Starting /dee2/code/volunteer_pipeline.sh SRR7171454 current disk space = 3115602657280 free memory = 1577899856 SRR7171454 SRAfilesize 4092c12a614d03158d7a13bdc8bc82e1 SRR7171454.sra SRR7171454.sra file validated SRR7171454 is paired end SRR7171454 is conventional basespace SRR7171454 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171454_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.039 33.0 33.0 34.0 31.0 34.0 2 32.71275 33.0 33.0 34.0 31.0 34.0 3 31.644 33.0 31.0 33.0 28.0 34.0 4 31.94275 33.0 32.0 33.0 31.0 34.0 5 32.0655 33.0 32.0 33.0 31.0 34.0 6 35.614 37.0 35.0 38.0 31.0 38.0 7 36.77125 38.0 37.0 38.0 34.0 38.0 8 37.30875 38.0 38.0 38.0 36.0 38.0 9 37.4525 38.0 38.0 38.0 37.0 38.0 10-14 37.53705 38.0 38.0 38.0 37.2 38.0 15-19 37.48165 38.0 38.0 38.0 37.2 38.0 20-24 37.51655 38.0 38.0 38.0 37.2 38.0 25-29 37.4873 38.0 38.0 38.0 37.0 38.0 30-34 37.47485 38.0 38.0 38.0 37.2 38.0 35-39 37.4534 38.0 38.0 38.0 37.0 38.0 40-44 37.446600000000004 38.0 38.0 38.0 37.0 38.0 45-49 37.38975000000001 38.0 38.0 38.0 37.0 38.0 50-54 37.4106 38.0 38.0 38.0 37.0 38.0 55-59 37.3304 38.0 38.0 38.0 37.0 38.0 60-64 37.30215 38.0 38.0 38.0 36.6 38.0 65-69 37.25985 38.0 38.0 38.0 36.2 38.0 70-74 37.18675 38.0 38.0 38.0 36.0 38.0 75-79 37.136849999999995 38.0 38.0 38.0 36.0 38.0 80-84 37.04495 38.0 38.0 38.0 36.0 38.0 85-89 37.01695 38.0 38.0 38.0 35.8 38.0 90-94 36.92295 38.0 38.0 38.0 35.6 38.0 95-99 36.779250000000005 38.0 38.0 38.0 34.8 38.0 100-104 36.7735 38.0 38.0 38.0 34.8 38.0 105-109 36.6409 38.0 38.0 38.0 34.4 38.0 110-114 36.61765 38.0 38.0 38.0 34.0 38.0 115-119 36.4252 38.0 37.8 38.0 33.8 38.0 120-124 36.3138 38.0 37.2 38.0 34.0 38.0 125-129 36.1607 38.0 37.0 38.0 33.4 38.0 130-134 36.0193 38.0 36.6 38.0 32.8 38.0 135-139 35.809400000000004 38.0 36.0 38.0 31.0 38.0 140-144 35.69235 38.0 36.0 38.0 31.0 38.0 145-149 35.4122 38.0 35.6 38.0 30.6 38.0 150-151 33.34325 36.5 31.5 38.0 21.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 1.0 22 4.0 23 3.0 24 3.0 25 5.0 26 8.0 27 11.0 28 18.0 29 27.0 30 31.0 31 42.0 32 54.0 33 70.0 34 143.0 35 253.0 36 659.0 37 2666.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.91507430997877 12.128450106157112 9.182590233545646 38.77388535031847 2 20.575 15.15 34.275 30.0 3 19.775000000000002 20.3 24.7 35.225 4 23.575 28.15 23.175 25.1 5 21.7 31.624999999999996 24.7 21.975 6 19.950000000000003 35.075 24.325 20.65 7 14.224999999999998 26.85 40.949999999999996 17.974999999999998 8 17.724999999999998 25.55 32.05 24.675 9 17.25 25.074999999999996 33.75 23.925 10-14 19.705000000000002 29.975 27.3 23.02 15-19 19.78 28.744999999999997 27.66 23.815 20-24 19.965 29.15 27.275 23.61 25-29 20.335 28.689999999999998 27.794999999999998 23.18 30-34 20.015 29.270000000000003 27.55 23.165 35-39 19.939999999999998 28.95 27.76 23.35 40-44 20.01 29.28 27.32 23.39 45-49 19.885 28.749999999999996 27.83 23.535 50-54 20.205000000000002 28.194999999999997 27.77 23.830000000000002 55-59 20.285 29.065 27.32 23.330000000000002 60-64 19.835 28.465 27.88 23.82 65-69 19.869999999999997 28.065 28.18 23.885 70-74 20.745 28.645 27.375 23.235 75-79 20.04 28.810000000000002 27.79 23.36 80-84 19.985 27.73 28.065 24.22 85-89 20.145 28.96 27.339999999999996 23.555 90-94 19.994999999999997 28.71 27.169999999999998 24.125 95-99 20.52 28.244999999999997 27.900000000000002 23.335 100-104 20.31 28.16 27.625 23.905 105-109 20.82 28.000000000000004 27.93 23.25 110-114 20.830000000000002 28.335 27.27 23.565 115-119 20.79 28.825 27.515 22.869999999999997 120-124 20.01 28.54 27.229999999999997 24.22 125-129 20.955 27.46 27.675 23.91 130-134 20.57 27.889999999999997 27.905 23.635 135-139 21.099999999999998 28.015 26.93 23.955000000000002 140-144 20.855 27.815 26.805 24.525 145-149 21.01 28.03 26.724999999999998 24.235 150-151 20.375 28.6875 26.900000000000002 24.0375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.5 9 0.5 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 1.0 20 1.0 21 1.0 22 1.0 23 1.0 24 2.0 25 3.0 26 4.5 27 4.0 28 6.0 29 10.0 30 14.0 31 18.0 32 27.5 33 47.5 34 59.0 35 71.0 36 94.5 37 109.5 38 124.0 39 168.0 40 217.0 41 234.0 42 248.0 43 259.0 44 263.0 45 285.5 46 272.5 47 236.0 48 228.5 49 215.0 50 175.5 51 135.0 52 107.0 53 89.0 54 66.5 55 46.5 56 36.0 57 27.5 58 24.5 59 18.5 60 13.0 61 9.5 62 5.5 63 2.0 64 2.5 65 2.5 66 2.0 67 1.5 68 0.5 69 1.5 70 2.0 71 0.5 72 0.5 73 0.5 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 warn #Base N-Count 1 5.800000000000001 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.8 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79959919839679 99.6 2 0.2004008016032064 0.4 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 warn #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 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.0875 0.0 0.0 0.0 0.0 82-83 0.1125 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.2875 0.0 0.0 0.0 0.0 92-93 0.375 0.0 0.0 0.0 0.0 94-95 0.5 0.0 0.0 0.0 0.0 96-97 0.675 0.0 0.0 0.0 0.0 98-99 0.8375 0.0 0.0 0.0 0.0 100-101 0.9624999999999999 0.0 0.0 0.0 0.0 102-103 1.1875 0.0 0.0 0.0 0.0 104-105 1.2875 0.0 0.0 0.0 0.0 106-107 1.425 0.0 0.0 0.0 0.0 108-109 1.75 0.0 0.0 0.0 0.0 110-111 2.025 0.0 0.0 0.0 0.0 112-113 2.3375 0.0 0.0 0.0 0.0 114-115 2.875 0.0 0.0 0.0 0.0 116-117 3.325 0.0 0.0 0.0 0.0 118-119 3.7375 0.0 0.0 0.0 0.0 120-121 4.025 0.0 0.0 0.0 0.0 122-123 4.612500000000001 0.0 0.0 0.0 0.0 124-125 5.1875 0.0 0.0 0.0 0.0 126-127 5.625 0.0 0.0 0.0 0.0 128-129 6.0875 0.0 0.0 0.0 0.0 130-131 6.6375 0.0 0.0 0.0 0.0 132-133 7.2125 0.0 0.0 0.0 0.0 134-135 7.85 0.0 0.0 0.0 0.0 136-137 8.6625 0.0 0.0 0.0 0.0 138-139 9.412500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGAGCA 30 0.0014474266 24.15625 140-144 AGAGCAC 30 0.0014474266 24.15625 140-144 TCGGAAG 35 0.0035454615 20.705357 135-139 ATCGGAA 35 0.0035454615 20.705357 135-139 >>END_MODULE SRR7171454 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171454_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.043 33.0 33.0 34.0 32.0 34.0 2 33.128 34.0 33.0 34.0 32.0 34.0 3 33.153 34.0 33.0 34.0 33.0 34.0 4 33.12525 34.0 33.0 34.0 33.0 34.0 5 33.057 34.0 33.0 34.0 32.0 34.0 6 37.298 38.0 38.0 38.0 37.0 38.0 7 37.269 38.0 38.0 38.0 37.0 38.0 8 37.392 38.0 38.0 38.0 37.0 38.0 9 37.28675 38.0 38.0 38.0 37.0 38.0 10-14 37.27470000000001 38.0 38.0 38.0 36.8 38.0 15-19 37.28114999999999 38.0 38.0 38.0 37.0 38.0 20-24 37.31445 38.0 38.0 38.0 37.0 38.0 25-29 37.2558 38.0 38.0 38.0 37.0 38.0 30-34 37.28865 38.0 38.0 38.0 37.0 38.0 35-39 37.251000000000005 38.0 38.0 38.0 36.8 38.0 40-44 37.20315 38.0 38.0 38.0 36.8 38.0 45-49 37.18919999999999 38.0 38.0 38.0 36.6 38.0 50-54 37.105149999999995 38.0 38.0 38.0 36.0 38.0 55-59 37.0706 38.0 38.0 38.0 36.0 38.0 60-64 37.034349999999996 38.0 38.0 38.0 36.0 38.0 65-69 37.00645 38.0 38.0 38.0 36.0 38.0 70-74 36.9748 38.0 38.0 38.0 35.8 38.0 75-79 36.842200000000005 38.0 38.0 38.0 35.2 38.0 80-84 36.8465 38.0 38.0 38.0 35.0 38.0 85-89 36.7256 38.0 38.0 38.0 34.8 38.0 90-94 36.60905 38.0 38.0 38.0 34.0 38.0 95-99 36.5857 38.0 38.0 38.0 34.0 38.0 100-104 36.421499999999995 38.0 38.0 38.0 34.0 38.0 105-109 36.342299999999994 38.0 37.4 38.0 34.0 38.0 110-114 36.03965 38.0 37.0 38.0 32.6 38.0 115-119 35.907599999999995 38.0 37.0 38.0 32.2 38.0 120-124 35.722150000000006 38.0 36.2 38.0 31.0 38.0 125-129 35.63565000000001 38.0 36.0 38.0 31.0 38.0 130-134 35.2705 38.0 35.6 38.0 28.2 38.0 135-139 34.8303 38.0 35.0 38.0 25.4 38.0 140-144 34.7097 38.0 34.8 38.0 25.2 38.0 145-149 34.1496 38.0 33.6 38.0 23.0 38.0 150-151 31.411 35.5 27.0 38.0 18.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 2.0 17 2.0 18 0.0 19 2.0 20 5.0 21 3.0 22 5.0 23 7.0 24 9.0 25 9.0 26 14.0 27 17.0 28 29.0 29 34.0 30 40.0 31 59.0 32 84.0 33 118.0 34 141.0 35 305.0 36 726.0 37 2389.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.125 20.75 14.649999999999999 27.474999999999998 2 26.8 26.400000000000002 29.975 16.825000000000003 3 20.825 28.549999999999997 30.725 19.900000000000002 4 24.6 33.575 23.1 18.725 5 23.200000000000003 36.525 22.5 17.775 6 21.325 39.050000000000004 22.375 17.25 7 19.825 21.55 38.65 19.975 8 21.8 25.25 28.725 24.224999999999998 9 22.400000000000002 24.425 29.725 23.45 10-14 23.825 28.525 26.595000000000002 21.055 15-19 23.29 27.889999999999997 28.1 20.72 20-24 23.615 28.24 27.47 20.674999999999997 25-29 23.14 27.939999999999998 28.125 20.794999999999998 30-34 23.235 28.18 27.985 20.599999999999998 35-39 23.400000000000002 27.889999999999997 27.584999999999997 21.125 40-44 22.79 28.1 28.24 20.87 45-49 23.39 27.775 28.175 20.66 50-54 23.41 28.475 27.71 20.405 55-59 23.21 28.055000000000003 27.515 21.22 60-64 23.66 27.865000000000002 27.87 20.605 65-69 23.1 27.634999999999998 28.299999999999997 20.965 70-74 23.91 27.685 28.185 20.22 75-79 23.94 27.500000000000004 28.03 20.53 80-84 23.39 28.055000000000003 27.935 20.62 85-89 23.919999999999998 27.805000000000003 27.66 20.615 90-94 23.62 27.905 27.77 20.705000000000002 95-99 23.325000000000003 28.125 28.1 20.45 100-104 23.885 28.17 27.939999999999998 20.005 105-109 23.965 27.825 28.105000000000004 20.105 110-114 23.66 27.815 27.839999999999996 20.685000000000002 115-119 23.84 28.515 27.205000000000002 20.44 120-124 24.46 28.599999999999998 27.27 19.67 125-129 24.36 28.050000000000004 27.325 20.265 130-134 24.815 27.755000000000003 27.595 19.835 135-139 25.480000000000004 27.905 27.065 19.55 140-144 25.36 28.01 27.47 19.16 145-149 25.405 27.785 27.465 19.345000000000002 150-151 26.187500000000004 26.3625 26.900000000000002 20.549999999999997 >>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 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 0.5 21 0.5 22 0.0 23 1.0 24 1.5 25 1.5 26 2.5 27 2.5 28 3.5 29 5.0 30 10.5 31 16.0 32 20.0 33 30.0 34 45.5 35 66.0 36 80.5 37 105.0 38 138.5 39 168.0 40 199.5 41 231.5 42 256.5 43 285.5 44 312.0 45 310.0 46 287.0 47 245.5 48 213.0 49 197.5 50 172.5 51 132.0 52 100.5 53 85.0 54 63.5 55 48.5 56 39.5 57 31.5 58 22.5 59 12.0 60 16.0 61 14.0 62 7.0 63 6.5 64 3.5 65 1.5 66 1.5 67 1.5 68 1.0 69 1.0 70 1.0 71 0.5 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 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.725 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79944848332916 99.52499999999999 2 0.17548257708698922 0.35000000000000003 3 0.0 0.0 4 0.0 0.0 5 0.0250689395838556 0.125 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 warn #Sequence Count Percentage Possible Source GTTAGGCTTGAGCAGATTCATTCGCCAACTAACCCTTTAATTTATCCTAT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.0875 0.0 0.0 0.0 0.0 82-83 0.1125 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.35 0.0 0.0 0.0 0.0 94-95 0.475 0.0 0.0 0.0 0.0 96-97 0.65 0.0 0.0 0.0 0.0 98-99 0.8125 0.0 0.0 0.0 0.0 100-101 0.9375 0.0 0.0 0.0 0.0 102-103 1.1625 0.0 0.0 0.0 0.0 104-105 1.2625 0.0 0.0 0.0 0.0 106-107 1.4 0.0 0.0 0.0 0.0 108-109 1.725 0.0 0.0 0.0 0.0 110-111 2.0 0.0 0.0 0.0 0.0 112-113 2.2875 0.0 0.0 0.0 0.0 114-115 2.8125 0.0 0.0 0.0 0.0 116-117 3.25 0.0 0.0 0.0 0.0 118-119 3.6625 0.0 0.0 0.0 0.0 120-121 3.95 0.0 0.0 0.0 0.0 122-123 4.550000000000001 0.0 0.0 0.0 0.0 124-125 5.112500000000001 0.0 0.0 0.0 0.0 126-127 5.5625 0.0 0.0 0.0 0.0 128-129 6.0375 0.0 0.0 0.0 0.0 130-131 6.5875 0.0 0.0 0.0 0.0 132-133 7.1625 0.0 0.0 0.0 0.0 134-135 7.800000000000001 0.0 0.0 0.0 0.0 136-137 8.6125 0.0 0.0 0.0 0.0 138-139 9.337499999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCTCTAC 10 0.006830828 145.0 1 AAGAGCG 25 4.977651E-4 29.0 140-144 AGAGCGT 25 4.977651E-4 29.0 140-144 TCGGAAG 35 0.0035366106 20.714287 135-139 ATCGGAA 40 0.0076550315 18.125 135-139 >>END_MODULE Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871881 spots for SRR7171454.sra Written 871881 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra Read 871877 spots for SRR7171454.sra Written 871877 spots for SRR7171454.sra SRR ids: ['SRR7171454.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_01jokvse SRR7171454.sra spots: 17437544 blocks: [[1, 871877], [871878, 1743754], [1743755, 2615631], [2615632, 3487508], [3487509, 4359385], [4359386, 5231262], [5231263, 6103139], [6103140, 6975016], [6975017, 7846893], [7846894, 8718770], [8718771, 9590647], [9590648, 10462524], [10462525, 11334401], [11334402, 12206278], [12206279, 13078155], [13078156, 13950032], [13950033, 14821909], [14821910, 15693786], [15693787, 16565663], [16565664, 17437544]] SRR7171454 file size 5887311 SRR7171454 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 SRR7171454 SRR7171454_1.fastq SRR7171454_2.fastq Input file: SRR7171454_1.fastq Paired file: SRR7171454_2.fastq trimmed: SRR7171454-trimmed-pair1.fastq, SRR7171454-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 10:24:22 2025 >> started Fri Feb 14 10:24:40 2025 >> done (17.679s) 17437544 read pairs processed; of these: 35 ( 0.00%) short read pairs filtered out after trimming by size control 1415 ( 0.01%) empty read pairs filtered out after trimming by size control 17436094 (99.99%) read pairs available; of these: 2550145 (14.63%) trimmed read pairs available after processing 14885949 (85.37%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 4 0.00% 21 5 0.00% 22 0 0.00% 23 1 0.00% 24 2 0.00% 25 4 0.00% 26 1 0.00% 27 2 0.00% 28 2 0.00% 29 2 0.00% 30 3 0.00% 31 1 0.00% 32 5 0.00% 33 0 0.00% 34 7 0.00% 35 2 0.00% 36 3 0.00% 37 7 0.00% 38 5 0.00% 39 4 0.00% 40 7 0.00% 41 9 0.00% 42 10 0.00% 43 8 0.00% 44 8 0.00% 45 14 0.00% 46 12 0.00% 47 12 0.00% 48 22 0.00% 49 17 0.00% 50 24 0.00% 51 44 0.00% 52 36 0.00% 53 47 0.00% 54 45 0.00% 55 50 0.00% 56 58 0.00% 57 88 0.00% 58 88 0.00% 59 105 0.00% 60 110 0.00% 61 134 0.00% 62 138 0.00% 63 204 0.00% 64 246 0.00% 65 280 0.00% 66 336 0.00% 67 361 0.00% 68 405 0.00% 69 488 0.00% 70 545 0.00% 71 720 0.00% 72 830 0.00% 73 982 0.01% 74 1040 0.01% 75 1227 0.01% 76 1454 0.01% 77 1474 0.01% 78 1822 0.01% 79 1941 0.01% 80 2355 0.01% 81 2785 0.02% 82 3179 0.02% 83 3566 0.02% 84 3901 0.02% 85 4527 0.03% 86 4875 0.03% 87 5380 0.03% 88 5667 0.03% 89 6318 0.04% 90 7154 0.04% 91 7898 0.05% 92 8897 0.05% 93 9996 0.06% 94 10759 0.06% 95 11633 0.07% 96 12251 0.07% 97 13099 0.08% 98 13855 0.08% 99 14805 0.08% 100 15735 0.09% 101 16926 0.10% 102 18186 0.10% 103 19845 0.11% 104 20893 0.12% 105 22275 0.13% 106 23366 0.13% 107 24267 0.14% 108 24546 0.14% 109 25882 0.15% 110 27146 0.16% 111 28113 0.16% 112 29561 0.17% 113 31273 0.18% 114 33423 0.19% 115 34782 0.20% 116 36075 0.21% 117 37048 0.21% 118 37631 0.22% 119 38348 0.22% 120 39483 0.23% 121 41082 0.24% 122 42924 0.25% 123 44460 0.25% 124 46597 0.27% 125 47930 0.27% 126 48746 0.28% 127 50601 0.29% 128 50985 0.29% 129 52380 0.30% 130 52547 0.30% 131 53521 0.31% 132 55618 0.32% 133 56689 0.33% 134 58621 0.34% 135 61015 0.35% 136 61945 0.36% 137 62741 0.36% 138 63549 0.36% 139 64069 0.37% 140 64005 0.37% 141 66326 0.38% 142 67348 0.39% 143 68094 0.39% 144 70527 0.40% 145 72215 0.41% 146 72626 0.42% 147 73992 0.42% 148 74815 0.43% 149 75081 0.43% 150 75888 0.44% 151 14885949 85.37% 17436094 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.98 fanout-score-rank=20 prefix-density=0.58 prefix-fanout=2.0 sequence=CACTTGCAGCCATTCTCAGCACCAGAGTTCATCTCAGACCTCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=146.61 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=15.9 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAA criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=3.17 fanout-score-rank=19 prefix-density=0.53 prefix-fanout=3.1 sequence=ATGTACCCTGACTT criterion=fanout-score sequence-density=0.08 sequence-density-rank=20 fanout-score=29.60 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=9.1 sequence=AAGGCCAAGATCCAGGACAAGGA SRR7171454 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 10:26:12 Started mapping on | Feb 14 10:26:12 Finished on | Feb 14 10:28:23 Mapping speed, Million of reads per hour | 479.16 Number of input reads | 17436094 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 16131568 Uniquely mapped reads % | 92.52% Average mapped length | 294.18 Number of splices: Total | 15634085 Number of splices: Annotated (sjdb) | 15345127 Number of splices: GT/AG | 15395378 Number of splices: GC/AG | 189974 Number of splices: AT/AC | 10740 Number of splices: Non-canonical | 37993 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.49 Insertion rate per base | 0.02% Insertion average length | 2.49 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 378488 % of reads mapped to multiple loci | 2.17% Number of reads mapped to too many loci | 224269 % of reads mapped to too many loci | 1.29% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.81% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 926038 926038 926038 N_multimapping 378488 378488 378488 N_noFeature 461404 15966317 530887 N_ambiguous 171519 1141 74981 UnstrandedReadsAssigned:15498645 PositiveStrandReadsAssigned:164110 NegativeStrandReadsAssigned:15525700 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171454 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: SRR7171454-trimmed-pair1.fastq SRR7171454-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,436,094 reads, 15,633,422 reads pseudoaligned [quant] estimated average fragment length: 220.782 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,139 rounds 52401 SRR7171454.ke.tsv 34699 SRR7171454.se.tsv 87100 total ==> SRR7171454.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1798.22 1286 44.3716 Potri.005G024800.1.v4.1 1035 815.218 634 48.2527 Potri.004G059700.1.v4.1 961 741.228 7 0.58594 Potri.007G009000.2.v4.1 1416 1196.22 0 0 Potri.003G141000.2.v4.1 2943 2723.22 866.235 19.736 Potri.016G087400.1.v4.1 270 87.4454 1159 822.343 Potri.015G069301.1.v4.1 564 346.619 0 0 Potri.010G195200.1.v4.1 1773 1553.22 377.841 15.0933 Potri.012G127500.1.v4.1 977 757.223 3882 318.081 ==> SRR7171454.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 87 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 512 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 175 SRR7171454 completed mapping pipeline successfully