Starting /dee2/code/volunteer_pipeline.sh SRR6257541 current disk space = 1544257576960 free memory = 1598720456 SRR6257541 SRAfilesize 6b4937b867f5ba6873b0fde4ea2f079b SRR6257541.sra SRR6257541.sra file validated SRR6257541 is paired end SRR6257541 is conventional basespace SRR6257541 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6257541_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.1275 32.0 25.0 33.0 18.0 34.0 2 30.70075 31.0 29.0 33.0 27.0 34.0 3 32.2785 33.0 31.0 33.0 30.0 34.0 4 32.9225 33.0 33.0 33.0 32.0 34.0 5 32.78775 33.0 33.0 33.0 32.0 34.0 6 37.11675 38.0 37.0 38.0 36.0 38.0 7 37.656 38.0 38.0 38.0 37.0 38.0 8 37.72675 38.0 38.0 38.0 38.0 38.0 9 37.78725 38.0 38.0 38.0 38.0 38.0 10-14 37.7947 38.0 38.0 38.0 38.0 38.0 15-19 37.787850000000006 38.0 38.0 38.0 38.0 38.0 20-24 37.795350000000006 38.0 38.0 38.0 38.0 38.0 25-29 37.78735 38.0 38.0 38.0 38.0 38.0 30-34 37.77775 38.0 38.0 38.0 38.0 38.0 35-39 37.773700000000005 38.0 38.0 38.0 38.0 38.0 40-44 37.7562 38.0 38.0 38.0 38.0 38.0 45-49 37.7413 38.0 38.0 38.0 38.0 38.0 50-54 37.7247 38.0 38.0 38.0 38.0 38.0 55-59 37.7102 38.0 38.0 38.0 38.0 38.0 60-64 37.6956 38.0 38.0 38.0 38.0 38.0 65-69 37.631449999999994 38.0 38.0 38.0 38.0 38.0 70-74 37.62785 38.0 38.0 38.0 38.0 38.0 75-79 37.61385 38.0 38.0 38.0 38.0 38.0 80-84 37.576350000000005 38.0 38.0 38.0 38.0 38.0 85-89 37.544149999999995 38.0 38.0 38.0 38.0 38.0 90-94 37.548 38.0 38.0 38.0 38.0 38.0 95-99 37.50795 38.0 38.0 38.0 37.8 38.0 100-104 37.49805 38.0 38.0 38.0 37.8 38.0 105-109 37.41845 38.0 38.0 38.0 37.0 38.0 110-114 37.394999999999996 38.0 38.0 38.0 37.2 38.0 115-119 37.31525 38.0 38.0 38.0 37.0 38.0 120-124 37.28915 38.0 38.0 38.0 36.6 38.0 125-129 37.1953 38.0 38.0 38.0 36.0 38.0 130-134 37.16375 38.0 38.0 38.0 36.0 38.0 135-139 37.0637 38.0 38.0 38.0 36.0 38.0 140-144 36.96515 38.0 38.0 38.0 35.6 38.0 145-149 36.77435 38.0 38.0 38.0 35.0 38.0 150-151 35.145875000000004 38.0 36.0 38.0 31.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 0.0 15 1.0 16 0.0 17 0.0 18 0.0 19 2.0 20 0.0 21 2.0 22 1.0 23 4.0 24 2.0 25 2.0 26 4.0 27 2.0 28 3.0 29 8.0 30 8.0 31 18.0 32 26.0 33 27.0 34 51.0 35 74.0 36 250.0 37 3514.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.57910750507099 10.16734279918864 7.834685598377282 42.418864097363084 2 23.3 16.275000000000002 36.725 23.7 3 21.5 20.424999999999997 23.95 34.125 4 27.400000000000002 28.125 21.125 23.35 5 25.074999999999996 32.1 23.7 19.125 6 20.125 34.325 24.825 20.724999999999998 7 15.525 22.15 43.3 19.025 8 19.2 23.400000000000002 30.925000000000004 26.474999999999998 9 19.650000000000002 21.275 32.6 26.474999999999998 10-14 22.63 27.400000000000002 26.08 23.89 15-19 22.86 26.265 26.455000000000002 24.42 20-24 22.705000000000002 26.5 26.625 24.169999999999998 25-29 22.465 26.08 26.75 24.705 30-34 22.085 26.14 27.29 24.485 35-39 22.84 26.334999999999997 26.305 24.52 40-44 22.525000000000002 25.995 26.884999999999998 24.595 45-49 22.63 25.86 26.584999999999997 24.925 50-54 22.35 25.869999999999997 26.71 25.069999999999997 55-59 22.155 26.19 26.32 25.335 60-64 22.285 25.729999999999997 26.779999999999998 25.205 65-69 22.945 26.06 25.83 25.165 70-74 22.6 25.755 26.88 24.765 75-79 22.63 25.825 26.19 25.355 80-84 22.025 26.095000000000002 26.279999999999998 25.6 85-89 22.634999999999998 25.724999999999998 26.240000000000002 25.4 90-94 22.259999999999998 25.540000000000003 27.02 25.180000000000003 95-99 22.465 25.77 26.255 25.509999999999998 100-104 23.189999999999998 25.629999999999995 26.07 25.11 105-109 23.365 25.505 26.5 24.63 110-114 23.494999999999997 26.325 25.94 24.240000000000002 115-119 23.35 26.13 25.82 24.7 120-124 23.25 25.515 25.91 25.324999999999996 125-129 22.93 26.105 25.455 25.509999999999998 130-134 23.265 25.335 26.090000000000003 25.31 135-139 23.095 25.580000000000002 25.75 25.575 140-144 23.35 26.3 25.445 24.905 145-149 22.97 25.645 25.75 25.635 150-151 22.95 25.837500000000002 25.412499999999998 25.8 >>END_MODULE >>Per sequence GC content warn #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 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.5 27 1.5 28 3.0 29 5.5 30 8.0 31 11.5 32 15.0 33 20.5 34 30.5 35 37.5 36 55.0 37 78.0 38 102.0 39 119.0 40 144.5 41 177.5 42 210.0 43 207.0 44 220.5 45 243.0 46 224.0 47 214.5 48 198.0 49 194.5 50 183.0 51 154.0 52 131.5 53 122.5 54 111.5 55 92.5 56 78.5 57 77.5 58 75.0 59 57.5 60 51.0 61 56.0 62 45.5 63 29.0 64 27.5 65 32.0 66 26.5 67 22.5 68 19.5 69 13.5 70 13.5 71 12.0 72 10.0 73 9.5 74 8.5 75 5.5 76 5.5 77 5.0 78 1.5 79 0.5 80 0.5 81 0.5 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 1.4000000000000001 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 99.175 #Duplication Level Percentage of deduplicated Percentage of total 1 99.26896899420217 98.45 2 0.6806150743634989 1.35 3 0.025207965717166627 0.075 4 0.0 0.0 5 0.025207965717166627 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 CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 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 0.025 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 0.05 0.0 0.0 0.0 0.0 68-69 0.0875 0.0 0.0 0.0 0.0 70-71 0.1375 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2375 0.0 0.0 0.0 0.0 82-83 0.2625 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.3125 0.0 0.0 0.0 0.0 90-91 0.42500000000000004 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.625 0.0 0.0 0.0 0.0 96-97 0.6875 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.9875 0.0 0.0 0.0 0.0 102-103 1.225 0.0 0.0 0.0 0.0 104-105 1.4375 0.0 0.0 0.0 0.0 106-107 1.725 0.0 0.0 0.0 0.0 108-109 1.9625000000000001 0.0 0.0 0.0 0.0 110-111 2.2375 0.0 0.0 0.0 0.0 112-113 2.475 0.0 0.0 0.0 0.0 114-115 2.7 0.0 0.0 0.0 0.0 116-117 2.9875 0.0 0.0 0.0 0.0 118-119 3.2375 0.0 0.0 0.0 0.0 120-121 3.625 0.0 0.0 0.0 0.0 122-123 4.125 0.0 0.0 0.0 0.0 124-125 4.475 0.0 0.0 0.0 0.0 126-127 4.8 0.0 0.0 0.0 0.0 128-129 5.3125 0.0 0.0 0.0 0.0 130-131 5.7375 0.0 0.0 0.0 0.0 132-133 6.1875 0.0 0.0 0.0 0.0 134-135 6.612500000000001 0.0 0.0 0.0 0.0 136-137 7.1625 0.0 0.0 0.0 0.0 138-139 7.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6257541 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6257541_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 48 >>END_MODULE >>Per base sequence quality warn #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.90425 33.0 33.0 34.0 32.0 34.0 2 33.03575 33.0 33.0 34.0 32.0 34.0 3 33.03225 33.0 33.0 34.0 31.0 34.0 4 33.035 33.0 33.0 34.0 33.0 34.0 5 33.06025 33.0 33.0 34.0 33.0 34.0 6 37.366 38.0 38.0 38.0 37.0 38.0 7 37.3685 38.0 38.0 38.0 37.0 38.0 8 37.41 38.0 38.0 38.0 37.0 38.0 9 37.36225 38.0 38.0 38.0 37.0 38.0 10-14 37.2752 38.0 38.0 38.0 37.0 38.0 15-19 37.307849999999995 38.0 38.0 38.0 37.0 38.0 20-24 37.211149999999996 38.0 38.0 38.0 36.4 38.0 25-29 37.1896 38.0 38.0 38.0 36.8 38.0 30-34 37.124249999999996 38.0 38.0 38.0 36.0 38.0 35-39 37.02055 38.0 38.0 38.0 36.0 38.0 40-44 36.9447 38.0 38.0 38.0 35.6 38.0 45-49 36.83715 38.0 38.0 38.0 35.2 38.0 50-54 36.73435 38.0 38.0 38.0 34.8 38.0 55-59 36.64705 38.0 38.0 38.0 34.2 38.0 60-64 36.5264 38.0 38.0 38.0 34.0 38.0 65-69 36.36565 38.0 37.4 38.0 33.8 38.0 70-74 36.227850000000004 38.0 37.2 38.0 33.4 38.0 75-79 35.9572 38.0 37.0 38.0 32.4 38.0 80-84 35.75449999999999 38.0 36.6 38.0 31.4 38.0 85-89 35.6354 38.0 36.2 38.0 30.2 38.0 90-94 35.415049999999994 38.0 36.0 38.0 29.6 38.0 95-99 35.1308 38.0 36.0 38.0 28.8 38.0 100-104 34.87205 38.0 35.0 38.0 28.0 38.0 105-109 34.41605 38.0 34.6 38.0 25.6 38.0 110-114 34.040350000000004 38.0 34.0 38.0 23.6 38.0 115-119 33.672799999999995 38.0 34.0 38.0 22.2 38.0 120-124 33.0298 37.6 33.2 38.0 16.2 38.0 125-129 32.32975 36.6 31.8 38.0 14.8 38.0 130-134 31.955350000000003 36.0 31.0 38.0 14.0 38.0 135-139 31.05285 35.6 29.2 38.0 13.8 38.0 140-144 30.06875 35.0 26.8 38.0 13.0 38.0 145-149 28.68505 35.0 23.2 38.0 2.0 38.0 150-151 24.159999999999997 33.0 8.0 36.5 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 1.0 4 1.0 5 0.0 6 0.0 7 1.0 8 2.0 9 1.0 10 1.0 11 3.0 12 8.0 13 2.0 14 2.0 15 7.0 16 3.0 17 10.0 18 11.0 19 4.0 20 10.0 21 13.0 22 14.0 23 11.0 24 13.0 25 15.0 26 17.0 27 26.0 28 32.0 29 46.0 30 65.0 31 102.0 32 134.0 33 242.0 34 417.0 35 741.0 36 1340.0 37 701.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.324999999999996 17.25 10.825 33.6 2 28.65 22.025 30.525000000000002 18.8 3 22.875 24.75 27.925 24.45 4 25.324999999999996 32.800000000000004 21.025 20.849999999999998 5 28.95 33.75 19.650000000000002 17.65 6 22.7 35.699999999999996 20.349999999999998 21.25 7 22.675 17.275 38.2 21.85 8 22.25 22.75 26.224999999999998 28.775000000000002 9 23.925 21.025 28.675 26.375 10-14 25.995 25.66 23.799999999999997 24.545 15-19 25.679999999999996 25.805 24.585 23.93 20-24 25.705 26.56 24.37 23.365 25-29 25.715 25.95 24.495 23.84 30-34 25.679999999999996 26.025 24.51 23.785 35-39 25.555 25.94 25.259999999999998 23.244999999999997 40-44 26.185000000000002 26.179999999999996 24.67 22.965 45-49 25.865 26.490000000000002 24.349999999999998 23.294999999999998 50-54 25.685000000000002 26.145000000000003 24.505 23.665 55-59 26.045 26.179999999999996 24.695 23.080000000000002 60-64 25.935000000000002 26.334999999999997 24.615000000000002 23.115 65-69 26.14 26.21 24.495 23.155 70-74 25.874999999999996 26.229999999999997 25.14 22.755 75-79 25.685000000000002 25.81 25.275 23.23 80-84 25.624999999999996 26.375 24.995 23.005 85-89 25.515 26.255 24.79 23.44 90-94 25.735000000000003 26.41 25.124999999999996 22.73 95-99 25.665 26.215 25.685000000000002 22.435 100-104 26.155 26.39 24.825 22.63 105-109 25.419999999999998 26.545 25.19 22.845 110-114 25.740000000000002 26.400000000000002 24.855 23.005 115-119 26.31 26.790000000000003 24.725 22.175 120-124 26.314999999999998 26.35 24.62 22.715 125-129 26.424999999999997 26.965 23.87 22.74 130-134 26.555 26.290000000000003 25.180000000000003 21.975 135-139 26.02 27.139999999999997 24.990000000000002 21.85 140-144 26.650000000000002 27.095000000000002 24.335 21.92 145-149 26.840000000000003 27.3 24.46 21.4 150-151 26.974999999999998 26.775 24.55 21.7 >>END_MODULE >>Per sequence GC content fail #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 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 0.0 25 0.5 26 1.5 27 1.0 28 1.5 29 3.5 30 6.5 31 9.5 32 12.5 33 19.5 34 27.0 35 32.0 36 42.0 37 51.0 38 75.5 39 112.0 40 128.5 41 144.5 42 171.0 43 196.0 44 208.0 45 215.0 46 212.5 47 209.5 48 199.0 49 182.5 50 167.5 51 145.5 52 132.0 53 114.0 54 103.0 55 103.0 56 100.0 57 85.5 58 78.5 59 87.5 60 72.5 61 55.5 62 58.5 63 61.5 64 58.0 65 48.0 66 41.5 67 42.0 68 41.5 69 34.0 70 28.0 71 23.0 72 16.5 73 13.5 74 10.5 75 6.5 76 4.0 77 2.5 78 1.5 79 1.0 80 0.5 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 99.125 #Duplication Level Percentage of deduplicated Percentage of total 1 99.21815889029004 98.35000000000001 2 0.7061790668348046 1.4000000000000001 3 0.05044136191677175 0.15 4 0.025220680958385876 0.1 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 0.05 0.0 0.0 0.0 0.0 68-69 0.0875 0.0 0.0 0.0 0.0 70-71 0.1375 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2375 0.0 0.0 0.0 0.0 82-83 0.2625 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.3125 0.0 0.0 0.0 0.0 90-91 0.42500000000000004 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.6125 0.0 0.0 0.0 0.0 96-97 0.6625000000000001 0.0 0.0 0.0 0.0 98-99 0.7749999999999999 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 1.3875000000000002 0.0 0.0 0.0 0.0 106-107 1.65 0.0 0.0 0.0 0.0 108-109 1.8875 0.0 0.0 0.0 0.0 110-111 2.125 0.0 0.0 0.0 0.0 112-113 2.35 0.0 0.0 0.0 0.0 114-115 2.5250000000000004 0.0 0.0 0.0 0.0 116-117 2.8 0.0 0.0 0.0 0.0 118-119 3.0125 0.0 0.0 0.0 0.0 120-121 3.4 0.0 0.0 0.0 0.0 122-123 3.8 0.0 0.0 0.0 0.0 124-125 4.1 0.0 0.0 0.0 0.0 126-127 4.425 0.0 0.0 0.0 0.0 128-129 4.887499999999999 0.0 0.0 0.0 0.0 130-131 5.275 0.0 0.0 0.0 0.0 132-133 5.6625 0.0 0.0 0.0 0.0 134-135 5.987500000000001 0.0 0.0 0.0 0.0 136-137 6.4875 0.0 0.0 0.0 0.0 138-139 6.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATGCTT 10 0.006830828 145.0 145 GTGGAGT 10 0.006830828 145.0 1 GGAAACT 10 0.006830828 145.0 3 >>END_MODULE Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372314 spots for SRR6257541.sra Written 372314 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra Read 372300 spots for SRR6257541.sra Written 372300 spots for SRR6257541.sra SRR ids: ['SRR6257541.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_uc9dxunq SRR6257541.sra spots: 7446014 blocks: [[1, 372300], [372301, 744600], [744601, 1116900], [1116901, 1489200], [1489201, 1861500], [1861501, 2233800], [2233801, 2606100], [2606101, 2978400], [2978401, 3350700], [3350701, 3723000], [3723001, 4095300], [4095301, 4467600], [4467601, 4839900], [4839901, 5212200], [5212201, 5584500], [5584501, 5956800], [5956801, 6329100], [6329101, 6701400], [6701401, 7073700], [7073701, 7446014]] SRR6257541 file size 2506497 SRR6257541 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 SRR6257541 SRR6257541_1.fastq SRR6257541_2.fastq Input file: SRR6257541_1.fastq Paired file: SRR6257541_2.fastq trimmed: SRR6257541-trimmed-pair1.fastq, SRR6257541-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 Sat Dec 7 09:07:46 2024 >> started Sat Dec 7 09:07:57 2024 >> done (10.665s) 7446014 read pairs processed; of these: 2738 ( 0.04%) short read pairs filtered out after trimming by size control 4090 ( 0.05%) empty read pairs filtered out after trimming by size control 7439186 (99.91%) read pairs available; of these: 2475467 (33.28%) trimmed read pairs available after processing 4963719 (66.72%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 10 0.00% 20 6 0.00% 21 17 0.00% 22 10 0.00% 23 10 0.00% 24 17 0.00% 25 15 0.00% 26 14 0.00% 27 13 0.00% 28 14 0.00% 29 13 0.00% 30 17 0.00% 31 11 0.00% 32 6 0.00% 33 14 0.00% 34 13 0.00% 35 20 0.00% 36 11 0.00% 37 14 0.00% 38 25 0.00% 39 22 0.00% 40 16 0.00% 41 22 0.00% 42 34 0.00% 43 22 0.00% 44 26 0.00% 45 42 0.00% 46 30 0.00% 47 48 0.00% 48 38 0.00% 49 38 0.00% 50 59 0.00% 51 52 0.00% 52 64 0.00% 53 57 0.00% 54 79 0.00% 55 94 0.00% 56 67 0.00% 57 85 0.00% 58 111 0.00% 59 126 0.00% 60 134 0.00% 61 133 0.00% 62 157 0.00% 63 189 0.00% 64 191 0.00% 65 251 0.00% 66 278 0.00% 67 289 0.00% 68 311 0.00% 69 394 0.01% 70 422 0.01% 71 454 0.01% 72 563 0.01% 73 626 0.01% 74 685 0.01% 75 787 0.01% 76 852 0.01% 77 1046 0.01% 78 1013 0.01% 79 1219 0.02% 80 1410 0.02% 81 1480 0.02% 82 1557 0.02% 83 1744 0.02% 84 2015 0.03% 85 2285 0.03% 86 2490 0.03% 87 2716 0.04% 88 3108 0.04% 89 3113 0.04% 90 3436 0.05% 91 3632 0.05% 92 3908 0.05% 93 4205 0.06% 94 4548 0.06% 95 5003 0.07% 96 5120 0.07% 97 5462 0.07% 98 5856 0.08% 99 6228 0.08% 100 6698 0.09% 101 7018 0.09% 102 7639 0.10% 103 7815 0.11% 104 8236 0.11% 105 8648 0.12% 106 9071 0.12% 107 9903 0.13% 108 9849 0.13% 109 10987 0.15% 110 11008 0.15% 111 10963 0.15% 112 11305 0.15% 113 11868 0.16% 114 12673 0.17% 115 13102 0.18% 116 13462 0.18% 117 13279 0.18% 118 13533 0.18% 119 13791 0.19% 120 14111 0.19% 121 14886 0.20% 122 15699 0.21% 123 15587 0.21% 124 15957 0.21% 125 16291 0.22% 126 17126 0.23% 127 17388 0.23% 128 17296 0.23% 129 18758 0.25% 130 19224 0.26% 131 19978 0.27% 132 19902 0.27% 133 20522 0.28% 134 21310 0.29% 135 22395 0.30% 136 22988 0.31% 137 23788 0.32% 138 24720 0.33% 139 26294 0.35% 140 27375 0.37% 141 29544 0.40% 142 32360 0.43% 143 35166 0.47% 144 39448 0.53% 145 46420 0.62% 146 56967 0.77% 147 75067 1.01% 148 112465 1.51% 149 214488 2.88% 150 1130376 15.19% 151 4963719 66.72% 7439186 reads passed initial QC criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.91 fanout-score-rank=14 prefix-density=0.84 prefix-fanout=2.7 sequence=GGTGTTGTCGAAGCCGATGATGCGGAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=30.45 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=4.7 sequence=TCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATGTTCTCTATTCCGGTT criterion=sequence-density sequence-density=0.56 sequence-density-rank=1 fanout-score=3.55 fanout-score-rank=19 prefix-density=0.61 prefix-fanout=3.2 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=42.76 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=8.2 sequence=GAGCTGCTCACGCGGCGAGAGCGGGTCGCCGCGTGCCGGCCGGGGGACGGACCGGGAGTCGCCCCTTCGGGGGCTTTCCCCGAGCGCTGAACAGTCGACTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCTCGCGGATGCTGACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCGGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCCTTTACGGGCGCAAGTGAAATACCACTACTTTTAACGTTATTTT SRR6257541 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 09:08:38 Started mapping on | Dec 07 09:08:38 Finished on | Dec 07 09:09:17 Mapping speed, Million of reads per hour | 686.69 Number of input reads | 7439186 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 6995343 Uniquely mapped reads % | 94.03% Average mapped length | 294.89 Number of splices: Total | 8251979 Number of splices: Annotated (sjdb) | 7775070 Number of splices: GT/AG | 8140214 Number of splices: GC/AG | 99996 Number of splices: AT/AC | 4442 Number of splices: Non-canonical | 7327 Mismatch rate per base, % | 0.09% Deletion rate per base | 0.00% Deletion average length | 1.43 Insertion rate per base | 0.00% Insertion average length | 1.28 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 149269 % of reads mapped to multiple loci | 2.01% Number of reads mapped to too many loci | 31670 % of reads mapped to too many loci | 0.43% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.99% % of reads unmapped: other | 2.54% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 296910 296910 296910 N_multimapping 149269 149269 149269 N_noFeature 346932 6785731 422917 N_ambiguous 160919 1210 27332 UnstrandedReadsAssigned:6487492 PositiveStrandReadsAssigned:208402 NegativeStrandReadsAssigned:6545094 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR6257541 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR6257541-trimmed-pair1.fastq SRR6257541-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,439,186 reads, 6,611,603 reads pseudoaligned [quant] estimated average fragment length: 262.501 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,022 rounds 52973 SRR6257541.ke.tsv 35125 SRR6257541.se.tsv 88098 total ==> SRR6257541.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 674.93 0 0 PNS24247 1044 782.499 19.3053 5.4142 PNS24249 1928 1666.5 12.7917 1.68447 PNS24246 1044 782.499 19.3053 5.4142 PNS24248 1044 782.499 19.3053 5.4142 PNS24244 1471 1209.5 13.2923 2.41178 PNS24243 293 90.0987 0 0 KQK14069 1603 1341.5 1422.64 232.727 KQK14071 474 229.244 42.3994 40.5885 ==> SRR6257541.se.tsv <== BRADI_1g14170v3 1722 BRADI_1g53295v3 45 BRADI_1g59795v3 197 BRADI_1g07683v3 0 BRADI_1g00485v3 11 BRADI_1g20270v3 807 BRADI_1g74790v3 63 BRADI_1g09890v3 0 BRADI_1g77505v3 119 BRADI_1g48960v3 0 SRR6257541 completed mapping pipeline successfully