Starting /dee2/code/volunteer_pipeline.sh SRR7814811 current disk space = 1551530307584 free memory = 1605426436 SRR7814811 SRAfilesize 24859bbb854d9e2fa99aaa79b84c7399 SRR7814811.sra SRR7814811.sra file validated SRR7814811 is paired end SRR7814811 is conventional basespace SRR7814811 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814811_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 36.31375 37.0 37.0 37.0 37.0 37.0 2 36.27475 37.0 37.0 37.0 37.0 37.0 3 36.4555 37.0 37.0 37.0 37.0 37.0 4 36.476 37.0 37.0 37.0 37.0 37.0 5 36.549 37.0 37.0 37.0 37.0 37.0 6 36.524 37.0 37.0 37.0 37.0 37.0 7 36.449 37.0 37.0 37.0 37.0 37.0 8 36.533 37.0 37.0 37.0 37.0 37.0 9 36.4815 37.0 37.0 37.0 37.0 37.0 10-14 36.5138 37.0 37.0 37.0 37.0 37.0 15-19 36.48870000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.5024 37.0 37.0 37.0 37.0 37.0 25-29 36.446400000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.379599999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.3438 37.0 37.0 37.0 37.0 37.0 40-44 36.30309999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.2669 37.0 37.0 37.0 37.0 37.0 50-54 36.3029 37.0 37.0 37.0 37.0 37.0 55-59 36.196 37.0 37.0 37.0 37.0 37.0 60-64 36.1786 37.0 37.0 37.0 37.0 37.0 65-69 36.1838 37.0 37.0 37.0 37.0 37.0 70-74 36.064699999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.0676 37.0 37.0 37.0 37.0 37.0 80-84 36.06179999999999 37.0 37.0 37.0 37.0 37.0 85-89 36.0574 37.0 37.0 37.0 37.0 37.0 90-94 35.965999999999994 37.0 37.0 37.0 37.0 37.0 95-99 35.8975 37.0 37.0 37.0 37.0 37.0 100-104 35.8778 37.0 37.0 37.0 37.0 37.0 105-109 35.83480000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.8095 37.0 37.0 37.0 37.0 37.0 115-119 35.694500000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.663199999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.5783 37.0 37.0 37.0 37.0 37.0 130-134 35.4964 37.0 37.0 37.0 37.0 37.0 135-139 35.3451 37.0 37.0 37.0 37.0 37.0 140-144 35.3229 37.0 37.0 37.0 32.2 37.0 145-149 35.1075 37.0 37.0 37.0 27.4 37.0 150-151 34.47825 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 0.0 20 0.0 21 1.0 22 3.0 23 4.0 24 1.0 25 7.0 26 13.0 27 13.0 28 13.0 29 25.0 30 44.0 31 51.0 32 73.0 33 99.0 34 163.0 35 398.0 36 2787.0 37 304.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.10373340015034 10.899523928839889 6.163868704585317 36.83287396642446 2 25.881470367591895 13.50337584396099 30.332583145786447 30.282570642660666 3 22.25 18.125 23.275000000000002 36.35 4 26.275 25.074999999999996 20.575 28.075 5 27.125 28.425 23.150000000000002 21.3 6 22.3 32.875 21.15 23.674999999999997 7 17.95 24.349999999999998 39.175 18.525 8 20.349999999999998 23.125 28.875 27.650000000000002 9 20.3 20.825 32.074999999999996 26.8 10-14 22.86 27.084999999999997 24.36 25.695 15-19 22.945 25.605 24.79 26.66 20-24 23.044999999999998 26.279999999999998 24.825 25.85 25-29 23.335 25.380000000000003 25.19 26.095000000000002 30-34 22.965 25.715 25.009999999999998 26.31 35-39 23.745 25.474999999999998 24.95 25.83 40-44 22.994999999999997 25.874999999999996 25.41 25.72 45-49 23.52 25.905 24.13 26.445 50-54 23.61 26.229999999999997 24.555 25.605 55-59 23.745 25.779999999999998 24.55 25.924999999999997 60-64 24.08 25.25 24.5 26.169999999999998 65-69 24.18 25.369999999999997 24.165 26.284999999999997 70-74 23.525 25.34 24.545 26.590000000000003 75-79 23.205000000000002 25.619999999999997 25.345000000000002 25.83 80-84 23.79 25.674999999999997 24.58 25.955000000000002 85-89 23.66 26.06 24.240000000000002 26.040000000000003 90-94 24.154999999999998 25.55 24.085 26.21 95-99 23.98 25.490000000000002 24.45 26.08 100-104 24.315 25.05 24.455 26.179999999999996 105-109 24.2 25.569999999999997 23.96 26.27 110-114 24.64 24.8 24.39 26.169999999999998 115-119 23.985 25.069999999999997 24.47 26.474999999999998 120-124 24.355 25.080000000000002 24.07 26.495 125-129 24.515 25.045 24.485 25.955000000000002 130-134 24.6 24.725 24.185000000000002 26.490000000000002 135-139 24.255 25.240000000000002 24.345 26.16 140-144 24.425 24.834999999999997 24.46 26.279999999999998 145-149 24.67 25.4 23.73 26.200000000000003 150-151 24.425 24.9375 24.125 26.5125 >>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 0.5 19 1.0 20 0.5 21 0.0 22 0.5 23 0.5 24 0.5 25 0.5 26 0.5 27 3.0 28 5.0 29 5.0 30 7.0 31 11.0 32 11.0 33 16.0 34 30.5 35 35.5 36 47.0 37 58.5 38 67.5 39 94.5 40 112.0 41 125.0 42 148.5 43 179.5 44 196.0 45 192.0 46 212.5 47 208.5 48 174.0 49 176.0 50 174.0 51 152.5 52 139.5 53 130.5 54 116.0 55 106.0 56 98.5 57 89.5 58 81.5 59 75.0 60 65.5 61 60.5 62 66.5 63 64.0 64 58.5 65 53.0 66 41.5 67 38.5 68 43.5 69 42.0 70 38.0 71 35.0 72 28.5 73 20.5 74 13.0 75 12.5 76 12.5 77 8.0 78 6.0 79 4.0 80 2.5 81 1.0 82 0.0 83 0.0 84 1.0 85 1.0 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 0.22499999999999998 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 94.475 #Duplication Level Percentage of deduplicated Percentage of total 1 94.62820852077269 89.4 2 4.92193702037576 9.3 3 0.42339243186028047 1.2 4 0.02646202699126753 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 0.0 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.075 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 0.1 0.0 0.0 0.0 0.0 82-83 0.1875 0.0 0.0 0.0 0.0 84-85 0.2375 0.0 0.0 0.0 0.0 86-87 0.2875 0.0 0.0 0.0 0.0 88-89 0.35 0.0 0.0 0.0 0.0 90-91 0.4375 0.0 0.0 0.0 0.0 92-93 0.5125 0.0 0.0 0.0 0.0 94-95 0.7124999999999999 0.0 0.0 0.0 0.0 96-97 0.9375 0.0 0.0 0.0 0.0 98-99 1.1 0.0 0.0 0.0 0.0 100-101 1.1375 0.0 0.0 0.0 0.0 102-103 1.25 0.0 0.0 0.0 0.0 104-105 1.4125 0.0 0.0 0.0 0.0 106-107 1.6 0.0 0.0 0.0 0.0 108-109 1.875 0.0 0.0 0.0 0.0 110-111 2.0125 0.0 0.0 0.0 0.0 112-113 2.3499999999999996 0.0 0.0 0.0 0.0 114-115 2.6500000000000004 0.0 0.0 0.0 0.0 116-117 3.1125 0.0 0.0 0.0 0.0 118-119 3.55 0.0 0.0 0.0 0.0 120-121 3.925 0.0 0.0 0.0 0.0 122-123 4.3375 0.0 0.0 0.0 0.0 124-125 4.6125 0.0 0.0 0.0 0.0 126-127 4.9875 0.0 0.0 0.0 0.0 128-129 5.4375 0.0 0.0 0.0 0.0 130-131 5.9125 0.0 0.0 0.0 0.0 132-133 6.4125 0.0 0.0 0.0 0.0 134-135 6.7625 0.0 0.0 0.0 0.0 136-137 7.2375 0.0 0.0 0.0 0.0 138-139 7.85 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCACCC 10 0.006830828 145.0 7 AGGAAGA 10 0.006830828 145.0 4 >>END_MODULE SRR7814811 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7814811_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.092 37.0 37.0 37.0 37.0 37.0 2 35.6325 37.0 37.0 37.0 37.0 37.0 3 35.864 37.0 37.0 37.0 37.0 37.0 4 35.8325 37.0 37.0 37.0 37.0 37.0 5 35.978 37.0 37.0 37.0 37.0 37.0 6 35.736 37.0 37.0 37.0 37.0 37.0 7 35.7515 37.0 37.0 37.0 37.0 37.0 8 35.9925 37.0 37.0 37.0 37.0 37.0 9 35.9145 37.0 37.0 37.0 37.0 37.0 10-14 35.8426 37.0 37.0 37.0 37.0 37.0 15-19 35.810700000000004 37.0 37.0 37.0 37.0 37.0 20-24 35.80200000000001 37.0 37.0 37.0 37.0 37.0 25-29 35.7774 37.0 37.0 37.0 37.0 37.0 30-34 35.6658 37.0 37.0 37.0 37.0 37.0 35-39 35.624199999999995 37.0 37.0 37.0 37.0 37.0 40-44 35.5857 37.0 37.0 37.0 37.0 37.0 45-49 35.5532 37.0 37.0 37.0 37.0 37.0 50-54 35.538 37.0 37.0 37.0 37.0 37.0 55-59 35.384 37.0 37.0 37.0 37.0 37.0 60-64 35.263999999999996 37.0 37.0 37.0 34.6 37.0 65-69 35.3145 37.0 37.0 37.0 37.0 37.0 70-74 35.2066 37.0 37.0 37.0 29.8 37.0 75-79 35.2829 37.0 37.0 37.0 34.6 37.0 80-84 35.130100000000006 37.0 37.0 37.0 29.8 37.0 85-89 35.0932 37.0 37.0 37.0 25.0 37.0 90-94 35.0741 37.0 37.0 37.0 25.0 37.0 95-99 34.9373 37.0 37.0 37.0 25.0 37.0 100-104 34.955600000000004 37.0 37.0 37.0 25.0 37.0 105-109 34.8688 37.0 37.0 37.0 25.0 37.0 110-114 34.6666 37.0 37.0 37.0 25.0 37.0 115-119 34.6249 37.0 37.0 37.0 25.0 37.0 120-124 34.6435 37.0 37.0 37.0 25.0 37.0 125-129 34.4775 37.0 37.0 37.0 25.0 37.0 130-134 34.383500000000005 37.0 37.0 37.0 25.0 37.0 135-139 34.0277 37.0 37.0 37.0 25.0 37.0 140-144 34.021699999999996 37.0 37.0 37.0 25.0 37.0 145-149 33.92 37.0 37.0 37.0 25.0 37.0 150-151 33.31625 37.0 37.0 37.0 18.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 4.0 14 7.0 15 5.0 16 6.0 17 4.0 18 1.0 19 1.0 20 6.0 21 9.0 22 10.0 23 10.0 24 10.0 25 11.0 26 18.0 27 17.0 28 22.0 29 50.0 30 52.0 31 71.0 32 105.0 33 195.0 34 398.0 35 1010.0 36 1909.0 37 68.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.699999999999996 18.099999999999998 9.8 30.4 2 29.675 22.05 26.950000000000003 21.325 3 23.025000000000002 24.925 27.700000000000003 24.349999999999998 4 27.800000000000004 29.549999999999997 19.25 23.400000000000002 5 28.825 30.85 19.125 21.2 6 24.025 34.775 18.525 22.675 7 23.7 18.9 34.475 22.925 8 25.124999999999996 21.425 24.45 28.999999999999996 9 24.575 22.375 25.025 28.025 10-14 26.784999999999997 25.619999999999997 22.125 25.47 15-19 26.375 25.314999999999998 23.24 25.069999999999997 20-24 26.25 24.625 23.285 25.840000000000003 25-29 27.0 24.47 23.09 25.44 30-34 26.875 24.98 23.9 24.245 35-39 26.405 25.025 23.45 25.119999999999997 40-44 26.735 23.935000000000002 24.5 24.83 45-49 26.625 24.945 23.544999999999998 24.884999999999998 50-54 26.52 25.55 22.915 25.014999999999997 55-59 27.200000000000003 24.625 23.84 24.335 60-64 26.590000000000003 24.959999999999997 23.835 24.615000000000002 65-69 26.505000000000003 24.525 24.315 24.654999999999998 70-74 27.029999999999998 24.795 23.599999999999998 24.575 75-79 26.58 24.67 24.035 24.715 80-84 26.540000000000003 25.495 23.669999999999998 24.295 85-89 27.12 25.085 23.735 24.060000000000002 90-94 27.060000000000002 24.740000000000002 24.38 23.82 95-99 27.275 24.884999999999998 23.525 24.315 100-104 27.615000000000002 24.335 24.395 23.655 105-109 27.875 24.55 23.925 23.65 110-114 26.974999999999998 25.655 23.330000000000002 24.04 115-119 27.534999999999997 25.924999999999997 23.375 23.165 120-124 27.58 25.25 23.98 23.189999999999998 125-129 28.625 25.080000000000002 23.830000000000002 22.465 130-134 28.349999999999998 24.685000000000002 23.96 23.005 135-139 28.735 25.415 23.855 21.995 140-144 28.355000000000004 25.674999999999997 23.575 22.395 145-149 28.754999999999995 25.245 23.369999999999997 22.63 150-151 28.8625 24.5125 24.0125 22.6125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.5 9 1.0 10 1.0 11 1.0 12 1.0 13 0.5 14 0.5 15 0.5 16 0.5 17 1.0 18 0.5 19 0.0 20 0.5 21 0.5 22 0.5 23 0.5 24 0.0 25 0.5 26 2.5 27 4.0 28 3.0 29 3.0 30 3.0 31 3.0 32 9.0 33 19.0 34 25.0 35 30.5 36 33.5 37 38.0 38 55.0 39 76.5 40 104.0 41 123.5 42 136.0 43 148.0 44 151.5 45 162.0 46 168.0 47 180.0 48 189.0 49 182.0 50 189.0 51 173.0 52 133.0 53 116.5 54 115.0 55 119.5 56 103.5 57 83.5 58 90.0 59 81.5 60 72.0 61 77.5 62 73.5 63 76.5 64 75.5 65 65.0 66 62.5 67 57.5 68 52.5 69 51.5 70 48.5 71 41.5 72 32.0 73 29.0 74 34.5 75 25.0 76 13.5 77 10.5 78 4.5 79 2.5 80 2.5 81 2.0 82 1.0 83 0.5 84 1.0 85 1.0 86 0.5 87 0.0 88 1.5 89 1.5 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.5 97 1.5 98 2.5 99 3.5 100 6.0 >>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 94.35 #Duplication Level Percentage of deduplicated Percentage of total 1 94.67408585055644 89.325 2 4.822469528351881 9.1 3 0.45045045045045046 1.275 4 0.026497085320614733 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.026497085320614733 0.2 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 8 0.2 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.075 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 0.1 0.0 0.0 0.0 0.0 82-83 0.21250000000000002 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.3125 0.0 0.0 0.0 0.0 88-89 0.375 0.0 0.0 0.0 0.0 90-91 0.4625 0.0 0.0 0.0 0.0 92-93 0.5375000000000001 0.0 0.0 0.0 0.0 94-95 0.7375 0.0 0.0 0.0 0.0 96-97 0.9624999999999999 0.0 0.0 0.0 0.0 98-99 1.15 0.0 0.0 0.0 0.0 100-101 1.1875 0.0 0.0 0.0 0.0 102-103 1.2999999999999998 0.0 0.0 0.0 0.0 104-105 1.4625 0.0 0.0 0.0 0.0 106-107 1.65 0.0 0.0 0.0 0.0 108-109 1.925 0.0 0.0 0.0 0.0 110-111 2.075 0.0 0.0 0.0 0.0 112-113 2.425 0.0 0.0 0.0 0.0 114-115 2.7249999999999996 0.0 0.0 0.0 0.0 116-117 3.1875 0.0 0.0 0.0 0.0 118-119 3.625 0.0 0.0 0.0 0.0 120-121 4.0 0.0 0.0 0.0 0.0 122-123 4.425 0.0 0.0 0.0 0.0 124-125 4.725 0.0 0.0 0.0 0.0 126-127 5.0625 0.0 0.0 0.0 0.0 128-129 5.487500000000001 0.0 0.0 0.0 0.0 130-131 5.925 0.0 0.0 0.0 0.0 132-133 6.4375 0.0 0.0 0.0 0.0 134-135 6.8 0.0 0.0 0.0 0.0 136-137 7.275 0.0 0.0 0.0 0.0 138-139 7.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GACGAGG 10 0.006830828 145.0 1 >>END_MODULE Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307801 spots for SRR7814811.sra Written 1307801 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra Read 1307782 spots for SRR7814811.sra Written 1307782 spots for SRR7814811.sra SRR ids: ['SRR7814811.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_721q0wsi SRR7814811.sra spots: 26155659 blocks: [[1, 1307782], [1307783, 2615564], [2615565, 3923346], [3923347, 5231128], [5231129, 6538910], [6538911, 7846692], [7846693, 9154474], [9154475, 10462256], [10462257, 11770038], [11770039, 13077820], [13077821, 14385602], [14385603, 15693384], [15693385, 17001166], [17001167, 18308948], [18308949, 19616730], [19616731, 20924512], [20924513, 22232294], [22232295, 23540076], [23540077, 24847858], [24847859, 26155659]] SRR7814811 file size 8841594 SRR7814811 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 SRR7814811 SRR7814811_1.fastq SRR7814811_2.fastq Input file: SRR7814811_1.fastq Paired file: SRR7814811_2.fastq trimmed: SRR7814811-trimmed-pair1.fastq, SRR7814811-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Fri Dec 6 10:51:07 2024 >> started Fri Dec 6 10:51:36 2024 >> done (29.338s) 26155659 read pairs processed; of these: 120 ( 0.00%) short read pairs filtered out after trimming by size control 14556 ( 0.06%) empty read pairs filtered out after trimming by size control 26140983 (99.94%) read pairs available; of these: 2986833 (11.43%) trimmed read pairs available after processing 23154150 (88.57%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 17 0.00% 20 19 0.00% 21 19 0.00% 22 16 0.00% 23 17 0.00% 24 10 0.00% 25 16 0.00% 26 15 0.00% 27 20 0.00% 28 29 0.00% 29 34 0.00% 30 50 0.00% 31 29 0.00% 32 55 0.00% 33 44 0.00% 34 37 0.00% 35 50 0.00% 36 60 0.00% 37 63 0.00% 38 65 0.00% 39 88 0.00% 40 76 0.00% 41 76 0.00% 42 81 0.00% 43 80 0.00% 44 83 0.00% 45 93 0.00% 46 103 0.00% 47 126 0.00% 48 128 0.00% 49 150 0.00% 50 183 0.00% 51 188 0.00% 52 228 0.00% 53 224 0.00% 54 204 0.00% 55 226 0.00% 56 286 0.00% 57 285 0.00% 58 364 0.00% 59 414 0.00% 60 461 0.00% 61 504 0.00% 62 580 0.00% 63 644 0.00% 64 691 0.00% 65 752 0.00% 66 832 0.00% 67 962 0.00% 68 1117 0.00% 69 1272 0.00% 70 1390 0.01% 71 1678 0.01% 72 1890 0.01% 73 2155 0.01% 74 2442 0.01% 75 2603 0.01% 76 3034 0.01% 77 3247 0.01% 78 3371 0.01% 79 3977 0.02% 80 4480 0.02% 81 5152 0.02% 82 5821 0.02% 83 6554 0.03% 84 7325 0.03% 85 7768 0.03% 86 8561 0.03% 87 9422 0.04% 88 10085 0.04% 89 10824 0.04% 90 11676 0.04% 91 12938 0.05% 92 13912 0.05% 93 15340 0.06% 94 16391 0.06% 95 17444 0.07% 96 18740 0.07% 97 20186 0.08% 98 20759 0.08% 99 21462 0.08% 100 22963 0.09% 101 24153 0.09% 102 25848 0.10% 103 26998 0.10% 104 28190 0.11% 105 29520 0.11% 106 31259 0.12% 107 32066 0.12% 108 32743 0.13% 109 34469 0.13% 110 35310 0.14% 111 36199 0.14% 112 38084 0.15% 113 39052 0.15% 114 40976 0.16% 115 42416 0.16% 116 43368 0.17% 117 44250 0.17% 118 45642 0.17% 119 46090 0.18% 120 46955 0.18% 121 48248 0.18% 122 49607 0.19% 123 51143 0.20% 124 53096 0.20% 125 54192 0.21% 126 55216 0.21% 127 56380 0.22% 128 57400 0.22% 129 57860 0.22% 130 58914 0.23% 131 59925 0.23% 132 61187 0.23% 133 63432 0.24% 134 63753 0.24% 135 65474 0.25% 136 66466 0.25% 137 67299 0.26% 138 68470 0.26% 139 69286 0.27% 140 69740 0.27% 141 71375 0.27% 142 71580 0.27% 143 72994 0.28% 144 74473 0.28% 145 75381 0.29% 146 77253 0.30% 147 78475 0.30% 148 79360 0.30% 149 79453 0.30% 150 80049 0.31% 151 23154150 88.57% 26140983 reads passed initial QC criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=5.46 fanout-score-rank=25 prefix-density=0.24 prefix-fanout=3.8 sequence=GGCAGCCTCCTT criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=339.19 fanout-score-rank=1 prefix-density=0.53 prefix-fanout=18.5 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.44 fanout-score-rank=37 prefix-density=0.43 prefix-fanout=2.3 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=32 fanout-score=453.21 fanout-score-rank=1 prefix-density=1.16 prefix-fanout=19.3 sequence=CGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR7814811 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 10:52:24 Started mapping on | Dec 06 10:52:24 Finished on | Dec 06 10:55:52 Mapping speed, Million of reads per hour | 452.44 Number of input reads | 26140983 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 24406827 Uniquely mapped reads % | 93.37% Average mapped length | 294.58 Number of splices: Total | 23944380 Number of splices: Annotated (sjdb) | 22526497 Number of splices: GT/AG | 23609641 Number of splices: GC/AG | 265874 Number of splices: AT/AC | 18555 Number of splices: Non-canonical | 50310 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.03% Deletion average length | 3.10 Insertion rate per base | 0.03% Insertion average length | 2.62 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 439581 % of reads mapped to multiple loci | 1.68% Number of reads mapped to too many loci | 25858 % of reads mapped to too many loci | 0.10% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.24% % of reads unmapped: other | 0.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1294575 1294575 1294575 N_multimapping 439581 439581 439581 N_noFeature 699022 23778088 936965 N_ambiguous 452999 3004 63313 UnstrandedReadsAssigned:23254806 PositiveStrandReadsAssigned:625735 NegativeStrandReadsAssigned:23406549 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7814811 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: SRR7814811-trimmed-pair1.fastq SRR7814811-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,140,983 reads, 23,865,214 reads pseudoaligned [quant] estimated average fragment length: 264.109 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,143 rounds 52973 SRR7814811.ke.tsv 35125 SRR7814811.se.tsv 88098 total ==> SRR7814811.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 673.418 0 0 PNS24247 1044 780.891 82.0754 6.08433 PNS24249 1928 1664.89 225.425 7.83801 PNS24246 1044 780.891 82.0754 6.08433 PNS24248 1044 780.891 82.0754 6.08433 PNS24244 1471 1207.89 161.349 7.73266 PNS24243 293 96.1969 0 0 KQK14069 1603 1339.89 1965.31 84.9088 KQK14071 474 235.17 4.41824 1.08757 ==> SRR7814811.se.tsv <== BRADI_1g14170v3 1980 BRADI_1g53295v3 732 BRADI_1g59795v3 71 BRADI_1g07683v3 0 BRADI_1g00485v3 68 BRADI_1g20270v3 3023 BRADI_1g74790v3 222 BRADI_1g09890v3 0 BRADI_1g77505v3 318 BRADI_1g48960v3 0 SRR7814811 completed mapping pipeline successfully