Starting /dee2/code/volunteer_pipeline.sh SRR7804077 current disk space = 1541896011776 free memory = 1607568056 SRR7804077 SRAfilesize 146ecaec4903815e07cf6519f3b2a60c SRR7804077.sra SRR7804077.sra file validated SRR7804077 is paired end SRR7804077 is conventional basespace SRR7804077 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7804077_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1655 37.0 37.0 37.0 37.0 37.0 2 36.17675 37.0 37.0 37.0 37.0 37.0 3 36.2655 37.0 37.0 37.0 37.0 37.0 4 36.351 37.0 37.0 37.0 37.0 37.0 5 36.5225 37.0 37.0 37.0 37.0 37.0 6 36.456 37.0 37.0 37.0 37.0 37.0 7 36.362 37.0 37.0 37.0 37.0 37.0 8 36.444 37.0 37.0 37.0 37.0 37.0 9 36.4455 37.0 37.0 37.0 37.0 37.0 10-14 36.4454 37.0 37.0 37.0 37.0 37.0 15-19 36.4688 37.0 37.0 37.0 37.0 37.0 20-24 36.392700000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.3899 37.0 37.0 37.0 37.0 37.0 30-34 36.412 37.0 37.0 37.0 37.0 37.0 35-39 36.3786 37.0 37.0 37.0 37.0 37.0 40-44 36.3519 37.0 37.0 37.0 37.0 37.0 45-49 36.3667 37.0 37.0 37.0 37.0 37.0 50-54 36.3364 37.0 37.0 37.0 37.0 37.0 55-59 36.3074 37.0 37.0 37.0 37.0 37.0 60-64 36.3237 37.0 37.0 37.0 37.0 37.0 65-69 36.2631 37.0 37.0 37.0 37.0 37.0 70-74 36.2437 37.0 37.0 37.0 37.0 37.0 75-79 36.201 37.0 37.0 37.0 37.0 37.0 80-84 36.163599999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.1503 37.0 37.0 37.0 37.0 37.0 90-94 36.1156 37.0 37.0 37.0 37.0 37.0 95-99 36.100199999999994 37.0 37.0 37.0 37.0 37.0 100-104 36.1068 37.0 37.0 37.0 37.0 37.0 105-109 35.98350000000001 37.0 37.0 37.0 37.0 37.0 110-114 36.012699999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.9906 37.0 37.0 37.0 37.0 37.0 120-124 35.8943 37.0 37.0 37.0 37.0 37.0 125-129 35.88399999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.7892 37.0 37.0 37.0 37.0 37.0 135-139 35.8317 37.0 37.0 37.0 37.0 37.0 140-144 35.71169999999999 37.0 37.0 37.0 37.0 37.0 145-149 35.746 37.0 37.0 37.0 37.0 37.0 150-151 35.210499999999996 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 0.0 22 0.0 23 0.0 24 2.0 25 2.0 26 7.0 27 12.0 28 15.0 29 19.0 30 25.0 31 50.0 32 68.0 33 65.0 34 139.0 35 362.0 36 2923.0 37 309.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 44.85 12.225 9.55 33.375 2 27.145359019264447 13.10983237428071 31.523642732049034 28.221165874405806 3 22.475 19.975 24.425 33.125 4 25.3 26.275 21.8 26.625 5 27.075 29.2 22.225 21.5 6 23.1 31.5 22.45 22.95 7 18.3 24.375 37.325 20.0 8 21.4 22.925 27.85 27.825 9 19.475 21.825 30.9 27.800000000000004 10-14 23.965 25.705 24.08 26.25 15-19 23.595 24.54 25.445 26.419999999999998 20-24 23.49 25.47 24.935 26.105 25-29 23.56 24.485 24.995 26.96 30-34 23.625 25.285000000000004 24.98 26.11 35-39 23.68 24.965 25.235000000000003 26.119999999999997 40-44 23.830000000000002 24.759999999999998 25.28 26.13 45-49 24.135 24.315 24.990000000000002 26.56 50-54 24.169999999999998 24.995 24.72 26.115 55-59 23.825 24.65 24.785 26.740000000000002 60-64 24.07 24.884999999999998 24.490000000000002 26.555 65-69 24.665 24.535 24.22 26.58 70-74 24.13 25.255 24.37 26.245 75-79 24.94 24.905 23.825 26.33 80-84 24.169999999999998 24.72 24.94 26.169999999999998 85-89 24.27 24.535 24.355 26.840000000000003 90-94 24.32 24.22 24.58 26.88 95-99 24.345 24.060000000000002 24.77 26.825 100-104 24.545 24.46 24.41 26.584999999999997 105-109 24.765 24.39 24.36 26.484999999999996 110-114 24.6 24.54 24.315 26.545 115-119 24.915000000000003 24.715 23.61 26.76 120-124 24.715 24.535 24.240000000000002 26.51 125-129 24.455 24.32 24.58 26.645000000000003 130-134 25.255 24.63 24.03 26.085 135-139 25.019999999999996 24.25 24.45 26.279999999999998 140-144 24.86 24.04 24.47 26.63 145-149 24.945 24.195 24.44 26.419999999999998 150-151 25.412499999999998 23.849999999999998 24.337500000000002 26.400000000000002 >>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 0.5 13 0.5 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 1.0 26 1.5 27 3.0 28 3.5 29 2.5 30 4.5 31 7.5 32 12.5 33 16.5 34 17.0 35 25.0 36 37.5 37 42.5 38 56.5 39 83.0 40 103.0 41 132.5 42 165.0 43 178.0 44 181.5 45 182.5 46 183.0 47 191.0 48 184.5 49 182.0 50 175.0 51 149.0 52 131.0 53 134.5 54 133.5 55 110.0 56 105.5 57 97.0 58 84.0 59 78.0 60 67.5 61 70.5 62 76.5 63 71.0 64 63.0 65 54.0 66 50.5 67 54.5 68 54.5 69 45.0 70 40.5 71 37.0 72 31.0 73 27.5 74 19.0 75 13.0 76 9.5 77 6.5 78 5.5 79 3.0 80 1.0 81 0.5 82 2.0 83 1.5 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 0.075 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 94.15 #Duplication Level Percentage of deduplicated Percentage of total 1 94.23791821561338 88.725 2 5.363781200212427 10.100000000000001 3 0.34519383961763145 0.975 4 0.05310674455655868 0.2 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 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.025 90-91 0.075 0.0 0.0 0.0 0.025 92-93 0.1 0.0 0.0 0.0 0.025 94-95 0.1 0.0 0.0 0.0 0.025 96-97 0.1125 0.0 0.0 0.0 0.025 98-99 0.15 0.0 0.0 0.0 0.025 100-101 0.1875 0.0 0.0 0.0 0.025 102-103 0.21250000000000002 0.0 0.0 0.0 0.025 104-105 0.225 0.0 0.0 0.0 0.025 106-107 0.2625 0.0 0.0 0.0 0.025 108-109 0.3125 0.0 0.0 0.0 0.025 110-111 0.3375 0.0 0.0 0.0 0.025 112-113 0.3625 0.0 0.0 0.0 0.025 114-115 0.375 0.0 0.0 0.0 0.025 116-117 0.4125 0.0 0.0 0.0 0.025 118-119 0.45 0.0 0.0 0.0 0.025 120-121 0.475 0.0 0.0 0.0 0.025 122-123 0.5125 0.0 0.0 0.0 0.025 124-125 0.5375000000000001 0.0 0.0 0.0 0.025 126-127 0.625 0.0 0.0 0.0 0.025 128-129 0.6625000000000001 0.0 0.0 0.0 0.025 130-131 0.825 0.0 0.0 0.0 0.025 132-133 0.975 0.0 0.0 0.0 0.025 134-135 1.05 0.0 0.0 0.0 0.025 136-137 1.125 0.0 0.0 0.0 0.025 138-139 1.2125 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7804077 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7804077_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.22175 37.0 37.0 37.0 37.0 37.0 2 35.994 37.0 37.0 37.0 37.0 37.0 3 36.0045 37.0 37.0 37.0 37.0 37.0 4 36.1585 37.0 37.0 37.0 37.0 37.0 5 36.1475 37.0 37.0 37.0 37.0 37.0 6 36.155 37.0 37.0 37.0 37.0 37.0 7 36.161 37.0 37.0 37.0 37.0 37.0 8 36.297 37.0 37.0 37.0 37.0 37.0 9 36.112 37.0 37.0 37.0 37.0 37.0 10-14 36.13289999999999 37.0 37.0 37.0 37.0 37.0 15-19 35.9938 37.0 37.0 37.0 37.0 37.0 20-24 36.000800000000005 37.0 37.0 37.0 37.0 37.0 25-29 35.933099999999996 37.0 37.0 37.0 37.0 37.0 30-34 35.929899999999996 37.0 37.0 37.0 37.0 37.0 35-39 35.9165 37.0 37.0 37.0 37.0 37.0 40-44 35.833 37.0 37.0 37.0 37.0 37.0 45-49 35.8195 37.0 37.0 37.0 37.0 37.0 50-54 35.7952 37.0 37.0 37.0 37.0 37.0 55-59 35.7036 37.0 37.0 37.0 37.0 37.0 60-64 35.7636 37.0 37.0 37.0 37.0 37.0 65-69 35.664300000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.69029999999999 37.0 37.0 37.0 37.0 37.0 75-79 35.6037 37.0 37.0 37.0 37.0 37.0 80-84 35.553900000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.6163 37.0 37.0 37.0 37.0 37.0 90-94 35.6007 37.0 37.0 37.0 37.0 37.0 95-99 35.538799999999995 37.0 37.0 37.0 37.0 37.0 100-104 35.5371 37.0 37.0 37.0 37.0 37.0 105-109 35.4813 37.0 37.0 37.0 37.0 37.0 110-114 35.3292 37.0 37.0 37.0 32.2 37.0 115-119 35.3711 37.0 37.0 37.0 37.0 37.0 120-124 35.3373 37.0 37.0 37.0 34.6 37.0 125-129 35.1989 37.0 37.0 37.0 27.4 37.0 130-134 35.2996 37.0 37.0 37.0 34.6 37.0 135-139 35.18879999999999 37.0 37.0 37.0 29.8 37.0 140-144 35.1796 37.0 37.0 37.0 32.2 37.0 145-149 35.06100000000001 37.0 37.0 37.0 25.0 37.0 150-151 34.646 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 3.0 14 8.0 15 6.0 16 4.0 17 0.0 18 5.0 19 4.0 20 4.0 21 4.0 22 6.0 23 7.0 24 10.0 25 15.0 26 11.0 27 11.0 28 14.0 29 27.0 30 34.0 31 42.0 32 70.0 33 117.0 34 227.0 35 631.0 36 2553.0 37 187.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.509877469367346 18.579644911227806 9.802450612653162 32.10802700675169 2 30.475 22.95 25.474999999999998 21.099999999999998 3 22.525000000000002 25.424999999999997 28.299999999999997 23.75 4 27.075 28.975 19.7 24.25 5 27.275 32.025 19.7 21.0 6 23.799999999999997 32.675 18.525 25.0 7 21.575 18.475 33.5 26.450000000000003 8 24.075 23.925 21.975 30.025000000000002 9 23.625 22.875 24.349999999999998 29.15 10-14 25.945 25.195 22.215 26.645000000000003 15-19 25.874999999999996 23.880000000000003 23.45 26.795 20-24 26.125 24.425 23.35 26.1 25-29 26.35 24.63 23.025000000000002 25.995 30-34 26.02 24.545 23.39 26.045 35-39 26.924999999999997 24.255 23.255 25.564999999999998 40-44 25.97 24.335 23.575 26.119999999999997 45-49 26.025 24.92 23.544999999999998 25.509999999999998 50-54 26.495 24.23 23.525 25.75 55-59 26.640000000000004 24.68 23.48 25.2 60-64 26.57 23.925 23.799999999999997 25.705 65-69 26.87 25.009999999999998 23.380000000000003 24.740000000000002 70-74 26.295 24.75 23.61 25.345000000000002 75-79 26.63 24.474999999999998 23.724999999999998 25.169999999999998 80-84 27.365000000000002 24.595 22.905 25.135 85-89 27.46 23.799999999999997 23.225 25.515 90-94 26.900000000000002 24.279999999999998 23.23 25.590000000000003 95-99 27.125 24.560000000000002 23.395 24.92 100-104 27.57 24.875 22.7 24.855 105-109 27.125 24.735 23.095 25.045 110-114 26.985 25.240000000000002 22.965 24.81 115-119 27.35 24.515 22.985 25.15 120-124 27.125 24.610000000000003 23.275000000000002 24.990000000000002 125-129 26.77 24.595 23.355 25.28 130-134 27.529999999999998 24.545 23.39 24.535 135-139 26.88 24.725 23.435 24.959999999999997 140-144 26.935 24.91 22.900000000000002 25.255 145-149 26.590000000000003 25.005 23.53 24.875 150-151 27.650000000000002 24.875 23.7 23.775 >>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 0.5 8 0.5 9 0.5 10 0.5 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 0.5 25 2.0 26 2.5 27 1.5 28 1.5 29 2.0 30 5.0 31 6.5 32 8.5 33 11.5 34 16.5 35 22.5 36 23.0 37 32.5 38 48.5 39 68.5 40 91.5 41 119.0 42 151.5 43 153.5 44 156.0 45 178.5 46 184.0 47 175.0 48 159.0 49 154.0 50 148.5 51 139.0 52 140.0 53 129.5 54 111.5 55 114.0 56 108.5 57 90.5 58 96.0 59 97.0 60 79.0 61 79.0 62 84.5 63 77.0 64 77.5 65 82.5 66 77.0 67 75.5 68 72.5 69 62.5 70 54.5 71 44.0 72 44.0 73 42.0 74 26.5 75 17.0 76 15.0 77 11.0 78 7.0 79 3.5 80 2.0 81 1.0 82 1.0 83 1.5 84 0.5 85 0.0 86 0.0 87 1.0 88 1.0 89 0.0 90 0.5 91 1.5 92 1.0 93 0.5 94 0.5 95 0.5 96 1.0 97 0.5 98 0.0 99 0.0 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.025 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 94.15 #Duplication Level Percentage of deduplicated Percentage of total 1 94.3441317047265 88.825 2 5.284121083377589 9.950000000000001 3 0.2655337227827934 0.75 4 0.07966011683483802 0.3 5 0.0 0.0 6 0.0 0.0 7 0.02655337227827934 0.17500000000000002 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit >>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 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.1 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.1125 0.0 0.0 0.0 0.0 98-99 0.15 0.0 0.0 0.0 0.0 100-101 0.1875 0.0 0.0 0.0 0.0 102-103 0.21250000000000002 0.0 0.0 0.0 0.0 104-105 0.225 0.0 0.0 0.0 0.0 106-107 0.2625 0.0 0.0 0.0 0.0 108-109 0.3125 0.0 0.0 0.0 0.0 110-111 0.3375 0.0 0.0 0.0 0.0 112-113 0.3625 0.0 0.0 0.0 0.0 114-115 0.375 0.0 0.0 0.0 0.0 116-117 0.4375 0.0 0.0 0.0 0.0 118-119 0.4875 0.0 0.0 0.0 0.0 120-121 0.525 0.0 0.0 0.0 0.0 122-123 0.575 0.0 0.0 0.0 0.0 124-125 0.6125 0.0 0.0 0.0 0.0 126-127 0.7 0.0 0.0 0.0 0.0 128-129 0.7375 0.0 0.0 0.0 0.0 130-131 0.8999999999999999 0.0 0.0 0.0 0.0 132-133 1.05 0.0 0.0 0.0 0.0 134-135 1.125 0.0 0.0 0.0 0.0 136-137 1.2 0.0 0.0 0.0 0.0 138-139 1.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGTTAGC 10 0.006830828 145.0 9 CAATCGG 10 0.006830828 145.0 4 GCAATCG 10 0.006830828 145.0 3 AGCAATC 10 0.006830828 145.0 2 ATCCGGT 10 0.006830828 145.0 5 >>END_MODULE Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264965 spots for SRR7804077.sra Written 1264965 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra Read 1264947 spots for SRR7804077.sra Written 1264947 spots for SRR7804077.sra SRR ids: ['SRR7804077.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2pvx0n70 SRR7804077.sra spots: 25298958 blocks: [[1, 1264947], [1264948, 2529894], [2529895, 3794841], [3794842, 5059788], [5059789, 6324735], [6324736, 7589682], [7589683, 8854629], [8854630, 10119576], [10119577, 11384523], [11384524, 12649470], [12649471, 13914417], [13914418, 15179364], [15179365, 16444311], [16444312, 17709258], [17709259, 18974205], [18974206, 20239152], [20239153, 21504099], [21504100, 22769046], [22769047, 24033993], [24033994, 25298958]] SRR7804077 file size 8551286 SRR7804077 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 SRR7804077 SRR7804077_1.fastq SRR7804077_2.fastq Input file: SRR7804077_1.fastq Paired file: SRR7804077_2.fastq trimmed: SRR7804077-trimmed-pair1.fastq, SRR7804077-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 16:23:48 2024 >> started Sat Dec 7 16:24:42 2024 >> done (54.205s) 25298958 read pairs processed; of these: 85 ( 0.00%) short read pairs filtered out after trimming by size control 512 ( 0.00%) empty read pairs filtered out after trimming by size control 25298361 (100.00%) read pairs available; of these: 561941 ( 2.22%) trimmed read pairs available after processing 24736420 (97.78%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 12 0.00% 20 9 0.00% 21 9 0.00% 22 16 0.00% 23 15 0.00% 24 14 0.00% 25 10 0.00% 26 13 0.00% 27 21 0.00% 28 22 0.00% 29 10 0.00% 30 16 0.00% 31 26 0.00% 32 28 0.00% 33 24 0.00% 34 26 0.00% 35 22 0.00% 36 30 0.00% 37 43 0.00% 38 33 0.00% 39 24 0.00% 40 34 0.00% 41 30 0.00% 42 45 0.00% 43 34 0.00% 44 34 0.00% 45 37 0.00% 46 52 0.00% 47 63 0.00% 48 59 0.00% 49 50 0.00% 50 56 0.00% 51 38 0.00% 52 57 0.00% 53 54 0.00% 54 45 0.00% 55 63 0.00% 56 60 0.00% 57 63 0.00% 58 63 0.00% 59 79 0.00% 60 67 0.00% 61 79 0.00% 62 79 0.00% 63 67 0.00% 64 90 0.00% 65 77 0.00% 66 95 0.00% 67 100 0.00% 68 102 0.00% 69 122 0.00% 70 121 0.00% 71 125 0.00% 72 146 0.00% 73 158 0.00% 74 189 0.00% 75 215 0.00% 76 217 0.00% 77 229 0.00% 78 229 0.00% 79 293 0.00% 80 313 0.00% 81 350 0.00% 82 427 0.00% 83 460 0.00% 84 530 0.00% 85 596 0.00% 86 605 0.00% 87 647 0.00% 88 702 0.00% 89 776 0.00% 90 851 0.00% 91 1014 0.00% 92 1070 0.00% 93 1274 0.01% 94 1380 0.01% 95 1437 0.01% 96 1562 0.01% 97 1688 0.01% 98 1780 0.01% 99 1845 0.01% 100 2054 0.01% 101 2196 0.01% 102 2502 0.01% 103 2799 0.01% 104 2882 0.01% 105 3208 0.01% 106 3343 0.01% 107 3514 0.01% 108 3566 0.01% 109 3917 0.02% 110 4221 0.02% 111 4366 0.02% 112 4731 0.02% 113 5039 0.02% 114 5333 0.02% 115 5816 0.02% 116 6009 0.02% 117 6319 0.02% 118 6527 0.03% 119 6783 0.03% 120 7120 0.03% 121 7262 0.03% 122 7967 0.03% 123 8560 0.03% 124 8959 0.04% 125 9517 0.04% 126 9792 0.04% 127 10252 0.04% 128 10214 0.04% 129 10789 0.04% 130 11446 0.05% 131 11521 0.05% 132 12434 0.05% 133 12760 0.05% 134 13638 0.05% 135 14258 0.06% 136 14934 0.06% 137 15139 0.06% 138 15796 0.06% 139 16394 0.06% 140 16586 0.07% 141 17292 0.07% 142 17935 0.07% 143 18739 0.07% 144 19721 0.08% 145 20691 0.08% 146 21669 0.09% 147 22278 0.09% 148 22598 0.09% 149 23364 0.09% 150 23640 0.09% 151 24736420 97.78% 25298361 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=12.08 fanout-score-rank=10 prefix-density=0.31 prefix-fanout=6.5 sequence=CTTGATGACACCAACAGCAACTGTTTGTCTCATGTCACGCACAGCAAAACGACCAAGAGGAGGGTACATGGCGAAGGTCTCCACAACCATGGGCTTGGTGGGAATCATCTTCACGATACCAGCATCACCGTTCTTCAAGAACTTGGGCTCCTTCTCCAGCTCCTTACCAGATCGCCTGTCAATCTTGGTCACCAGCTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=33 fanout-score=310.98 fanout-score-rank=1 prefix-density=0.48 prefix-fanout=19.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCAC criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=8.46 fanout-score-rank=19 prefix-density=1.29 prefix-fanout=3.4 sequence=TCTTCTTCTTCTCCTCCTTGATTTCATCAGCTTGAGGTTAAAAGATTTGGAAGATGTCTTGCAGCTGTGGATCAAGCTGCAACTGTGGCTCAAACTGCACTTGCGGGAAGATGTACCCAGACCTGGCAGAGCAGGGCAGCACCAACACTAGCACCCAGGCCCAGGTGGTGGTTCTCGGCATGGTGCCGGAGAAGAAGCAGGAGCAGCTCGAGATGGCCGGCGTGTCCGGCAGCGAGGGGTGCAGCTGCGGCGACAACTGCAAGTGCAACCCTTGCAACTGTTAGCCCACTAATCAATCATGATGCATTTGTGGTTAATAAATAAGCGCCGAGTCAGAGCGTGTGTTGTGGTTTACTTGTGAGTAACTGGTGTGTCCTTCCTTGTGAGTATGTATGTATTCGTGTGTGTCTGCGTGTAATTGGTTCATTTGATCAAGCTCTCTGCACTTGGGAGTTTGGCCAATGAACCAATCATCAGTATGTAAGAAAGGCAGAGGCTCTGTATGTCTGTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=36 fanout-score=736.40 fanout-score-rank=1 prefix-density=1.03 prefix-fanout=19.4 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGACTGTGCCGTGCTTATCATTGACTCCACGACTGGAGGTTTTGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCATGCCCTCCTTGCTTTCACTCTTGGAGTGAAGCAGATGATCTGCTGCTGCAACAAGATGGA SRR7804077 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 17:38:01 Started mapping on | Dec 07 17:38:01 Finished on | Dec 07 17:51:15 Mapping speed, Million of reads per hour | 114.70 Number of input reads | 25298361 Average input read length | 301 UNIQUE READS: Uniquely mapped reads number | 23144450 Uniquely mapped reads % | 91.49% Average mapped length | 299.75 Number of splices: Total | 24906145 Number of splices: Annotated (sjdb) | 23486648 Number of splices: GT/AG | 24538193 Number of splices: GC/AG | 275789 Number of splices: AT/AC | 19073 Number of splices: Non-canonical | 73090 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.02% Deletion average length | 2.66 Insertion rate per base | 0.02% Insertion average length | 2.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 375536 % of reads mapped to multiple loci | 1.48% Number of reads mapped to too many loci | 26608 % of reads mapped to too many loci | 0.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.14% % of reads unmapped: other | 0.79% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1778375 1778375 1778375 N_multimapping 375536 375536 375536 N_noFeature 496829 22522530 676581 N_ambiguous 516383 4068 76295 UnstrandedReadsAssigned:22131238 PositiveStrandReadsAssigned:617852 NegativeStrandReadsAssigned:22391574 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7804077 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: SRR7804077-trimmed-pair1.fastq SRR7804077-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,298,361 reads, 22,748,999 reads pseudoaligned [quant] estimated average fragment length: 323.265 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,255 rounds 52973 SRR7804077.ke.tsv 35125 SRR7804077.se.tsv 88098 total ==> SRR7804077.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 614.663 0 0 PNS24247 1044 721.735 101.031 8.15823 PNS24249 1928 1605.73 245.564 8.91271 PNS24246 1044 721.735 101.031 8.15823 PNS24248 1044 721.735 101.031 8.15823 PNS24244 1471 1148.73 85.3423 4.32975 PNS24243 293 70.7934 0 0 KQK14069 1603 1280.73 11149.9 507.374 KQK14071 474 190.484 66.9596 20.4867 ==> SRR7804077.se.tsv <== BRADI_1g14170v3 11544 BRADI_1g53295v3 991 BRADI_1g59795v3 201 BRADI_1g07683v3 0 BRADI_1g00485v3 56 BRADI_1g20270v3 1508 BRADI_1g74790v3 75 BRADI_1g09890v3 0 BRADI_1g77505v3 302 BRADI_1g48960v3 0 SRR7804077 completed mapping pipeline successfully