 30.0 29.775000000000002 10-14 19.3 31.740000000000002 25.83 23.13 15-19 19.78 29.895 27.43 22.895 20-24 19.96 29.28 27.839999999999996 22.919999999999998 25-29 19.25 29.86 28.144999999999996 22.745 30-34 19.24 29.555 28.235 22.97 35-39 19.814999999999998 29.599999999999998 26.995 23.59 40-44 19.85 30.270000000000003 27.034999999999997 22.845 45-49 19.950000000000003 29.195 27.345000000000002 23.51 50-54 19.58700882117081 29.535886126704092 27.490978348035284 23.386126704089815 55-59 20.25642319923275 29.902579375094646 27.040533037201552 22.80046438847105 60-64 19.64518392302295 28.766162172997895 27.854064348000403 23.73458955597875 65-69 19.8 29.235 27.73 23.235 70-74 19.869999999999997 29.849999999999998 27.415 22.865 75-79 19.71 29.494999999999997 27.639999999999997 23.155 80-84 20.119999999999997 29.12 27.485 23.275000000000002 85-89 20.375 29.07 27.43 23.125 90-94 19.715 29.330000000000002 27.584999999999997 23.369999999999997 95-99 20.325 29.21 27.455000000000002 23.01 100-104 20.555 29.095 26.75 23.599999999999998 105-109 20.47650032534161 29.24570799339306 26.988337754642373 23.289453926622954 110-114 20.630000000000003 29.12 27.229999999999997 23.02 115-119 21.235 28.82 26.965 22.98 120-124 21.01 29.725 26.205000000000002 23.06 125-129 21.42 28.810000000000002 26.275 23.494999999999997 130-134 20.86 29.015 26.495 23.630000000000003 135-139 21.2 28.194999999999997 26.645000000000003 23.96 140-144 21.36 28.060000000000002 27.01 23.57 145-149 20.75 28.299999999999997 27.05 23.9 150-151 21.613832853025936 27.57799774464353 26.688384914171152 24.11978448815938 >>END_MODULE >>Per sequence GC content pass #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 1.0 12 1.0 13 0.0 14 0.0 15 0.0 16 1.0 17 1.0 18 2.0 19 2.5 20 0.5 21 0.0 22 1.0 23 2.0 24 3.0 25 4.0 26 6.0 27 11.5 28 14.5 29 19.0 30 36.0 31 45.0 32 50.5 33 59.5 34 74.0 35 103.0 36 117.0 37 135.0 38 164.0 39 185.0 40 207.5 41 235.0 42 242.5 43 249.5 44 276.0 45 259.0 46 224.5 47 223.0 48 208.0 49 171.0 50 141.0 51 121.0 52 95.0 53 72.0 54 53.0 55 37.0 56 32.5 57 26.5 58 21.5 59 14.5 60 10.0 61 7.0 62 5.0 63 7.0 64 7.0 65 5.0 66 2.5 67 2.0 68 3.0 69 2.0 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 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 1.7999999999999998 2 0.0 3 0.0 4 0.0 5 0.15 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 0.24 55-59 0.9450000000000001 60-64 0.22999999999999998 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 0.105 110-114 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 0.2375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.775 #Duplication Level Percentage of deduplicated Percentage of total 1 99.77449260836883 99.55000000000001 2 0.22550739163117012 0.44999999999999996 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 fail #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 0.0125 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.44999999999999996 0.0 0.0 0.0 0.0 88-89 0.5875 0.0 0.0 0.0 0.0 90-91 0.7625 0.0 0.0 0.0 0.0 92-93 1.0125 0.0 0.0 0.0 0.0 94-95 1.125 0.0 0.0 0.0 0.0 96-97 1.3625 0.0 0.0 0.0 0.0 98-99 1.625 0.0 0.0 0.0 0.0 100-101 2.0 0.0 0.0 0.0 0.0 102-103 2.45 0.0 0.0 0.0 0.0 104-105 2.9125 0.0 0.0 0.0 0.0 106-107 3.3125 0.0 0.0 0.0 0.0 108-109 3.7625 0.0 0.0 0.0 0.0 110-111 4.1375 0.0 0.0 0.0 0.0 112-113 4.637499999999999 0.0 0.0 0.0 0.0 114-115 5.2625 0.0 0.0 0.0 0.0 116-117 5.975 0.0 0.0 0.0 0.0 118-119 6.8375 0.0 0.0 0.0 0.0 120-121 7.55 0.0 0.0 0.0 0.0 122-123 8.575 0.0 0.0 0.0 0.0 124-125 9.162500000000001 0.0 0.0 0.0 0.0 126-127 9.7875 0.0 0.0 0.0 0.0 128-129 10.2125 0.0 0.0 0.0 0.0 130-131 10.8125 0.0 0.0 0.0 0.0 132-133 11.6125 0.0 0.0 0.0 0.0 134-135 12.3875 0.0 0.0 0.0 0.0 136-137 13.1875 0.0 0.0 0.0 0.0 138-139 14.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7166171 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7166171_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.95475 33.0 33.0 34.0 32.0 34.0 2 33.032 34.0 33.0 34.0 32.0 34.0 3 33.06175 34.0 33.0 34.0 32.0 34.0 4 33.04725 34.0 33.0 34.0 32.0 34.0 5 32.9575 34.0 33.0 34.0 32.0 34.0 6 37.16375 38.0 38.0 38.0 37.0 38.0 7 37.192 38.0 38.0 38.0 37.0 38.0 8 37.17675 38.0 38.0 38.0 37.0 38.0 9 37.12975 38.0 38.0 38.0 37.0 38.0 10-14 37.116 38.0 38.0 38.0 37.0 38.0 15-19 37.13484999999999 38.0 38.0 38.0 37.0 38.0 20-24 37.070299999999996 38.0 38.0 38.0 36.8 38.0 25-29 37.06945 38.0 38.0 38.0 36.4 38.0 30-34 36.987300000000005 38.0 38.0 38.0 36.2 38.0 35-39 36.96865 38.0 38.0 38.0 36.0 38.0 40-44 36.94495 38.0 38.0 38.0 36.0 38.0 45-49 36.91780000000001 38.0 38.0 38.0 36.0 38.0 50-54 36.755849999999995 38.0 38.0 38.0 35.6 38.0 55-59 36.6592 38.0 38.0 38.0 35.2 38.0 60-64 36.6835 38.0 38.0 38.0 35.0 38.0 65-69 36.62705 38.0 38.0 38.0 34.8 38.0 70-74 36.554199999999994 38.0 38.0 38.0 34.6 38.0 75-79 36.52525 38.0 38.0 38.0 34.0 38.0 80-84 36.363949999999996 38.0 38.0 38.0 34.0 38.0 85-89 36.245850000000004 38.0 38.0 38.0 33.8 38.0 90-94 36.050850000000004 38.0 37.8 38.0 33.2 38.0 95-99 35.9557 38.0 37.2 38.0 33.0 38.0 100-104 35.793150000000004 38.0 37.0 38.0 32.2 38.0 105-109 35.629149999999996 38.0 37.0 38.0 31.0 38.0 110-114 35.4145 38.0 36.8 38.0 30.2 38.0 115-119 35.17935 38.0 36.0 38.0 28.6 38.0 120-124 34.84265 38.0 36.0 38.0 27.4 38.0 125-129 34.700450000000004 38.0 35.4 38.0 27.2 38.0 130-134 34.230500000000006 38.0 35.0 38.0 23.6 38.0 135-139 33.73885 38.0 34.6 38.0 21.0 38.0 140-144 33.0308 38.0 34.0 38.0 15.6 38.0 145-149 31.7301 38.0 32.8 38.0 8.8 38.0 150-151 27.746625 36.0 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 3.0 4 4.0 5 1.0 6 1.0 7 1.0 8 1.0 9 3.0 10 1.0 11 1.0 12 1.0 13 4.0 14 6.0 15 1.0 16 4.0 17 5.0 18 5.0 19 5.0 20 7.0 21 8.0 22 20.0 23 12.0 24 25.0 25 26.0 26 14.0 27 28.0 28 25.0 29 30.0 30 59.0 31 65.0 32 96.0 33 102.0 34 213.0 35 300.0 36 705.0 37 2212.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.35 17.875 14.899999999999999 26.875 2 24.275 23.7 34.25 17.775 3 20.549999999999997 25.924999999999997 33.324999999999996 20.200000000000003 4 23.175 36.05 20.9 19.875 5 23.799999999999997 36.975 21.775 17.45 6 18.55 37.15 23.45 20.849999999999998 7 18.125 16.575 43.925 21.375 8 21.224999999999998 21.15 26.875 30.75 9 21.9 23.825 27.950000000000003 26.325 10-14 22.770000000000003 28.49 26.705000000000002 22.035 15-19 23.405 27.73 28.48 20.385 20-24 22.64 28.475 28.255000000000003 20.630000000000003 25-29 23.27 28.095 28.475 20.16 30-34 22.945 28.425 28.389999999999997 20.24 35-39 22.6 27.83 29.01 20.560000000000002 40-44 22.655 27.575 29.03 20.74 45-49 22.84 28.000000000000004 28.389999999999997 20.77 50-54 22.869999999999997 28.32 28.32 20.49 55-59 23.18 27.779999999999998 28.544999999999998 20.495 60-64 23.075000000000003 27.800000000000004 28.689999999999998 20.435 65-69 23.285 27.255000000000003 29.165000000000003 20.294999999999998 70-74 22.845 28.294999999999998 28.754999999999995 20.105 75-79 23.7 27.925 28.595 19.78 80-84 23.345 27.700000000000003 28.775000000000002 20.18 85-89 23.755000000000003 27.355 28.444999999999997 20.445 90-94 23.075000000000003 27.33 28.854999999999997 20.74 95-99 23.565 27.810000000000002 28.634999999999998 19.99 100-104 23.885 28.360000000000003 28.044999999999998 19.71 105-109 23.72 27.765 28.415000000000003 20.1 110-114 24.02 28.26 27.650000000000002 20.07 115-119 24.83 27.785 28.125 19.259999999999998 120-124 24.995 27.805000000000003 27.905 19.295 125-129 25.0 27.865000000000002 27.74 19.395 130-134 25.695 27.694999999999997 27.495000000000005 19.115 135-139 26.165 27.145000000000003 27.77 18.92 140-144 25.825 27.884999999999998 27.915 18.375 145-149 26.284999999999997 28.050000000000004 27.52 18.145 150-151 26.36977733299975 27.08281210908181 28.15861896422317 18.388791593695274 >>END_MODULE >>Per sequence GC content pass #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 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 0.0 22 0.0 23 0.0 24 2.5 25 4.0 26 4.5 27 8.0 28 14.5 29 20.5 30 21.5 31 21.0 32 27.0 33 37.0 34 56.5 35 79.5 36 97.5 37 117.5 38 143.5 39 170.5 40 192.0 41 222.5 42 255.5 43 277.0 44 298.0 45 286.5 46 255.0 47 243.5 48 221.5 49 189.5 50 162.0 51 130.5 52 103.0 53 77.5 54 58.0 55 46.5 56 32.5 57 25.5 58 21.0 59 19.0 60 14.5 61 8.5 62 8.0 63 6.0 64 3.5 65 4.5 66 3.0 67 0.5 68 1.5 69 1.5 70 1.5 71 1.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.0 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 10-14 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 0.0 150-151 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.775 #Duplication Level Percentage of deduplicated Percentage of total 1 99.77449260836883 99.55000000000001 2 0.22550739163117012 0.44999999999999996 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 fail #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 0.0125 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.44999999999999996 0.0 0.0 0.0 0.0 88-89 0.5875 0.0 0.0 0.0 0.0 90-91 0.7625 0.0 0.0 0.0 0.0 92-93 1.0125 0.0 0.0 0.0 0.0 94-95 1.15 0.0 0.0 0.0 0.0 96-97 1.3875 0.0 0.0 0.0 0.0 98-99 1.65 0.0 0.0 0.0 0.0 100-101 2.05 0.0 0.0 0.0 0.0 102-103 2.525 0.0 0.0 0.0 0.0 104-105 2.9625 0.0 0.0 0.0 0.0 106-107 3.425 0.0 0.0 0.0 0.0 108-109 3.8875 0.0 0.0 0.0 0.0 110-111 4.325 0.0 0.0 0.0 0.0 112-113 4.85 0.0 0.0 0.0 0.0 114-115 5.4625 0.0 0.0 0.0 0.0 116-117 6.1625 0.0 0.0 0.0 0.0 118-119 7.025 0.0 0.0 0.0 0.0 120-121 7.7125 0.0 0.0 0.0 0.0 122-123 8.7 0.0 0.0 0.0 0.0 124-125 9.287500000000001 0.0 0.0 0.0 0.0 126-127 9.8875 0.0 0.0 0.0 0.0 128-129 10.3125 0.0 0.0 0.0 0.0 130-131 10.925 0.0 0.0 0.0 0.0 132-133 11.7375 0.0 0.0 0.0 0.0 134-135 12.5 0.0 0.0 0.0 0.0 136-137 13.3 0.0 0.0 0.0 0.0 138-139 14.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCTGCAG 10 0.006830828 145.0 7 AAGTGAG 10 0.006830828 145.0 5 CTCTGTG 10 0.006830828 145.0 9 >>END_MODULE Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra Read 651575 spots for SRR7166171.sra Written 651575 spots for SRR7166171.sra Read 651573 spots for SRR7166171.sra Written 651573 spots for SRR7166171.sra SRR ids: ['SRR7166171.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_be_o1i1g SRR7166171.sra spots: 13031462 blocks: [[1, 651573], [651574, 1303146], [1303147, 1954719], [1954720, 2606292], [2606293, 3257865], [3257866, 3909438], [3909439, 4561011], [4561012, 5212584], [5212585, 5864157], [5864158, 6515730], [6515731, 7167303], [7167304, 7818876], [7818877, 8470449], [8470450, 9122022], [9122023, 9773595], [9773596, 10425168], [10425169, 11076741], [11076742, 11728314], [11728315, 12379887], [12379888, 13031462]] SRR7166171 file size 4394234 SRR7166171 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 SRR7166171 SRR7166171_1.fastq SRR7166171_2.fastq Input file: SRR7166171_1.fastq Paired file: SRR7166171_2.fastq trimmed: SRR7166171-trimmed-pair1.fastq, SRR7166171-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 Fri Feb 14 20:10:36 2025 >> started Fri Feb 14 20:11:04 2025 >> done (28.682s) 13031462 read pairs processed; of these: 9072 ( 0.07%) short read pairs filtered out after trimming by size control 9086 ( 0.07%) empty read pairs filtered out after trimming by size control 13013304 (99.86%) read pairs available; of these: 6342019 (48.73%) trimmed read pairs available after processing 6671285 (51.27%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 8 0.00% 20 8 0.00% 21 5 0.00% 22 8 0.00% 23 7 0.00% 24 10 0.00% 25 4 0.00% 26 6 0.00% 27 5 0.00% 28 6 0.00% 29 5 0.00% 30 9 0.00% 31 9 0.00% 32 7 0.00% 33 6 0.00% 34 6 0.00% 35 4 0.00% 36 9 0.00% 37 13 0.00% 38 14 0.00% 39 10 0.00% 40 20 0.00% 41 20 0.00% 42 29 0.00% 43 28 0.00% 44 32 0.00% 45 41 0.00% 46 45 0.00% 47 46 0.00% 48 62 0.00% 49 85 0.00% 50 79 0.00% 51 95 0.00% 52 121 0.00% 53 128 0.00% 54 134 0.00% 55 182 0.00% 56 196 0.00% 57 214 0.00% 58 266 0.00% 59 327 0.00% 60 351 0.00% 61 434 0.00% 62 466 0.00% 63 557 0.00% 64 558 0.00% 65 697 0.01% 66 722 0.01% 67 806 0.01% 68 916 0.01% 69 1169 0.01% 70 1413 0.01% 71 1650 0.01% 72 1886 0.01% 73 2156 0.02% 74 2410 0.02% 75 2683 0.02% 76 2929 0.02% 77 3155 0.02% 78 3583 0.03% 79 3902 0.03% 80 4539 0.03% 81 5456 0.04% 82 6302 0.05% 83 6885 0.05% 84 8255 0.06% 85 8888 0.07% 86 9448 0.07% 87 9964 0.08% 88 10541 0.08% 89 11234 0.09% 90 12331 0.09% 91 13681 0.11% 92 15092 0.12% 93 16698 0.13% 94 17780 0.14% 95 18966 0.15% 96 19367 0.15% 97 19928 0.15% 98 20454 0.16% 99 21805 0.17% 100 22166 0.17% 101 24410 0.19% 102 26433 0.20% 103 28179 0.22% 104 30307 0.23% 105 31300 0.24% 106 31970 0.25% 107 31966 0.25% 108 32082 0.25% 109 33209 0.26% 110 34177 0.26% 111 35825 0.28% 112 38173 0.29% 113 40180 0.31% 114 42976 0.33% 115 44163 0.34% 116 44817 0.34% 117 45414 0.35% 118 45291 0.35% 119 45641 0.35% 120 46318 0.36% 121 47902 0.37% 122 50054 0.38% 123 52830 0.41% 124 55440 0.43% 125 56999 0.44% 126 58040 0.45% 127 58255 0.45% 128 57955 0.45% 129 58298 0.45% 130 59187 0.45% 131 60531 0.47% 132 63277 0.49% 133 66028 0.51% 134 69450 0.53% 135 72569 0.56% 136 74405 0.57% 137 76263 0.59% 138 77944 0.60% 139 78903 0.61% 140 81476 0.63% 141 86108 0.66% 142 91449 0.70% 143 99370 0.76% 144 112341 0.86% 145 128602 0.99% 146 151448 1.16% 147 190095 1.46% 148 268043 2.06% 149 494452 3.80% 150 2396939 18.42% 151 6671285 51.27% 13013304 reads passed initial QC criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=3.27 fanout-score-rank=19 prefix-density=0.48 prefix-fanout=2.1 sequence=CACTTGCAGCCATTCTCAGCACCAGAGTTCATCTCAGACC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=111.54 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=12.4 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=4.07 fanout-score-rank=11 prefix-density=0.61 prefix-fanout=3.0 sequence=CTGCAAATGTGG criterion=fanout-score sequence-density=0.09 sequence-density-rank=27 fanout-score=33.82 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=8.7 sequence=AAGGCCAAGATCCAGGACAAGGA SRR7166171 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 20:12:31 Started mapping on | Feb 14 20:12:32 Finished on | Feb 14 20:14:40 Mapping speed, Million of reads per hour | 366.00 Number of input reads | 13013304 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 11967539 Uniquely mapped reads % | 91.96% Average mapped length | 288.62 Number of splices: Total | 10773363 Number of splices: Annotated (sjdb) | 10537519 Number of splices: GT/AG | 10593711 Number of splices: GC/AG | 132725 Number of splices: AT/AC | 10218 Number of splices: Non-canonical | 36709 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 2.23 Insertion rate per base | 0.02% Insertion average length | 2.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 334050 % of reads mapped to multiple loci | 2.57% Number of reads mapped to too many loci | 84936 % of reads mapped to too many loci | 0.65% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.64% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 720527 720527 720527 N_multimapping 334050 334050 334050 N_noFeature 432128 11797054 529644 N_ambiguous 136832 947 63272 UnstrandedReadsAssigned:11398579 PositiveStrandReadsAssigned:169538 NegativeStrandReadsAssigned:11374623 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=145 echo kmer=141 SRR7166171 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7166171-trimmed-pair1.fastq SRR7166171-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,013,304 reads, 11,364,829 reads pseudoaligned [quant] estimated average fragment length: 214.332 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,050 rounds 52401 SRR7166171.ke.tsv 34699 SRR7166171.se.tsv 87100 total ==> SRR7166171.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1804.67 981 41.6244 Potri.005G024800.1.v4.1 1035 821.668 274 25.5347 Potri.004G059700.1.v4.1 961 747.672 36 3.68695 Potri.007G009000.2.v4.1 1416 1202.67 0 0 Potri.003G141000.2.v4.1 2943 2729.67 303.302 8.50829 Potri.016G087400.1.v4.1 270 97.1044 782.472 617.03 Potri.015G069301.1.v4.1 564 354.046 0 0 Potri.010G195200.1.v4.1 1773 1559.67 428 21.013 Potri.012G127500.1.v4.1 977 763.668 2519 252.581 ==> SRR7166171.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 15 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 552 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 171 SRR7166171 completed mapping pipeline successfully