Starting /dee2/code/volunteer_pipeline.sh SRR7171866 current disk space = 3088543313920 free memory = 1427583312 SRR7171866 SRAfilesize 1b6ef437c1dcb154382ea5c9b69757e3 SRR7171866.sra SRR7171866.sra file validated SRR7171866 is paired end SRR7171866 is conventional basespace SRR7171866 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171866_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 28.7485 32.0 25.0 33.0 18.0 34.0 2 32.33425 33.0 32.0 33.0 32.0 34.0 3 32.127 33.0 33.0 33.0 29.0 34.0 4 32.7545 33.0 33.0 34.0 31.0 34.0 5 32.9665 33.0 33.0 34.0 32.0 34.0 6 36.216 38.0 36.0 38.0 33.0 38.0 7 37.1045 38.0 38.0 38.0 36.0 38.0 8 37.17875 38.0 38.0 38.0 36.0 38.0 9 37.41575 38.0 38.0 38.0 37.0 38.0 10-14 37.55615 38.0 38.0 38.0 37.4 38.0 15-19 37.52635 38.0 38.0 38.0 37.2 38.0 20-24 37.513250000000006 38.0 38.0 38.0 37.6 38.0 25-29 37.54445 38.0 38.0 38.0 37.8 38.0 30-34 37.48885 38.0 38.0 38.0 37.2 38.0 35-39 37.4604 38.0 38.0 38.0 37.2 38.0 40-44 37.452650000000006 38.0 38.0 38.0 37.0 38.0 45-49 37.4223 38.0 38.0 38.0 37.0 38.0 50-54 37.3776 38.0 38.0 38.0 37.0 38.0 55-59 37.3108 38.0 38.0 38.0 36.8 38.0 60-64 37.2701 38.0 38.0 38.0 36.6 38.0 65-69 37.2002 38.0 38.0 38.0 36.0 38.0 70-74 37.1343 38.0 38.0 38.0 36.0 38.0 75-79 37.04705 38.0 38.0 38.0 36.0 38.0 80-84 37.001549999999995 38.0 38.0 38.0 36.0 38.0 85-89 36.95255 38.0 38.0 38.0 35.6 38.0 90-94 36.8522 38.0 38.0 38.0 35.0 38.0 95-99 36.765100000000004 38.0 38.0 38.0 35.0 38.0 100-104 36.6609 38.0 38.0 38.0 34.8 38.0 105-109 36.42575000000001 38.0 37.8 38.0 34.0 38.0 110-114 36.3544 38.0 37.8 38.0 34.0 38.0 115-119 36.1971 38.0 37.0 38.0 33.6 38.0 120-124 36.00985 38.0 37.0 38.0 33.0 38.0 125-129 35.872400000000006 38.0 36.8 38.0 33.0 38.0 130-134 35.647749999999995 38.0 36.2 38.0 31.4 38.0 135-139 35.31565 38.0 36.0 38.0 30.6 38.0 140-144 34.929449999999996 38.0 35.2 38.0 28.2 38.0 145-149 34.47525 38.0 35.0 38.0 27.6 38.0 150-151 31.306625 36.5 31.5 38.0 12.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 2.0 15 2.0 16 1.0 17 1.0 18 4.0 19 1.0 20 2.0 21 3.0 22 8.0 23 6.0 24 6.0 25 8.0 26 8.0 27 18.0 28 16.0 29 29.0 30 22.0 31 46.0 32 52.0 33 84.0 34 141.0 35 284.0 36 733.0 37 2523.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.550000000000004 13.350000000000001 12.65 34.449999999999996 2 21.355338834708675 20.005001250312578 36.05901475368842 22.58064516129032 3 19.0 27.450000000000003 25.5 28.050000000000004 4 23.200000000000003 36.0 20.849999999999998 19.950000000000003 5 21.75 35.3 24.45 18.5 6 18.65 36.225 25.75 19.375 7 13.55 21.875 44.3 20.275000000000002 8 16.925 22.575 29.875 30.625000000000004 9 19.0 23.025000000000002 31.025000000000002 26.950000000000003 10-14 20.315 29.154999999999998 26.834999999999997 23.695 15-19 20.385 28.139999999999997 28.005000000000003 23.47 20-24 20.25 27.925 27.87 23.955000000000002 25-29 19.685 28.48 27.935 23.9 30-34 19.814999999999998 28.21 28.144999999999996 23.830000000000002 35-39 20.119999999999997 28.425 27.98 23.474999999999998 40-44 19.71 28.15 27.76 24.38 45-49 20.305 27.950000000000003 28.275 23.47 50-54 20.04 28.754999999999995 27.32 23.885 55-59 20.674999999999997 28.22 27.700000000000003 23.405 60-64 20.325 27.950000000000003 27.815 23.91 65-69 20.265 28.285 27.785 23.665 70-74 20.195 28.16 27.67 23.974999999999998 75-79 20.615 27.92 27.93 23.535 80-84 20.515 28.235 27.474999999999998 23.775 85-89 20.24 28.12 27.355 24.285 90-94 21.115000000000002 27.625 27.61 23.65 95-99 20.474999999999998 27.825 27.815 23.885 100-104 20.455000000000002 28.275 27.71 23.56 105-109 20.580000000000002 28.51 27.88 23.03 110-114 20.8 28.08 27.200000000000003 23.919999999999998 115-119 20.74 28.02 27.82 23.419999999999998 120-124 21.13 28.16 27.365000000000002 23.345 125-129 20.765 27.639999999999997 27.77 23.825 130-134 20.735 27.455000000000002 27.97 23.84 135-139 20.625 28.09 27.855 23.43 140-144 21.14 28.384999999999998 27.38 23.095 145-149 20.46 27.755000000000003 27.705000000000002 24.08 150-151 20.8625 27.3 28.799999999999997 23.0375 >>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 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 1.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.5 23 0.5 24 1.0 25 2.0 26 4.0 27 8.5 28 11.0 29 11.5 30 17.0 31 22.0 32 28.0 33 35.5 34 53.0 35 75.0 36 85.0 37 93.5 38 121.5 39 163.5 40 197.5 41 224.0 42 232.5 43 256.5 44 280.0 45 266.0 46 256.0 47 246.0 48 239.5 49 229.5 50 191.5 51 152.0 52 126.0 53 94.5 54 66.0 55 52.5 56 37.5 57 27.0 58 21.0 59 12.0 60 12.0 61 13.0 62 7.5 63 6.0 64 5.5 65 3.0 66 2.0 67 3.5 68 2.0 69 0.5 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 0.0 2 0.025 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 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.037500000000000006 0.0 0.0 0.0 0.0 88-89 0.0625 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.075 0.0 0.0 0.0 0.0 94-95 0.075 0.0 0.0 0.0 0.0 96-97 0.1 0.0 0.0 0.0 0.0 98-99 0.125 0.0 0.0 0.0 0.0 100-101 0.1375 0.0 0.0 0.0 0.0 102-103 0.2 0.0 0.0 0.0 0.0 104-105 0.225 0.0 0.0 0.0 0.0 106-107 0.2875 0.0 0.0 0.0 0.0 108-109 0.3625 0.0 0.0 0.0 0.0 110-111 0.4125 0.0 0.0 0.0 0.0 112-113 0.4875 0.0 0.0 0.0 0.0 114-115 0.5875 0.0 0.0 0.0 0.0 116-117 0.6875 0.0 0.0 0.0 0.0 118-119 0.7875 0.0 0.0 0.0 0.0 120-121 1.0 0.0 0.0 0.0 0.0 122-123 1.1625 0.0 0.0 0.0 0.0 124-125 1.2875 0.0 0.0 0.0 0.0 126-127 1.475 0.0 0.0 0.0 0.0 128-129 1.6 0.0 0.0 0.0 0.0 130-131 1.7625000000000002 0.0 0.0 0.0 0.0 132-133 1.875 0.0 0.0 0.0 0.0 134-135 2.1 0.0 0.0 0.0 0.0 136-137 2.45 0.0 0.0 0.0 0.0 138-139 2.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTATAGA 10 0.0065789125 146.81013 1 >>END_MODULE SRR7171866 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171866_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 33.09675 33.0 33.0 34.0 32.0 34.0 2 33.10825 34.0 33.0 34.0 32.0 34.0 3 33.1895 34.0 33.0 34.0 33.0 34.0 4 33.223 34.0 33.0 34.0 33.0 34.0 5 33.251 34.0 33.0 34.0 33.0 34.0 6 37.4785 38.0 38.0 38.0 38.0 38.0 7 37.43625 38.0 38.0 38.0 37.0 38.0 8 37.37675 38.0 38.0 38.0 38.0 38.0 9 37.33325 38.0 38.0 38.0 37.0 38.0 10-14 37.446999999999996 38.0 38.0 38.0 37.4 38.0 15-19 37.41105 38.0 38.0 38.0 37.2 38.0 20-24 37.3649 38.0 38.0 38.0 37.0 38.0 25-29 37.38595 38.0 38.0 38.0 37.2 38.0 30-34 37.3314 38.0 38.0 38.0 37.0 38.0 35-39 37.2654 38.0 38.0 38.0 37.0 38.0 40-44 37.10830000000001 38.0 38.0 38.0 36.8 38.0 45-49 37.27845 38.0 38.0 38.0 37.0 38.0 50-54 37.26635 38.0 38.0 38.0 37.0 38.0 55-59 37.221799999999995 38.0 38.0 38.0 37.0 38.0 60-64 37.1475 38.0 38.0 38.0 36.2 38.0 65-69 37.0923 38.0 38.0 38.0 36.0 38.0 70-74 36.984899999999996 38.0 38.0 38.0 36.0 38.0 75-79 37.0101 38.0 38.0 38.0 36.0 38.0 80-84 36.91995 38.0 38.0 38.0 36.0 38.0 85-89 36.86215 38.0 38.0 38.0 35.6 38.0 90-94 36.68035 38.0 38.0 38.0 35.0 38.0 95-99 36.628 38.0 38.0 38.0 34.6 38.0 100-104 36.444950000000006 38.0 38.0 38.0 34.0 38.0 105-109 36.2686 38.0 37.8 38.0 33.8 38.0 110-114 36.1961 38.0 37.6 38.0 33.8 38.0 115-119 36.0484 38.0 37.0 38.0 33.2 38.0 120-124 35.904900000000005 38.0 37.0 38.0 33.0 38.0 125-129 35.68025 38.0 36.6 38.0 31.8 38.0 130-134 35.2753 38.0 36.0 38.0 29.6 38.0 135-139 35.0718 38.0 35.6 38.0 29.0 38.0 140-144 34.753499999999995 38.0 35.0 38.0 28.0 38.0 145-149 34.1075 38.0 35.0 38.0 25.0 38.0 150-151 30.576625 36.5 29.0 38.0 8.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 3 0.0 4 2.0 5 1.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 1.0 13 1.0 14 2.0 15 2.0 16 2.0 17 2.0 18 0.0 19 4.0 20 6.0 21 10.0 22 11.0 23 8.0 24 6.0 25 12.0 26 12.0 27 18.0 28 28.0 29 18.0 30 27.0 31 47.0 32 44.0 33 83.0 34 125.0 35 261.0 36 656.0 37 2608.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.225 16.35 16.275000000000002 28.15 2 25.575 23.150000000000002 34.225 17.05 3 21.8 27.6 30.125 20.474999999999998 4 24.55 36.175000000000004 20.875 18.4 5 22.85 37.775 21.725 17.65 6 18.75 38.074999999999996 23.95 19.225 7 18.65 16.875 43.425000000000004 21.05 8 22.075 22.35 27.05 28.525 9 21.125 25.95 28.725 24.2 10-14 22.875 28.58 26.8 21.745 15-19 22.455 28.675 27.694999999999997 21.175 20-24 23.119999999999997 28.345 27.26 21.275 25-29 23.18 28.27 27.865000000000002 20.685000000000002 30-34 22.755 28.275 27.355 21.615000000000002 35-39 22.899579915983196 27.970594118823765 27.775555111022204 21.354270854170835 40-44 23.166023166023166 28.02487088201374 27.934613648899365 20.874492303063732 45-49 23.225 27.884999999999998 27.52 21.37 50-54 23.18 28.28 27.644999999999996 20.895 55-59 23.3 27.894999999999996 27.62 21.185000000000002 60-64 23.064999999999998 28.215 27.639999999999997 21.08 65-69 23.89 27.839999999999996 27.095000000000002 21.175 70-74 22.75 28.76 27.565 20.925 75-79 23.785 27.894999999999996 27.150000000000002 21.17 80-84 23.32 28.044999999999998 27.495000000000005 21.14 85-89 23.46 28.249999999999996 27.575 20.715 90-94 23.66 28.225 27.694999999999997 20.419999999999998 95-99 23.65 28.060000000000002 27.345000000000002 20.945 100-104 23.855 27.915 27.42 20.810000000000002 105-109 23.775 28.544999999999998 27.51 20.169999999999998 110-114 24.11 28.185 27.169999999999998 20.535 115-119 24.165 28.050000000000004 27.445000000000004 20.34 120-124 23.585 28.435 27.11 20.87 125-129 23.905 28.15 27.52 20.424999999999997 130-134 23.71 27.584999999999997 27.689999999999998 21.015 135-139 24.345 28.110000000000003 26.8 20.745 140-144 24.635 27.73 27.139999999999997 20.495 145-149 24.505 27.975 27.105 20.415 150-151 24.2375 27.8375 27.187499999999996 20.7375 >>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 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 0.0 23 0.5 24 2.0 25 1.5 26 1.0 27 3.0 28 4.5 29 5.0 30 6.5 31 12.5 32 21.0 33 25.5 34 34.0 35 49.0 36 68.0 37 107.0 38 139.5 39 153.5 40 182.0 41 231.5 42 278.5 43 288.5 44 289.0 45 294.5 46 279.5 47 274.5 48 261.5 49 212.0 50 175.0 51 144.0 52 115.0 53 92.5 54 59.0 55 44.0 56 37.5 57 29.0 58 20.5 59 11.0 60 9.5 61 9.5 62 7.0 63 4.5 64 3.5 65 2.0 66 1.5 67 1.5 68 1.5 69 1.5 70 1.5 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 0.02 40-44 0.28500000000000003 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 99.675 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67394030599448 99.35000000000001 2 0.32605969400551793 0.65 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 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.037500000000000006 0.0 0.0 0.0 0.0 88-89 0.0625 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.075 0.0 0.0 0.0 0.0 94-95 0.075 0.0 0.0 0.0 0.0 96-97 0.1 0.0 0.0 0.0 0.0 98-99 0.125 0.0 0.0 0.0 0.0 100-101 0.1375 0.0 0.0 0.0 0.0 102-103 0.2 0.0 0.0 0.0 0.0 104-105 0.225 0.0 0.0 0.0 0.0 106-107 0.2875 0.0 0.0 0.0 0.0 108-109 0.3875 0.0 0.0 0.0 0.0 110-111 0.4375 0.0 0.0 0.0 0.0 112-113 0.4875 0.0 0.0 0.0 0.0 114-115 0.5875 0.0 0.0 0.0 0.0 116-117 0.6875 0.0 0.0 0.0 0.0 118-119 0.7875 0.0 0.0 0.0 0.0 120-121 1.0 0.0 0.0 0.0 0.0 122-123 1.1625 0.0 0.0 0.0 0.0 124-125 1.2875 0.0 0.0 0.0 0.0 126-127 1.475 0.0 0.0 0.0 0.0 128-129 1.6 0.0 0.0 0.0 0.0 130-131 1.7625000000000002 0.0 0.0 0.0 0.0 132-133 1.875 0.0 0.0 0.0 0.0 134-135 2.0875000000000004 0.0 0.0 0.0 0.0 136-137 2.425 0.0 0.0 0.0 0.0 138-139 2.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677254 spots for SRR7171866.sra Written 677254 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra Read 677246 spots for SRR7171866.sra Written 677246 spots for SRR7171866.sra SRR ids: ['SRR7171866.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_eocpplr7 SRR7171866.sra spots: 13544928 blocks: [[1, 677246], [677247, 1354492], [1354493, 2031738], [2031739, 2708984], [2708985, 3386230], [3386231, 4063476], [4063477, 4740722], [4740723, 5417968], [5417969, 6095214], [6095215, 6772460], [6772461, 7449706], [7449707, 8126952], [8126953, 8804198], [8804199, 9481444], [9481445, 10158690], [10158691, 10835936], [10835937, 11513182], [11513183, 12190428], [12190429, 12867674], [12867675, 13544928]] SRR7171866 file size 4568231 SRR7171866 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 SRR7171866 SRR7171866_1.fastq SRR7171866_2.fastq Input file: SRR7171866_1.fastq Paired file: SRR7171866_2.fastq trimmed: SRR7171866-trimmed-pair1.fastq, SRR7171866-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 22:03:33 2025 >> started Thu Feb 13 22:03:57 2025 >> done (23.687s) 13544928 read pairs processed; of these: 8048 ( 0.06%) short read pairs filtered out after trimming by size control 5342 ( 0.04%) empty read pairs filtered out after trimming by size control 13531538 (99.90%) read pairs available; of these: 5290107 (39.09%) trimmed read pairs available after processing 8241431 (60.91%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 1 0.00% 21 3 0.00% 22 4 0.00% 23 4 0.00% 24 2 0.00% 25 3 0.00% 26 3 0.00% 27 2 0.00% 28 5 0.00% 29 4 0.00% 30 4 0.00% 31 0 0.00% 32 2 0.00% 33 5 0.00% 34 0 0.00% 35 1 0.00% 36 0 0.00% 37 1 0.00% 38 4 0.00% 39 4 0.00% 40 3 0.00% 41 2 0.00% 42 6 0.00% 43 2 0.00% 44 10 0.00% 45 7 0.00% 46 4 0.00% 47 8 0.00% 48 7 0.00% 49 9 0.00% 50 8 0.00% 51 13 0.00% 52 13 0.00% 53 11 0.00% 54 23 0.00% 55 21 0.00% 56 25 0.00% 57 27 0.00% 58 29 0.00% 59 39 0.00% 60 34 0.00% 61 53 0.00% 62 56 0.00% 63 43 0.00% 64 71 0.00% 65 73 0.00% 66 86 0.00% 67 79 0.00% 68 109 0.00% 69 109 0.00% 70 126 0.00% 71 162 0.00% 72 183 0.00% 73 205 0.00% 74 241 0.00% 75 263 0.00% 76 322 0.00% 77 366 0.00% 78 366 0.00% 79 427 0.00% 80 490 0.00% 81 612 0.00% 82 638 0.00% 83 750 0.01% 84 1142 0.01% 85 1524 0.01% 86 1684 0.01% 87 1871 0.01% 88 1988 0.01% 89 2106 0.02% 90 2101 0.02% 91 2471 0.02% 92 2594 0.02% 93 2681 0.02% 94 2892 0.02% 95 3026 0.02% 96 3226 0.02% 97 3473 0.03% 98 3627 0.03% 99 3946 0.03% 100 4155 0.03% 101 4609 0.03% 102 4700 0.03% 103 5333 0.04% 104 5527 0.04% 105 5865 0.04% 106 6261 0.05% 107 6373 0.05% 108 7082 0.05% 109 7359 0.05% 110 7893 0.06% 111 8486 0.06% 112 8972 0.07% 113 9397 0.07% 114 10173 0.08% 115 10753 0.08% 116 11191 0.08% 117 11619 0.09% 118 12149 0.09% 119 12917 0.10% 120 13408 0.10% 121 14155 0.10% 122 14661 0.11% 123 15462 0.11% 124 16597 0.12% 125 17246 0.13% 126 18206 0.13% 127 19302 0.14% 128 20203 0.15% 129 21212 0.16% 130 22389 0.17% 131 24240 0.18% 132 25811 0.19% 133 27547 0.20% 134 28948 0.21% 135 31180 0.23% 136 33481 0.25% 137 36252 0.27% 138 39253 0.29% 139 42526 0.31% 140 46863 0.35% 141 52610 0.39% 142 59382 0.44% 143 67923 0.50% 144 80763 0.60% 145 99782 0.74% 146 127806 0.94% 147 177472 1.31% 148 285841 2.11% 149 590959 4.37% 150 3011274 22.25% 151 8241431 60.91% 13531538 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=4.94 fanout-score-rank=18 prefix-density=0.34 prefix-fanout=3.2 sequence=TCCTTGTCCTGGATCTTGGCCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=130.93 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=11.3 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCAC criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=4.69 fanout-score-rank=15 prefix-density=0.42 prefix-fanout=3.4 sequence=CTGCAAATGTGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=28.84 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=5.6 sequence=GAAGGATCTGTTTAATTTGAGACAGAAAACATGAAATCCTCCTACACTTTCTTCATTCTTTTCTCACTCTTTTCGTTTGCTAACGTGATCGGTGCTAGAAAAGACACTGGAGAGTATTGGAGAGCTGTCATGAAAGATCAGCCCATGCCAGAAGCAATACAAGGCCTTATTCGCGAAACCACATTGTCATCAGTCTCCAATGAGAAAGCCGATTGCCACACAACCGAGTCCAATGAAAAGAATAATTTTGTCAAGGATTTTGGCCCACAGCCTACTGCTACATCTTATGACAATGGTATAAAACCAGCAAAAGACAAGTCCTTCTCGAAAGATTTCCACCCAAACTCTCAGTTGTTCCTTTACAATGATGGTGTCGTTAAAGGAGAGAGATCCTTTGCTGAGGATCTTGAGCCGAGGCCTAATGTGTCCGTTTACCACGACGACGCTCCTCTTAAAGGAGAAAAATCTTTTCCGGAGGACTTCGAACCAGGGCCTAACATATCAGTTTATG SRR7171866 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 22:04:43 Started mapping on | Feb 13 22:04:44 Finished on | Feb 13 22:06:33 Mapping speed, Million of reads per hour | 446.91 Number of input reads | 13531538 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 12631409 Uniquely mapped reads % | 93.35% Average mapped length | 297.22 Number of splices: Total | 12914171 Number of splices: Annotated (sjdb) | 12689509 Number of splices: GT/AG | 12711330 Number of splices: GC/AG | 160681 Number of splices: AT/AC | 10437 Number of splices: Non-canonical | 31723 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.59 Insertion rate per base | 0.02% Insertion average length | 2.57 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 371236 % of reads mapped to multiple loci | 2.74% Number of reads mapped to too many loci | 53342 % of reads mapped to too many loci | 0.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.44% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 537580 537580 537580 N_multimapping 371236 371236 371236 N_noFeature 261698 12524440 308134 N_ambiguous 137693 857 76589 UnstrandedReadsAssigned:12232018 PositiveStrandReadsAssigned:106112 NegativeStrandReadsAssigned:12246686 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7171866 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: SRR7171866-trimmed-pair1.fastq SRR7171866-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,531,538 reads, 12,088,216 reads pseudoaligned [quant] estimated average fragment length: 268.906 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,098 rounds 52401 SRR7171866.ke.tsv 34699 SRR7171866.se.tsv 87100 total ==> SRR7171866.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1750.09 1022 47.2948 Potri.005G024800.1.v4.1 1035 767.094 260 27.4504 Potri.004G059700.1.v4.1 961 693.123 12 1.40215 Potri.007G009000.2.v4.1 1416 1148.09 0 0 Potri.003G141000.2.v4.1 2943 2675.09 590.199 17.8683 Potri.016G087400.1.v4.1 270 66.2101 739 903.951 Potri.015G069301.1.v4.1 564 302.038 0 0 Potri.010G195200.1.v4.1 1773 1505.09 143 7.69479 Potri.012G127500.1.v4.1 977 709.106 2022 230.937 ==> SRR7171866.se.tsv <== Potri.001G166300.v4.1 2 Potri.001G448400.v4.1 33 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 307 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 87 SRR7171866 completed mapping pipeline successfully