Starting /dee2/code/volunteer_pipeline.sh SRR12666366 current disk space = 1543243395072 free memory = 1599346104 SRR12666366 SRAfilesize 5d2bf40971fe5ad2e3d0b0fc0b256776 SRR12666366.sra SRR12666366.sra file validated SRR12666366 is paired end SRR12666366 is conventional basespace SRR12666366 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666366_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3605 37.0 37.0 37.0 37.0 37.0 2 36.28075 37.0 37.0 37.0 37.0 37.0 3 36.377 37.0 37.0 37.0 37.0 37.0 4 36.5235 37.0 37.0 37.0 37.0 37.0 5 36.5235 37.0 37.0 37.0 37.0 37.0 6 36.539 37.0 37.0 37.0 37.0 37.0 7 36.3675 37.0 37.0 37.0 37.0 37.0 8 36.437 37.0 37.0 37.0 37.0 37.0 9 36.4895 37.0 37.0 37.0 37.0 37.0 10-14 36.5046 37.0 37.0 37.0 37.0 37.0 15-19 36.5114 37.0 37.0 37.0 37.0 37.0 20-24 36.4637 37.0 37.0 37.0 37.0 37.0 25-29 36.43390000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.3669 37.0 37.0 37.0 37.0 37.0 35-39 36.3323 37.0 37.0 37.0 37.0 37.0 40-44 36.33560000000001 37.0 37.0 37.0 37.0 37.0 45-49 36.2768 37.0 37.0 37.0 37.0 37.0 50-54 36.248599999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.1948 37.0 37.0 37.0 37.0 37.0 60-64 36.2274 37.0 37.0 37.0 37.0 37.0 65-69 36.1808 37.0 37.0 37.0 37.0 37.0 70-74 36.137600000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.1401 37.0 37.0 37.0 37.0 37.0 80-84 36.1027 37.0 37.0 37.0 37.0 37.0 85-89 36.1367 37.0 37.0 37.0 37.0 37.0 90-94 36.0732 37.0 37.0 37.0 37.0 37.0 95-99 36.0264 37.0 37.0 37.0 37.0 37.0 100-104 36.028 37.0 37.0 37.0 37.0 37.0 105-109 36.0918 37.0 37.0 37.0 37.0 37.0 110-114 35.9221 37.0 37.0 37.0 37.0 37.0 115-119 35.9159 37.0 37.0 37.0 37.0 37.0 120-124 35.8789 37.0 37.0 37.0 37.0 37.0 125-129 35.9159 37.0 37.0 37.0 37.0 37.0 130-134 35.8399 37.0 37.0 37.0 37.0 37.0 135-139 35.870400000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.6385 37.0 37.0 37.0 37.0 37.0 145-149 35.483 37.0 37.0 37.0 37.0 37.0 150-151 35.30025 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 1.0 22 2.0 23 4.0 24 3.0 25 3.0 26 7.0 27 13.0 28 11.0 29 24.0 30 30.0 31 42.0 32 71.0 33 99.0 34 156.0 35 316.0 36 2767.0 37 449.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.175 12.0 8.825 40.0 2 22.327909887359198 16.720901126408013 35.51939924906133 25.431789737171464 3 20.875 22.35 26.025 30.75 4 26.275 28.9 20.65 24.175 5 25.174999999999997 33.0 22.225 19.6 6 20.3 33.6 23.025000000000002 23.075000000000003 7 17.349999999999998 21.15 40.725 20.775 8 20.200000000000003 21.4 28.199999999999996 30.2 9 20.7 20.65 30.7 27.950000000000003 10-14 23.285 26.93 24.75 25.035 15-19 22.8 26.07 25.540000000000003 25.590000000000003 20-24 22.52 25.669999999999998 25.869999999999997 25.94 25-29 23.150000000000002 25.979999999999997 25.115 25.755 30-34 22.89 25.655 25.11 26.345000000000002 35-39 23.285 25.419999999999998 25.205 26.090000000000003 40-44 23.315 25.759999999999998 25.224999999999998 25.7 45-49 23.135 25.795 24.759999999999998 26.31 50-54 23.395 25.83 24.865000000000002 25.91 55-59 23.31 25.865 24.645 26.179999999999996 60-64 23.05 25.835 24.75 26.365 65-69 22.905 25.115 25.615 26.365 70-74 23.415 24.945 25.669999999999998 25.97 75-79 23.53 25.064999999999998 25.585 25.82 80-84 23.86 25.115 24.98 26.045 85-89 23.549999999999997 25.09 25.46 25.900000000000002 90-94 24.404999999999998 24.895 24.8 25.900000000000002 95-99 23.474999999999998 25.06 25.05 26.415 100-104 24.115000000000002 24.884999999999998 24.875 26.125 105-109 24.065 25.05 24.654999999999998 26.229999999999997 110-114 24.25 24.52 25.290000000000003 25.94 115-119 23.745 25.165 25.195 25.895000000000003 120-124 24.0 25.25 24.735 26.015 125-129 24.44 25.055 24.565 25.94 130-134 24.36 24.985 24.69 25.965 135-139 24.09 24.709999999999997 24.83 26.369999999999997 140-144 24.2 24.654999999999998 24.77 26.375 145-149 24.34 25.674999999999997 24.365000000000002 25.619999999999997 150-151 24.675 25.1 23.8125 26.4125 >>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 0.5 14 0.5 15 0.0 16 0.5 17 1.0 18 0.5 19 0.5 20 0.5 21 1.0 22 1.0 23 0.0 24 0.0 25 0.0 26 2.0 27 3.5 28 4.0 29 4.0 30 4.5 31 8.0 32 13.0 33 23.0 34 28.5 35 33.0 36 47.5 37 55.0 38 76.0 39 106.5 40 128.5 41 141.5 42 156.5 43 185.5 44 200.0 45 203.0 46 200.0 47 209.5 48 203.0 49 175.5 50 164.0 51 151.0 52 143.0 53 126.5 54 111.0 55 103.5 56 95.0 57 81.0 58 64.5 59 65.5 60 69.5 61 63.5 62 56.0 63 51.0 64 53.5 65 58.5 66 59.0 67 54.0 68 43.0 69 35.5 70 34.0 71 29.5 72 23.0 73 18.0 74 11.0 75 8.0 76 5.0 77 1.5 78 0.0 79 1.0 80 1.0 81 0.0 82 1.0 83 1.0 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 0.125 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 91.225 #Duplication Level Percentage of deduplicated Percentage of total 1 91.23047410249383 83.22500000000001 2 8.05700191833379 14.7 3 0.6577144423129624 1.7999999999999998 4 0.027404768429706773 0.1 5 0.0 0.0 6 0.0 0.0 7 0.027404768429706773 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 CTCGGCTTCAGGGTACATGTTGCAGCCGTTGCAGCCGCTGCCGCACTTGC 7 0.17500000000000002 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 0.0 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 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.21250000000000002 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.2875 0.0 0.0 0.0 0.0 92-93 0.42500000000000004 0.0 0.0 0.0 0.0 94-95 0.45 0.0 0.0 0.0 0.0 96-97 0.4625 0.0 0.0 0.0 0.0 98-99 0.5375 0.0 0.0 0.0 0.0 100-101 0.7250000000000001 0.0 0.0 0.0 0.0 102-103 0.825 0.0 0.0 0.0 0.0 104-105 1.025 0.0 0.0 0.0 0.0 106-107 1.1625 0.0 0.0 0.0 0.0 108-109 1.375 0.0 0.0 0.0 0.0 110-111 1.625 0.0 0.0 0.0 0.0 112-113 1.775 0.0 0.0 0.0 0.0 114-115 1.95 0.0 0.0 0.0 0.0 116-117 2.2249999999999996 0.0 0.0 0.0 0.0 118-119 2.55 0.0 0.0 0.0 0.0 120-121 2.825 0.0 0.0 0.0 0.0 122-123 3.075 0.0 0.0 0.0 0.0 124-125 3.4749999999999996 0.0 0.0 0.0 0.0 126-127 3.8875 0.0 0.0 0.0 0.0 128-129 4.275 0.0 0.0 0.0 0.0 130-131 4.7 0.0 0.0 0.0 0.0 132-133 5.125 0.0 0.0 0.0 0.0 134-135 5.4 0.0 0.0 0.0 0.0 136-137 5.887499999999999 0.0 0.0 0.0 0.0 138-139 6.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCGGA 65 4.1823133E-4 15.615384 140-144 ATCGGAA 65 0.0076375785 13.384615 140-144 >>END_MODULE SRR12666366 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666366_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 36.0565 37.0 37.0 37.0 37.0 37.0 2 35.888 37.0 37.0 37.0 37.0 37.0 3 36.199 37.0 37.0 37.0 37.0 37.0 4 36.163 37.0 37.0 37.0 37.0 37.0 5 36.2395 37.0 37.0 37.0 37.0 37.0 6 36.05 37.0 37.0 37.0 37.0 37.0 7 36.149 37.0 37.0 37.0 37.0 37.0 8 36.3085 37.0 37.0 37.0 37.0 37.0 9 36.237 37.0 37.0 37.0 37.0 37.0 10-14 36.19089999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.1777 37.0 37.0 37.0 37.0 37.0 20-24 36.1973 37.0 37.0 37.0 37.0 37.0 25-29 36.1184 37.0 37.0 37.0 37.0 37.0 30-34 36.0899 37.0 37.0 37.0 37.0 37.0 35-39 36.063599999999994 37.0 37.0 37.0 37.0 37.0 40-44 36.0244 37.0 37.0 37.0 37.0 37.0 45-49 36.0289 37.0 37.0 37.0 37.0 37.0 50-54 35.970600000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.0252 37.0 37.0 37.0 37.0 37.0 60-64 35.891000000000005 37.0 37.0 37.0 37.0 37.0 65-69 35.96419999999999 37.0 37.0 37.0 37.0 37.0 70-74 35.8851 37.0 37.0 37.0 37.0 37.0 75-79 35.89319999999999 37.0 37.0 37.0 37.0 37.0 80-84 35.8498 37.0 37.0 37.0 37.0 37.0 85-89 35.8549 37.0 37.0 37.0 37.0 37.0 90-94 35.8478 37.0 37.0 37.0 37.0 37.0 95-99 35.819599999999994 37.0 37.0 37.0 37.0 37.0 100-104 35.822900000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.803799999999995 37.0 37.0 37.0 37.0 37.0 110-114 35.7264 37.0 37.0 37.0 37.0 37.0 115-119 35.7452 37.0 37.0 37.0 37.0 37.0 120-124 35.690099999999994 37.0 37.0 37.0 37.0 37.0 125-129 35.7017 37.0 37.0 37.0 37.0 37.0 130-134 35.6906 37.0 37.0 37.0 37.0 37.0 135-139 35.49550000000001 37.0 37.0 37.0 37.0 37.0 140-144 35.466899999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.3974 37.0 37.0 37.0 34.6 37.0 150-151 34.9655 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 4.0 13 3.0 14 3.0 15 7.0 16 0.0 17 0.0 18 2.0 19 5.0 20 1.0 21 3.0 22 5.0 23 8.0 24 6.0 25 9.0 26 7.0 27 7.0 28 18.0 29 21.0 30 24.0 31 50.0 32 75.0 33 95.0 34 167.0 35 435.0 36 2588.0 37 457.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.2 15.925 10.75 33.125 2 27.725 20.5 31.35 20.424999999999997 3 24.375 23.625 27.175 24.825 4 27.55 31.474999999999998 18.0 22.975 5 26.474999999999998 34.050000000000004 18.625 20.849999999999998 6 23.325000000000003 33.375 20.175 23.125 7 22.825 15.65 37.1 24.425 8 22.8 19.75 24.275 33.175 9 23.799999999999997 20.275000000000002 26.5 29.425 10-14 26.534999999999997 25.36 22.31 25.795 15-19 25.97 24.625 24.215 25.19 20-24 25.91 24.925 23.705000000000002 25.46 25-29 26.66 23.71 23.255 26.375 30-34 26.155 24.48 24.185000000000002 25.180000000000003 35-39 25.945 24.005000000000003 24.560000000000002 25.490000000000002 40-44 26.25 24.83 23.845 25.074999999999996 45-49 26.465 25.240000000000002 23.105 25.19 50-54 25.635 24.535 24.4 25.430000000000003 55-59 27.005000000000003 24.66 23.68 24.654999999999998 60-64 26.229999999999997 25.019999999999996 23.799999999999997 24.95 65-69 26.11 24.834999999999997 24.09 24.965 70-74 26.384999999999998 24.315 24.57 24.73 75-79 26.400000000000002 24.395 24.57 24.635 80-84 27.065 25.419999999999998 23.189999999999998 24.325 85-89 26.3 25.1 24.15 24.45 90-94 25.979999999999997 24.73 24.224999999999998 25.064999999999998 95-99 26.77 24.92 24.46 23.849999999999998 100-104 26.840000000000003 24.59 24.23 24.34 105-109 27.355 24.65 24.099999999999998 23.895 110-114 26.83 25.195 23.84 24.135 115-119 27.21 25.085 23.630000000000003 24.075 120-124 26.705000000000002 25.795 23.925 23.575 125-129 27.13 25.995 23.69 23.185 130-134 27.439999999999998 24.91 23.98 23.669999999999998 135-139 27.615000000000002 25.779999999999998 23.669999999999998 22.935 140-144 27.310000000000002 25.215 24.22 23.255 145-149 27.66 26.02 23.555 22.765 150-151 28.249999999999996 25.575 23.7875 22.3875 >>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 1.0 7 1.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 1.0 15 1.0 16 0.5 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 1.0 23 1.0 24 0.0 25 1.0 26 2.0 27 2.0 28 3.0 29 2.5 30 3.0 31 6.0 32 8.5 33 10.5 34 17.0 35 27.0 36 29.5 37 42.0 38 56.5 39 78.5 40 102.5 41 107.0 42 125.5 43 166.0 44 198.0 45 198.5 46 188.0 47 179.5 48 171.5 49 163.5 50 157.0 51 149.0 52 130.0 53 122.5 54 122.5 55 105.5 56 91.0 57 87.0 58 91.5 59 94.0 60 81.5 61 80.0 62 85.5 63 85.0 64 77.0 65 60.0 66 67.0 67 80.5 68 66.5 69 49.0 70 48.0 71 48.0 72 32.5 73 22.5 74 18.0 75 10.0 76 8.0 77 9.5 78 6.5 79 1.5 80 0.5 81 0.0 82 0.5 83 0.5 84 0.0 85 0.5 86 1.5 87 1.0 88 0.5 89 0.5 90 0.0 91 1.0 92 1.5 93 1.0 94 1.0 95 0.5 96 0.0 97 0.5 98 0.5 99 0.5 100 2.5 >>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 91.225 #Duplication Level Percentage of deduplicated Percentage of total 1 91.34009317621266 83.325 2 7.919978076185257 14.45 3 0.6303096738832557 1.725 4 0.027404768429706773 0.1 5 0.054809536859413546 0.25 6 0.027404768429706773 0.15 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 GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 6 0.15 No Hit CGGATGGCGGATGGTTCATGGATGTGTTTCATGTGCTGAATAAGCAAGGG 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 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 0.0 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 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.21250000000000002 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.2875 0.0 0.0 0.0 0.0 92-93 0.42500000000000004 0.0 0.0 0.0 0.0 94-95 0.45 0.0 0.0 0.0 0.0 96-97 0.4625 0.0 0.0 0.0 0.0 98-99 0.5375 0.0 0.0 0.0 0.0 100-101 0.7250000000000001 0.0 0.0 0.0 0.0 102-103 0.8374999999999999 0.0 0.0 0.0 0.0 104-105 1.05 0.0 0.0 0.0 0.0 106-107 1.2125 0.0 0.0 0.0 0.0 108-109 1.4249999999999998 0.0 0.0 0.0 0.0 110-111 1.675 0.0 0.0 0.0 0.0 112-113 1.825 0.0 0.0 0.0 0.0 114-115 2.0 0.0 0.0 0.0 0.0 116-117 2.2750000000000004 0.0 0.0 0.0 0.0 118-119 2.5999999999999996 0.0 0.0 0.0 0.0 120-121 2.875 0.0 0.0 0.0 0.0 122-123 3.125 0.0 0.0 0.0 0.0 124-125 3.5250000000000004 0.0 0.0 0.0 0.0 126-127 3.9125 0.0 0.0 0.0 0.0 128-129 4.3 0.0 0.0 0.0 0.0 130-131 4.7 0.0 0.0 0.0 0.0 132-133 5.125 0.0 0.0 0.0 0.0 134-135 5.4 0.0 0.0 0.0 0.0 136-137 5.887499999999999 0.0 0.0 0.0 0.0 138-139 6.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATCCTG 10 0.006830828 145.0 145 GATCGGA 60 0.004491891 14.500001 140-144 >>END_MODULE Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683985 spots for SRR12666366.sra Written 1683985 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra Read 1683978 spots for SRR12666366.sra Written 1683978 spots for SRR12666366.sra SRR ids: ['SRR12666366.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lgbhpjly SRR12666366.sra spots: 33679567 blocks: [[1, 1683978], [1683979, 3367956], [3367957, 5051934], [5051935, 6735912], [6735913, 8419890], [8419891, 10103868], [10103869, 11787846], [11787847, 13471824], [13471825, 15155802], [15155803, 16839780], [16839781, 18523758], [18523759, 20207736], [20207737, 21891714], [21891715, 23575692], [23575693, 25259670], [25259671, 26943648], [26943649, 28627626], [28627627, 30311604], [30311605, 31995582], [31995583, 33679567]] SRR12666366 file size 11424089 SRR12666366 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 SRR12666366 SRR12666366_1.fastq SRR12666366_2.fastq Input file: SRR12666366_1.fastq Paired file: SRR12666366_2.fastq trimmed: SRR12666366-trimmed-pair1.fastq, SRR12666366-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 13:19:01 2024 >> started Sat Dec 7 13:19:59 2024 >> done (57.844s) 33679567 read pairs processed; of these: 81 ( 0.00%) short read pairs filtered out after trimming by size control 15295 ( 0.05%) empty read pairs filtered out after trimming by size control 33664191 (99.95%) read pairs available; of these: 3228884 ( 9.59%) trimmed read pairs available after processing 30435307 (90.41%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 10 0.00% 20 11 0.00% 21 15 0.00% 22 14 0.00% 23 23 0.00% 24 18 0.00% 25 30 0.00% 26 15 0.00% 27 31 0.00% 28 32 0.00% 29 44 0.00% 30 22 0.00% 31 33 0.00% 32 40 0.00% 33 47 0.00% 34 41 0.00% 35 53 0.00% 36 35 0.00% 37 40 0.00% 38 55 0.00% 39 51 0.00% 40 28 0.00% 41 59 0.00% 42 67 0.00% 43 73 0.00% 44 59 0.00% 45 71 0.00% 46 65 0.00% 47 79 0.00% 48 83 0.00% 49 94 0.00% 50 107 0.00% 51 104 0.00% 52 131 0.00% 53 133 0.00% 54 151 0.00% 55 174 0.00% 56 177 0.00% 57 153 0.00% 58 194 0.00% 59 235 0.00% 60 264 0.00% 61 241 0.00% 62 340 0.00% 63 381 0.00% 64 419 0.00% 65 427 0.00% 66 504 0.00% 67 511 0.00% 68 626 0.00% 69 707 0.00% 70 831 0.00% 71 978 0.00% 72 1158 0.00% 73 1332 0.00% 74 1404 0.00% 75 1529 0.00% 76 1815 0.01% 77 1945 0.01% 78 2332 0.01% 79 2590 0.01% 80 2981 0.01% 81 3285 0.01% 82 3865 0.01% 83 4390 0.01% 84 4884 0.01% 85 5359 0.02% 86 5925 0.02% 87 6600 0.02% 88 7076 0.02% 89 7833 0.02% 90 8656 0.03% 91 9738 0.03% 92 10910 0.03% 93 12304 0.04% 94 13412 0.04% 95 14390 0.04% 96 15246 0.05% 97 16173 0.05% 98 17194 0.05% 99 18474 0.05% 100 19744 0.06% 101 21075 0.06% 102 22926 0.07% 103 24950 0.07% 104 26339 0.08% 105 28186 0.08% 106 29313 0.09% 107 30255 0.09% 108 31868 0.09% 109 33228 0.10% 110 34158 0.10% 111 36318 0.11% 112 38644 0.11% 113 39924 0.12% 114 42392 0.13% 115 44441 0.13% 116 44906 0.13% 117 46722 0.14% 118 47949 0.14% 119 48433 0.14% 120 49959 0.15% 121 52316 0.16% 122 53657 0.16% 123 55911 0.17% 124 58965 0.18% 125 60485 0.18% 126 61944 0.18% 127 63325 0.19% 128 64453 0.19% 129 65467 0.19% 130 66212 0.20% 131 67707 0.20% 132 69715 0.21% 133 71622 0.21% 134 74466 0.22% 135 77116 0.23% 136 78444 0.23% 137 79206 0.24% 138 80690 0.24% 139 82056 0.24% 140 81809 0.24% 141 82681 0.25% 142 84846 0.25% 143 86766 0.26% 144 88689 0.26% 145 92380 0.27% 146 93807 0.28% 147 94718 0.28% 148 95671 0.28% 149 94728 0.28% 150 95364 0.28% 151 30435307 90.41% 33664191 reads passed initial QC criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=4.52 fanout-score-rank=22 prefix-density=0.18 prefix-fanout=3.6 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.04 sequence-density-rank=24 fanout-score=205.81 fanout-score-rank=1 prefix-density=0.48 prefix-fanout=16.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.41 fanout-score-rank=34 prefix-density=0.35 prefix-fanout=2.3 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=33 fanout-score=648.97 fanout-score-rank=1 prefix-density=0.97 prefix-fanout=20.2 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12666366 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:20:40 Started mapping on | Dec 07 13:20:40 Finished on | Dec 07 13:25:03 Mapping speed, Million of reads per hour | 460.80 Number of input reads | 33664191 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 32018626 Uniquely mapped reads % | 95.11% Average mapped length | 296.40 Number of splices: Total | 35008395 Number of splices: Annotated (sjdb) | 32828273 Number of splices: GT/AG | 34510226 Number of splices: GC/AG | 391322 Number of splices: AT/AC | 26357 Number of splices: Non-canonical | 80490 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.89 Insertion rate per base | 0.02% Insertion average length | 2.53 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 475677 % of reads mapped to multiple loci | 1.41% Number of reads mapped to too many loci | 45417 % of reads mapped to too many loci | 0.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.56% % of reads unmapped: other | 0.78% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1169888 1169888 1169888 N_multimapping 475677 475677 475677 N_noFeature 991588 31273254 1231994 N_ambiguous 596995 4287 92568 UnstrandedReadsAssigned:30430043 PositiveStrandReadsAssigned:741085 NegativeStrandReadsAssigned:30694064 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666366 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: SRR12666366-trimmed-pair1.fastq SRR12666366-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,664,191 reads, 30,958,800 reads pseudoaligned [quant] estimated average fragment length: 282.727 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,277 rounds 52973 SRR12666366.ke.tsv 35125 SRR12666366.se.tsv 88098 total ==> SRR12666366.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 655.133 0 0 PNS24247 1044 762.273 121.432 7.54765 PNS24249 1928 1646.27 212.017 6.10181 PNS24246 1044 762.273 121.432 7.54765 PNS24248 1044 762.273 121.432 7.54765 PNS24244 1471 1189.27 244.688 9.74814 PNS24243 293 93.1892 1 0.508423 KQK14069 1603 1321.27 4994.91 179.112 KQK14071 474 225.958 50.3564 10.5589 ==> SRR12666366.se.tsv <== BRADI_1g14170v3 5331 BRADI_1g53295v3 1571 BRADI_1g59795v3 126 BRADI_1g07683v3 0 BRADI_1g00485v3 114 BRADI_1g20270v3 3664 BRADI_1g74790v3 164 BRADI_1g09890v3 0 BRADI_1g77505v3 301 BRADI_1g48960v3 0 SRR12666366 completed mapping pipeline successfully