Starting /dee2/code/volunteer_pipeline.sh SRR7171482 current disk space = 3087338614784 free memory = 1450082572 SRR7171482 SRAfilesize beb3baa3a7f4d39994fb110b16d03f06 SRR7171482.sra SRR7171482.sra file validated SRR7171482 is paired end SRR7171482 is conventional basespace SRR7171482 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171482_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 31.80275 33.0 33.0 34.0 32.0 34.0 2 33.00225 34.0 33.0 34.0 32.0 34.0 3 32.103 33.0 33.0 33.0 29.0 34.0 4 32.66825 33.0 33.0 34.0 32.0 34.0 5 32.9015 33.0 33.0 34.0 32.0 34.0 6 36.3785 38.0 36.0 38.0 34.0 38.0 7 37.116 38.0 38.0 38.0 35.0 38.0 8 37.3025 38.0 38.0 38.0 36.0 38.0 9 37.46225 38.0 38.0 38.0 37.0 38.0 10-14 37.5731 38.0 38.0 38.0 37.8 38.0 15-19 37.54845 38.0 38.0 38.0 37.4 38.0 20-24 37.539100000000005 38.0 38.0 38.0 37.6 38.0 25-29 37.5126 38.0 38.0 38.0 37.4 38.0 30-34 37.5009 38.0 38.0 38.0 37.6 38.0 35-39 37.468900000000005 38.0 38.0 38.0 37.0 38.0 40-44 37.49805 38.0 38.0 38.0 37.0 38.0 45-49 37.440450000000006 38.0 38.0 38.0 37.0 38.0 50-54 37.425799999999995 38.0 38.0 38.0 37.0 38.0 55-59 37.37885 38.0 38.0 38.0 37.0 38.0 60-64 37.32359999999999 38.0 38.0 38.0 36.8 38.0 65-69 37.2642 38.0 38.0 38.0 36.8 38.0 70-74 37.2554 38.0 38.0 38.0 36.6 38.0 75-79 37.205650000000006 38.0 38.0 38.0 36.0 38.0 80-84 37.116749999999996 38.0 38.0 38.0 36.0 38.0 85-89 37.061800000000005 38.0 38.0 38.0 36.0 38.0 90-94 37.05055 38.0 38.0 38.0 36.0 38.0 95-99 36.8116 38.0 38.0 38.0 35.0 38.0 100-104 36.818000000000005 38.0 38.0 38.0 35.0 38.0 105-109 36.6995 38.0 38.0 38.0 34.6 38.0 110-114 36.650400000000005 38.0 38.0 38.0 34.0 38.0 115-119 36.457499999999996 38.0 38.0 38.0 34.0 38.0 120-124 36.335350000000005 38.0 37.8 38.0 34.0 38.0 125-129 36.31765 38.0 37.2 38.0 33.8 38.0 130-134 36.14095 38.0 37.0 38.0 33.0 38.0 135-139 35.995850000000004 38.0 36.4 38.0 32.6 38.0 140-144 35.852850000000004 38.0 36.0 38.0 32.6 38.0 145-149 35.598949999999995 38.0 36.0 38.0 31.0 38.0 150-151 33.748000000000005 36.5 33.5 38.0 22.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 0.0 23 1.0 24 3.0 25 7.0 26 9.0 27 13.0 28 12.0 29 23.0 30 27.0 31 45.0 32 49.0 33 98.0 34 120.0 35 211.0 36 564.0 37 2817.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.417490890161375 12.129099427381572 11.114003123373244 38.33940655908381 2 22.375 14.475 32.800000000000004 30.349999999999998 3 20.925 18.125 25.174999999999997 35.775 4 23.025000000000002 24.95 22.825 29.2 5 21.349999999999998 30.225 25.5 22.925 6 20.05 34.325 25.124999999999996 20.5 7 15.0 25.900000000000002 40.875 18.224999999999998 8 17.875 26.525 30.2 25.4 9 16.75 24.325 34.925 24.0 10-14 19.31 29.189999999999998 28.165000000000003 23.335 15-19 19.225 28.28 28.645 23.849999999999998 20-24 19.595000000000002 28.465 28.13 23.810000000000002 25-29 19.785 29.110000000000003 27.555000000000003 23.549999999999997 30-34 19.48 29.54 27.279999999999998 23.7 35-39 20.055 28.51 27.525 23.91 40-44 20.285 28.87 27.384999999999998 23.46 45-49 20.06 28.115000000000002 27.97 23.855 50-54 19.830000000000002 29.095 27.744999999999997 23.330000000000002 55-59 19.475 28.87 27.705000000000002 23.95 60-64 19.715 28.675 27.925 23.685000000000002 65-69 19.875 27.99 28.01 24.125 70-74 20.13 28.83 27.389999999999997 23.65 75-79 20.015 28.33 28.005000000000003 23.65 80-84 20.02 27.865000000000002 28.09 24.025 85-89 19.805 28.49 28.01 23.695 90-94 20.349999999999998 27.88 27.889999999999997 23.880000000000003 95-99 20.5 28.365000000000002 27.79 23.345 100-104 20.23 27.815 28.315 23.64 105-109 20.415 27.465 28.095 24.025 110-114 20.724999999999998 28.335 27.365000000000002 23.575 115-119 21.04 28.655 26.834999999999997 23.47 120-124 21.05 27.915 27.279999999999998 23.755000000000003 125-129 20.315 28.605000000000004 26.83 24.25 130-134 20.73 28.355000000000004 26.985 23.93 135-139 20.43 28.144999999999996 26.905 24.52 140-144 21.16 27.744999999999997 26.605 24.490000000000002 145-149 21.125 27.994999999999997 27.060000000000002 23.82 150-151 21.5375 27.287499999999998 27.187499999999996 23.9875 >>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 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.5 23 1.0 24 1.5 25 2.5 26 6.0 27 10.5 28 11.5 29 12.0 30 16.5 31 22.0 32 28.5 33 41.0 34 56.0 35 72.0 36 91.0 37 104.5 38 124.0 39 156.0 40 184.0 41 221.0 42 244.5 43 272.0 44 297.0 45 288.0 46 269.0 47 254.5 48 246.0 49 210.5 50 172.5 51 145.0 52 108.5 53 73.5 54 51.0 55 48.5 56 39.5 57 30.0 58 25.5 59 11.0 60 8.5 61 11.0 62 7.5 63 5.0 64 4.0 65 3.0 66 2.5 67 2.5 68 2.0 69 0.5 70 0.5 71 0.5 72 0.0 73 0.0 74 0.5 75 0.5 76 0.0 77 0.5 78 0.5 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 3.95 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 99.75 #Duplication Level Percentage of deduplicated Percentage of total 1 99.74937343358395 99.5 2 0.2506265664160401 0.5 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 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 0.05 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.15 0.0 0.0 0.0 0.0 86-87 0.275 0.0 0.0 0.0 0.0 88-89 0.4 0.0 0.0 0.0 0.0 90-91 0.475 0.0 0.0 0.0 0.0 92-93 0.5375000000000001 0.0 0.0 0.0 0.0 94-95 0.6125 0.0 0.0 0.0 0.0 96-97 0.7124999999999999 0.0 0.0 0.0 0.0 98-99 0.875 0.0 0.0 0.0 0.0 100-101 1.0625 0.0 0.0 0.0 0.0 102-103 1.3875000000000002 0.0 0.0 0.0 0.0 104-105 1.675 0.0 0.0 0.0 0.0 106-107 1.85 0.0 0.0 0.0 0.0 108-109 2.1375 0.0 0.0 0.0 0.0 110-111 2.55 0.0 0.0 0.0 0.0 112-113 2.9 0.0 0.0 0.0 0.0 114-115 3.3375000000000004 0.0 0.0 0.0 0.0 116-117 3.7874999999999996 0.0 0.0 0.0 0.0 118-119 4.1875 0.0 0.0 0.0 0.0 120-121 4.5125 0.0 0.0 0.0 0.0 122-123 4.975 0.0 0.0 0.0 0.0 124-125 5.5375 0.0 0.0 0.0 0.0 126-127 5.887499999999999 0.0 0.0 0.0 0.0 128-129 6.2625 0.0 0.0 0.0 0.0 130-131 7.0 0.0 0.0 0.0 0.0 132-133 7.7 0.0 0.0 0.0 0.0 134-135 8.3875 0.0 0.0 0.0 0.0 136-137 9.0625 0.0 0.0 0.0 0.0 138-139 9.775 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7171482 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171482_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 33.07675 33.0 33.0 34.0 32.0 34.0 2 33.16875 34.0 33.0 34.0 33.0 34.0 3 33.15025 34.0 33.0 34.0 33.0 34.0 4 33.1105 34.0 33.0 34.0 33.0 34.0 5 33.11125 34.0 33.0 34.0 33.0 34.0 6 37.33725 38.0 38.0 38.0 37.0 38.0 7 37.39425 38.0 38.0 38.0 37.0 38.0 8 37.4105 38.0 38.0 38.0 37.0 38.0 9 37.32025 38.0 38.0 38.0 37.0 38.0 10-14 37.25854999999999 38.0 38.0 38.0 37.0 38.0 15-19 37.27805000000001 38.0 38.0 38.0 37.0 38.0 20-24 37.2645 38.0 38.0 38.0 37.0 38.0 25-29 37.236000000000004 38.0 38.0 38.0 37.0 38.0 30-34 37.243399999999994 38.0 38.0 38.0 37.0 38.0 35-39 37.24515 38.0 38.0 38.0 36.8 38.0 40-44 37.1772 38.0 38.0 38.0 36.6 38.0 45-49 37.16985 38.0 38.0 38.0 37.0 38.0 50-54 37.14645 38.0 38.0 38.0 36.2 38.0 55-59 37.096 38.0 38.0 38.0 36.0 38.0 60-64 37.05645 38.0 38.0 38.0 36.0 38.0 65-69 37.0433 38.0 38.0 38.0 36.0 38.0 70-74 36.971500000000006 38.0 38.0 38.0 36.0 38.0 75-79 36.89515 38.0 38.0 38.0 35.8 38.0 80-84 36.88785 38.0 38.0 38.0 35.6 38.0 85-89 36.760799999999996 38.0 38.0 38.0 34.8 38.0 90-94 36.71810000000001 38.0 38.0 38.0 34.8 38.0 95-99 36.622249999999994 38.0 38.0 38.0 34.4 38.0 100-104 36.4499 38.0 38.0 38.0 34.0 38.0 105-109 36.322199999999995 38.0 38.0 38.0 34.0 38.0 110-114 36.1632 38.0 37.2 38.0 33.2 38.0 115-119 35.97195 38.0 37.0 38.0 32.4 38.0 120-124 35.798249999999996 38.0 36.6 38.0 31.8 38.0 125-129 35.7018 38.0 36.0 38.0 31.0 38.0 130-134 35.433499999999995 38.0 36.0 38.0 30.4 38.0 135-139 35.0411 38.0 35.2 38.0 27.6 38.0 140-144 34.8808 38.0 35.0 38.0 27.4 38.0 145-149 34.44225 38.0 33.8 38.0 24.6 38.0 150-151 31.57925 35.5 28.0 38.0 18.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 2.0 17 3.0 18 2.0 19 2.0 20 5.0 21 1.0 22 8.0 23 6.0 24 8.0 25 16.0 26 20.0 27 23.0 28 19.0 29 23.0 30 43.0 31 65.0 32 75.0 33 91.0 34 126.0 35 273.0 36 688.0 37 2501.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.199999999999996 20.625 16.175 27.0 2 26.674999999999997 27.400000000000002 29.5 16.425 3 22.400000000000002 27.925 29.599999999999998 20.075000000000003 4 24.175 33.875 23.625 18.325 5 25.674999999999997 35.825 21.575 16.925 6 22.25 37.0 23.65 17.1 7 21.375 21.3 37.974999999999994 19.35 8 21.875 26.400000000000002 27.224999999999998 24.5 9 22.15 25.624999999999996 28.825 23.400000000000002 10-14 24.02 29.005 26.085 20.89 15-19 23.52 28.515 27.165 20.8 20-24 24.285 28.075 27.145000000000003 20.495 25-29 24.29 28.395 27.115000000000002 20.200000000000003 30-34 24.485 28.34 27.455000000000002 19.72 35-39 24.11 28.360000000000003 26.985 20.544999999999998 40-44 23.82 28.74 26.615 20.825 45-49 23.46 27.805000000000003 28.044999999999998 20.69 50-54 23.605 28.044999999999998 27.685 20.665 55-59 24.044999999999998 28.355000000000004 27.400000000000002 20.200000000000003 60-64 23.765 28.144999999999996 27.36 20.73 65-69 23.735 28.415000000000003 27.485 20.365 70-74 23.98 28.294999999999998 27.384999999999998 20.34 75-79 24.12 27.685 27.375 20.82 80-84 24.0 27.779999999999998 28.29 19.93 85-89 23.799999999999997 28.185 27.500000000000004 20.515 90-94 24.3 28.050000000000004 27.800000000000004 19.85 95-99 24.235 27.71 27.345000000000002 20.71 100-104 24.345 27.48 27.965 20.21 105-109 23.849999999999998 28.42 27.889999999999997 19.84 110-114 24.015 28.444999999999997 27.405 20.135 115-119 24.255 28.134999999999998 27.57 20.04 120-124 24.6 27.965 27.575 19.86 125-129 25.290000000000003 28.275 27.21 19.225 130-134 25.595000000000002 28.375 27.265 18.765 135-139 25.685000000000002 27.925 27.169999999999998 19.220000000000002 140-144 25.895000000000003 28.38 26.745 18.98 145-149 26.484999999999996 27.455000000000002 27.195000000000004 18.865000000000002 150-151 25.7125 27.575 26.825 19.8875 >>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 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.5 24 1.5 25 2.0 26 1.5 27 2.5 28 5.5 29 8.0 30 10.0 31 8.5 32 11.0 33 18.0 34 36.0 35 58.0 36 72.0 37 92.0 38 125.5 39 156.0 40 196.0 41 241.0 42 264.5 43 293.5 44 298.0 45 293.0 46 290.5 47 258.0 48 229.5 49 209.5 50 181.0 51 156.0 52 125.5 53 91.5 54 73.0 55 49.5 56 32.0 57 26.5 58 22.5 59 18.5 60 10.5 61 6.5 62 5.5 63 5.0 64 3.5 65 2.5 66 1.5 67 0.5 68 0.5 69 1.0 70 1.0 71 0.0 72 0.0 73 0.0 74 0.5 75 1.0 76 0.5 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 99.72424166457759 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 warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.025 0.0 5 0.025 0.0 0.0 0.025 0.0 6 0.025 0.0 0.0 0.025 0.0 7 0.025 0.0 0.0 0.025 0.0 8 0.025 0.0 0.0 0.025 0.0 9 0.025 0.0 0.0 0.025 0.0 10-11 0.025 0.0 0.0 0.025 0.0 12-13 0.025 0.0 0.0 0.025 0.0 14-15 0.025 0.0 0.0 0.025 0.0 16-17 0.025 0.0 0.0 0.025 0.0 18-19 0.025 0.0 0.0 0.025 0.0 20-21 0.025 0.0 0.0 0.025 0.0 22-23 0.025 0.0 0.0 0.025 0.0 24-25 0.025 0.0 0.0 0.025 0.0 26-27 0.025 0.0 0.0 0.025 0.0 28-29 0.025 0.0 0.0 0.025 0.0 30-31 0.025 0.0 0.0 0.025 0.0 32-33 0.025 0.0 0.0 0.025 0.0 34-35 0.025 0.0 0.0 0.025 0.0 36-37 0.025 0.0 0.0 0.025 0.0 38-39 0.025 0.0 0.0 0.025 0.0 40-41 0.025 0.0 0.0 0.025 0.0 42-43 0.025 0.0 0.0 0.025 0.0 44-45 0.025 0.0 0.0 0.025 0.0 46-47 0.025 0.0 0.0 0.025 0.0 48-49 0.025 0.0 0.0 0.025 0.0 50-51 0.025 0.0 0.0 0.025 0.0 52-53 0.025 0.0 0.0 0.025 0.0 54-55 0.025 0.0 0.0 0.025 0.0 56-57 0.025 0.0 0.0 0.025 0.0 58-59 0.025 0.0 0.0 0.025 0.0 60-61 0.025 0.0 0.0 0.025 0.0 62-63 0.025 0.0 0.0 0.025 0.0 64-65 0.025 0.0 0.0 0.025 0.0 66-67 0.025 0.0 0.0 0.025 0.0 68-69 0.025 0.0 0.0 0.025 0.0 70-71 0.025 0.0 0.0 0.025 0.0 72-73 0.05 0.0 0.0 0.025 0.0 74-75 0.1 0.0 0.0 0.025 0.0 76-77 0.1125 0.0 0.0 0.025 0.0 78-79 0.125 0.0 0.0 0.025 0.0 80-81 0.125 0.0 0.0 0.025 0.0 82-83 0.125 0.0 0.0 0.025 0.0 84-85 0.15 0.0 0.0 0.025 0.0 86-87 0.275 0.0 0.0 0.025 0.0 88-89 0.425 0.0 0.0 0.025 0.0 90-91 0.5 0.0 0.0 0.025 0.0 92-93 0.5625 0.0 0.0 0.025 0.0 94-95 0.6375 0.0 0.0 0.025 0.0 96-97 0.7375 0.0 0.0 0.025 0.0 98-99 0.8999999999999999 0.0 0.0 0.025 0.0 100-101 1.0625 0.0 0.0 0.025 0.0 102-103 1.4125 0.0 0.0 0.025 0.0 104-105 1.7 0.0 0.0 0.025 0.0 106-107 1.8624999999999998 0.0 0.0 0.025 0.0 108-109 2.1375 0.0 0.0 0.025 0.0 110-111 2.5125 0.0 0.0 0.025 0.0 112-113 2.8375 0.0 0.0 0.025 0.0 114-115 3.2625 0.0 0.0 0.025 0.0 116-117 3.725 0.0 0.0 0.025 0.0 118-119 4.112500000000001 0.0 0.0 0.025 0.0 120-121 4.425 0.0 0.0 0.025 0.0 122-123 4.875 0.0 0.0 0.025 0.0 124-125 5.4625 0.0 0.0 0.025 0.0 126-127 5.824999999999999 0.0 0.0 0.025 0.0 128-129 6.2125 0.0 0.0 0.025 0.0 130-131 6.925 0.0 0.0 0.025 0.0 132-133 7.612500000000001 0.0 0.0 0.025 0.0 134-135 8.287500000000001 0.0 0.0 0.025 0.0 136-137 8.95 0.0 0.0 0.025 0.0 138-139 9.625 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAATGGC 10 0.006830828 145.0 3 AGTGTGT 20 0.00593511 29.0 140-144 >>END_MODULE Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586138 spots for SRR7171482.sra Written 586138 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra Read 586119 spots for SRR7171482.sra Written 586119 spots for SRR7171482.sra SRR ids: ['SRR7171482.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t7f236qi SRR7171482.sra spots: 11722399 blocks: [[1, 586119], [586120, 1172238], [1172239, 1758357], [1758358, 2344476], [2344477, 2930595], [2930596, 3516714], [3516715, 4102833], [4102834, 4688952], [4688953, 5275071], [5275072, 5861190], [5861191, 6447309], [6447310, 7033428], [7033429, 7619547], [7619548, 8205666], [8205667, 8791785], [8791786, 9377904], [9377905, 9964023], [9964024, 10550142], [10550143, 11136261], [11136262, 11722399]] SRR7171482 file size 3950636 SRR7171482 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 SRR7171482 SRR7171482_1.fastq SRR7171482_2.fastq Input file: SRR7171482_1.fastq Paired file: SRR7171482_2.fastq trimmed: SRR7171482-trimmed-pair1.fastq, SRR7171482-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 Thu Feb 13 19:34:15 2025 >> started Thu Feb 13 19:34:28 2025 >> done (12.469s) 11722399 read pairs processed; of these: 17 ( 0.00%) short read pairs filtered out after trimming by size control 1561 ( 0.01%) empty read pairs filtered out after trimming by size control 11720821 (99.99%) read pairs available; of these: 1852455 (15.80%) trimmed read pairs available after processing 9868366 (84.20%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 2 0.00% 21 0 0.00% 22 0 0.00% 23 1 0.00% 24 1 0.00% 25 0 0.00% 26 2 0.00% 27 2 0.00% 28 3 0.00% 29 0 0.00% 30 4 0.00% 31 0 0.00% 32 1 0.00% 33 3 0.00% 34 1 0.00% 35 2 0.00% 36 2 0.00% 37 1 0.00% 38 3 0.00% 39 6 0.00% 40 4 0.00% 41 9 0.00% 42 8 0.00% 43 2 0.00% 44 9 0.00% 45 8 0.00% 46 7 0.00% 47 11 0.00% 48 12 0.00% 49 13 0.00% 50 17 0.00% 51 25 0.00% 52 28 0.00% 53 30 0.00% 54 35 0.00% 55 40 0.00% 56 42 0.00% 57 53 0.00% 58 63 0.00% 59 62 0.00% 60 80 0.00% 61 93 0.00% 62 107 0.00% 63 141 0.00% 64 164 0.00% 65 146 0.00% 66 212 0.00% 67 245 0.00% 68 292 0.00% 69 305 0.00% 70 318 0.00% 71 456 0.00% 72 472 0.00% 73 651 0.01% 74 705 0.01% 75 828 0.01% 76 974 0.01% 77 968 0.01% 78 1123 0.01% 79 1292 0.01% 80 1537 0.01% 81 1723 0.01% 82 1956 0.02% 83 2251 0.02% 84 2603 0.02% 85 2827 0.02% 86 3117 0.03% 87 3549 0.03% 88 3826 0.03% 89 4296 0.04% 90 4760 0.04% 91 5208 0.04% 92 5827 0.05% 93 6577 0.06% 94 7125 0.06% 95 7877 0.07% 96 8438 0.07% 97 9175 0.08% 98 9781 0.08% 99 10463 0.09% 100 11214 0.10% 101 12123 0.10% 102 13208 0.11% 103 14024 0.12% 104 15063 0.13% 105 15985 0.14% 106 17134 0.15% 107 17713 0.15% 108 18599 0.16% 109 19340 0.17% 110 19827 0.17% 111 21017 0.18% 112 21931 0.19% 113 23245 0.20% 114 24390 0.21% 115 25503 0.22% 116 26495 0.23% 117 27530 0.23% 118 27866 0.24% 119 28909 0.25% 120 29548 0.25% 121 30784 0.26% 122 31488 0.27% 123 33055 0.28% 124 34352 0.29% 125 35031 0.30% 126 36169 0.31% 127 37168 0.32% 128 37555 0.32% 129 38701 0.33% 130 38904 0.33% 131 39808 0.34% 132 40487 0.35% 133 41782 0.36% 134 42805 0.37% 135 43965 0.38% 136 44689 0.38% 137 45679 0.39% 138 46197 0.39% 139 46914 0.40% 140 46927 0.40% 141 47981 0.41% 142 49048 0.42% 143 49648 0.42% 144 50651 0.43% 145 52004 0.44% 146 52071 0.44% 147 53251 0.45% 148 53483 0.46% 149 53467 0.46% 150 54726 0.47% 151 9868366 84.20% 11720821 reads passed initial QC criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=3.04 fanout-score-rank=27 prefix-density=0.54 prefix-fanout=2.1 sequence=CACTTGCAGCCATTCTCAGCACCAAAGTTCATCTCAGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=162.59 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=12.4 sequence=TCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAG criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=2.93 fanout-score-rank=24 prefix-density=0.44 prefix-fanout=2.9 sequence=ATGTACCCTGACTTAGGTTTCTCAGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=88.59 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=8.9 sequence=AGAAAAGATAAGCTAGGCAAGATGGTTTTACTAGACAAGATGTGGGATGATGTTGTTGCTGGACCTCAGCCAGAACGTGGCCTTGG SRR7171482 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 19:35:14 Started mapping on | Feb 13 19:35:14 Finished on | Feb 13 19:36:38 Mapping speed, Million of reads per hour | 502.32 Number of input reads | 11720821 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 10939957 Uniquely mapped reads % | 93.34% Average mapped length | 293.58 Number of splices: Total | 10400859 Number of splices: Annotated (sjdb) | 10170526 Number of splices: GT/AG | 10229585 Number of splices: GC/AG | 133682 Number of splices: AT/AC | 8471 Number of splices: Non-canonical | 29121 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.04% Deletion average length | 2.54 Insertion rate per base | 0.02% Insertion average length | 2.50 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 264626 % of reads mapped to multiple loci | 2.26% Number of reads mapped to too many loci | 124777 % of reads mapped to too many loci | 1.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.12% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 516238 516238 516238 N_multimapping 264626 264626 264626 N_noFeature 324872 10840751 360910 N_ambiguous 118051 637 54527 UnstrandedReadsAssigned:10497034 PositiveStrandReadsAssigned:98569 NegativeStrandReadsAssigned:10524520 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171482 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: SRR7171482-trimmed-pair1.fastq SRR7171482-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,720,821 reads, 10,596,747 reads pseudoaligned [quant] estimated average fragment length: 214.995 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,102 rounds 52401 SRR7171482.ke.tsv 34699 SRR7171482.se.tsv 87100 total ==> SRR7171482.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1804.01 1049 50.8249 Potri.005G024800.1.v4.1 1035 821.005 511 54.4019 Potri.004G059700.1.v4.1 961 747.015 29 3.39319 Potri.007G009000.2.v4.1 1416 1202.01 0 0 Potri.003G141000.2.v4.1 2943 2729.01 567 18.1601 Potri.016G087400.1.v4.1 270 88.1406 736 729.862 Potri.015G069301.1.v4.1 564 351.325 0 0 Potri.010G195200.1.v4.1 1773 1559.01 202 11.3251 Potri.012G127500.1.v4.1 977 763.005 6739 771.982 ==> SRR7171482.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 152 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 485 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 299 SRR7171482 completed mapping pipeline successfully