Starting /dee2/code/volunteer_pipeline.sh SRR12666362 current disk space = 1543049039872 free memory = 1597499512 SRR12666362 SRAfilesize 995e88fbf95cda2768ef82e94e710560 SRR12666362.sra SRR12666362.sra file validated SRR12666362 is paired end SRR12666362 is conventional basespace SRR12666362 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666362_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 36.253 37.0 37.0 37.0 37.0 37.0 2 36.127 37.0 37.0 37.0 37.0 37.0 3 36.3635 37.0 37.0 37.0 37.0 37.0 4 36.462 37.0 37.0 37.0 37.0 37.0 5 36.478 37.0 37.0 37.0 37.0 37.0 6 36.428 37.0 37.0 37.0 37.0 37.0 7 36.3655 37.0 37.0 37.0 37.0 37.0 8 36.569 37.0 37.0 37.0 37.0 37.0 9 36.461 37.0 37.0 37.0 37.0 37.0 10-14 36.4565 37.0 37.0 37.0 37.0 37.0 15-19 36.456399999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.3805 37.0 37.0 37.0 37.0 37.0 25-29 36.362700000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.313599999999994 37.0 37.0 37.0 37.0 37.0 35-39 36.3139 37.0 37.0 37.0 37.0 37.0 40-44 36.2626 37.0 37.0 37.0 37.0 37.0 45-49 36.2568 37.0 37.0 37.0 37.0 37.0 50-54 36.2192 37.0 37.0 37.0 37.0 37.0 55-59 36.2025 37.0 37.0 37.0 37.0 37.0 60-64 36.1762 37.0 37.0 37.0 37.0 37.0 65-69 36.1703 37.0 37.0 37.0 37.0 37.0 70-74 36.132600000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.132799999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.028200000000005 37.0 37.0 37.0 37.0 37.0 85-89 36.0347 37.0 37.0 37.0 37.0 37.0 90-94 36.0329 37.0 37.0 37.0 37.0 37.0 95-99 35.9653 37.0 37.0 37.0 37.0 37.0 100-104 36.0166 37.0 37.0 37.0 37.0 37.0 105-109 36.0631 37.0 37.0 37.0 37.0 37.0 110-114 35.9348 37.0 37.0 37.0 37.0 37.0 115-119 35.8625 37.0 37.0 37.0 37.0 37.0 120-124 35.8601 37.0 37.0 37.0 37.0 37.0 125-129 35.863899999999994 37.0 37.0 37.0 37.0 37.0 130-134 35.8645 37.0 37.0 37.0 37.0 37.0 135-139 35.91330000000001 37.0 37.0 37.0 37.0 37.0 140-144 35.62820000000001 37.0 37.0 37.0 37.0 37.0 145-149 35.5829 37.0 37.0 37.0 37.0 37.0 150-151 35.338499999999996 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 1.0 23 2.0 24 6.0 25 10.0 26 8.0 27 16.0 28 19.0 29 31.0 30 27.0 31 49.0 32 66.0 33 88.0 34 136.0 35 304.0 36 2772.0 37 463.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.974999999999994 12.35 8.799999999999999 34.875 2 21.5607803901951 18.10905452726363 35.36768384192096 24.96248124062031 3 21.15 22.775000000000002 24.975 31.1 4 25.374999999999996 31.275 19.650000000000002 23.7 5 24.7 32.625 21.8 20.875 6 20.974999999999998 33.800000000000004 23.95 21.275 7 16.7 22.175 41.099999999999994 20.025000000000002 8 21.525 21.525 28.475 28.475 9 22.0 20.225 30.125 27.650000000000002 10-14 22.634999999999998 26.655 24.905 25.805 15-19 22.695 25.6 25.540000000000003 26.165 20-24 22.56 25.955000000000002 25.455 26.029999999999998 25-29 23.385 25.605 25.345000000000002 25.665 30-34 22.785 25.72 25.130000000000003 26.365 35-39 23.005 25.55 24.9 26.545 40-44 23.155 26.06 25.040000000000003 25.745 45-49 23.810000000000002 25.374999999999996 24.92 25.895000000000003 50-54 24.055 25.545 24.865000000000002 25.535000000000004 55-59 23.23 25.840000000000003 24.77 26.16 60-64 23.47 25.96 24.709999999999997 25.86 65-69 23.305 25.814999999999998 25.15 25.729999999999997 70-74 23.43 25.53 25.155 25.885 75-79 23.880000000000003 25.285000000000004 25.130000000000003 25.705 80-84 23.39 25.6 25.03 25.979999999999997 85-89 23.810000000000002 25.369999999999997 25.080000000000002 25.740000000000002 90-94 22.8 25.985000000000003 24.995 26.22 95-99 23.65 25.52 25.11 25.72 100-104 24.245 25.324999999999996 25.0 25.430000000000003 105-109 23.41 25.865 24.75 25.974999999999998 110-114 23.985 25.205 24.925 25.885 115-119 24.285 25.590000000000003 24.38 25.745 120-124 24.595 24.935 24.555 25.915 125-129 24.66 25.3 24.335 25.705 130-134 23.755000000000003 25.124999999999996 24.905 26.215 135-139 23.955000000000002 25.525 24.72 25.8 140-144 24.474999999999998 26.275 24.445 24.805 145-149 23.905 25.825 24.375 25.895000000000003 150-151 23.799999999999997 24.9875 24.975 26.237500000000004 >>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 0.5 20 0.0 21 0.0 22 0.5 23 0.5 24 1.0 25 1.5 26 1.5 27 2.5 28 2.0 29 4.5 30 8.0 31 10.0 32 15.5 33 17.0 34 21.5 35 33.0 36 43.5 37 58.0 38 84.5 39 108.5 40 112.0 41 139.0 42 176.5 43 189.0 44 186.0 45 196.0 46 204.5 47 188.0 48 184.0 49 187.5 50 184.5 51 164.5 52 142.0 53 123.0 54 119.0 55 115.0 56 95.0 57 89.5 58 85.0 59 76.5 60 73.5 61 69.5 62 59.5 63 47.0 64 46.5 65 53.0 66 55.5 67 50.0 68 38.5 69 32.5 70 27.0 71 19.5 72 17.0 73 13.0 74 9.0 75 5.5 76 2.0 77 4.0 78 2.5 79 1.0 80 1.5 81 0.5 82 0.5 83 0.5 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 0.05 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 91.2 #Duplication Level Percentage of deduplicated Percentage of total 1 91.1732456140351 83.15 2 8.086622807017543 14.75 3 0.6853070175438596 1.875 4 0.027412280701754384 0.1 5 0.027412280701754384 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 GTCCATTGAAAATCCTTGGAGATTCATGAACAAACCGACCTCACATTAGG 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.07500000000000001 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.15 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.2625 0.0 0.0 0.0 0.0 92-93 0.2875 0.0 0.0 0.0 0.0 94-95 0.3625 0.0 0.0 0.0 0.0 96-97 0.45 0.0 0.0 0.0 0.0 98-99 0.5875 0.0 0.0 0.0 0.0 100-101 0.7124999999999999 0.0 0.0 0.0 0.0 102-103 0.8125 0.0 0.0 0.0 0.0 104-105 0.9125 0.0 0.0 0.0 0.0 106-107 1.15 0.0 0.0 0.0 0.0 108-109 1.3125 0.0 0.0 0.0 0.0 110-111 1.425 0.0 0.0 0.0 0.0 112-113 1.5875 0.0 0.0 0.0 0.0 114-115 1.85 0.0 0.0 0.0 0.0 116-117 2.0125 0.0 0.0 0.0 0.0 118-119 2.325 0.0 0.0 0.0 0.0 120-121 2.6 0.0 0.0 0.0 0.0 122-123 2.825 0.0 0.0 0.0 0.0 124-125 3.075 0.0 0.0 0.0 0.0 126-127 3.375 0.0 0.0 0.0 0.0 128-129 3.75 0.0 0.0 0.0 0.0 130-131 4.05 0.0 0.0 0.0 0.0 132-133 4.575 0.0 0.0 0.0 0.0 134-135 4.9875 0.0 0.0 0.0 0.0 136-137 5.550000000000001 0.0 0.0 0.0 0.0 138-139 6.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTT 40 0.005621335 54.375 1 >>END_MODULE SRR12666362 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666362_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 35.978 37.0 37.0 37.0 37.0 37.0 2 35.7435 37.0 37.0 37.0 37.0 37.0 3 35.976 37.0 37.0 37.0 37.0 37.0 4 36.06 37.0 37.0 37.0 37.0 37.0 5 36.163 37.0 37.0 37.0 37.0 37.0 6 35.9945 37.0 37.0 37.0 37.0 37.0 7 35.957 37.0 37.0 37.0 37.0 37.0 8 36.179 37.0 37.0 37.0 37.0 37.0 9 36.1325 37.0 37.0 37.0 37.0 37.0 10-14 36.1589 37.0 37.0 37.0 37.0 37.0 15-19 36.0899 37.0 37.0 37.0 37.0 37.0 20-24 36.012299999999996 37.0 37.0 37.0 37.0 37.0 25-29 35.9935 37.0 37.0 37.0 37.0 37.0 30-34 35.921299999999995 37.0 37.0 37.0 37.0 37.0 35-39 35.9631 37.0 37.0 37.0 37.0 37.0 40-44 35.8831 37.0 37.0 37.0 37.0 37.0 45-49 35.8801 37.0 37.0 37.0 37.0 37.0 50-54 35.85119999999999 37.0 37.0 37.0 37.0 37.0 55-59 35.87349999999999 37.0 37.0 37.0 37.0 37.0 60-64 35.7967 37.0 37.0 37.0 37.0 37.0 65-69 35.8409 37.0 37.0 37.0 37.0 37.0 70-74 35.7819 37.0 37.0 37.0 37.0 37.0 75-79 35.797799999999995 37.0 37.0 37.0 37.0 37.0 80-84 35.8065 37.0 37.0 37.0 37.0 37.0 85-89 35.7381 37.0 37.0 37.0 37.0 37.0 90-94 35.728699999999996 37.0 37.0 37.0 37.0 37.0 95-99 35.6314 37.0 37.0 37.0 37.0 37.0 100-104 35.7086 37.0 37.0 37.0 37.0 37.0 105-109 35.63590000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.578199999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.5921 37.0 37.0 37.0 37.0 37.0 120-124 35.5312 37.0 37.0 37.0 37.0 37.0 125-129 35.556200000000004 37.0 37.0 37.0 37.0 37.0 130-134 35.5818 37.0 37.0 37.0 37.0 37.0 135-139 35.41180000000001 37.0 37.0 37.0 34.6 37.0 140-144 35.3239 37.0 37.0 37.0 37.0 37.0 145-149 35.2932 37.0 37.0 37.0 34.6 37.0 150-151 34.99325 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 1.0 14 8.0 15 4.0 16 2.0 17 2.0 18 3.0 19 3.0 20 3.0 21 4.0 22 8.0 23 10.0 24 10.0 25 9.0 26 16.0 27 23.0 28 15.0 29 29.0 30 26.0 31 49.0 32 58.0 33 99.0 34 168.0 35 504.0 36 2573.0 37 372.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.625 14.524999999999999 9.725 31.125000000000004 2 28.95 20.7 29.075 21.275 3 25.224999999999998 23.325000000000003 26.775 24.675 4 27.85 31.05 18.325 22.775000000000002 5 28.525 32.9 18.4 20.175 6 22.425 32.5 19.35 25.724999999999998 7 21.9 16.400000000000002 37.525 24.175 8 24.25 20.8 23.599999999999998 31.35 9 25.525 21.2 24.75 28.525 10-14 26.14 24.745 23.044999999999998 26.07 15-19 26.13 24.735 23.39 25.745 20-24 25.679999999999996 25.224999999999998 23.825 25.27 25-29 25.765 24.59 24.25 25.395 30-34 26.150000000000002 25.165 23.630000000000003 25.055 35-39 25.869999999999997 24.59 24.22 25.319999999999997 40-44 26.06 24.709999999999997 23.625 25.605 45-49 26.150000000000002 24.695 24.245 24.91 50-54 26.790000000000003 25.405 23.54 24.265 55-59 26.834999999999997 24.375 23.905 24.884999999999998 60-64 26.06 24.63 24.65 24.66 65-69 26.525 24.735 24.490000000000002 24.25 70-74 26.534999999999997 24.725 24.94 23.799999999999997 75-79 26.395000000000003 24.075 24.635 24.895 80-84 26.31 24.955 24.005000000000003 24.73 85-89 26.305 24.905 24.66 24.13 90-94 26.605 24.68 24.545 24.169999999999998 95-99 26.905 24.66 24.845 23.59 100-104 26.865 24.98 24.21 23.945 105-109 26.55 25.135 24.03 24.285 110-114 25.929999999999996 25.035 24.88 24.154999999999998 115-119 26.325 26.055 24.245 23.375 120-124 27.084999999999997 25.419999999999998 24.21 23.285 125-129 27.21 25.540000000000003 24.310000000000002 22.939999999999998 130-134 27.455000000000002 24.73 24.48 23.335 135-139 27.884999999999998 25.515 23.385 23.215 140-144 27.150000000000002 25.09 24.37 23.39 145-149 27.950000000000003 25.490000000000002 24.095 22.465 150-151 28.212500000000002 24.4125 24.3125 23.0625 >>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 0.5 6 0.5 7 0.5 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.5 28 2.5 29 7.5 30 10.0 31 6.5 32 10.5 33 13.5 34 16.0 35 26.0 36 35.5 37 43.0 38 59.5 39 83.0 40 96.5 41 130.5 42 145.0 43 146.5 44 174.5 45 180.0 46 176.5 47 170.5 48 177.5 49 173.0 50 158.0 51 155.0 52 143.5 53 128.0 54 117.5 55 103.0 56 91.0 57 102.0 58 104.0 59 94.0 60 84.5 61 82.0 62 79.0 63 77.0 64 72.5 65 67.0 66 65.5 67 61.0 68 60.0 69 53.0 70 49.5 71 40.5 72 26.5 73 22.0 74 16.5 75 12.0 76 8.5 77 8.0 78 6.5 79 2.5 80 1.0 81 1.0 82 0.5 83 0.5 84 1.0 85 1.0 86 1.0 87 1.0 88 0.5 89 0.5 90 0.5 91 0.0 92 0.5 93 0.5 94 0.5 95 1.5 96 2.0 97 1.0 98 0.5 99 1.0 100 2.0 >>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 91.475 #Duplication Level Percentage of deduplicated Percentage of total 1 91.58239956272205 83.775 2 7.65236403388904 14.000000000000002 3 0.6832467887400929 1.875 4 0.027329871549603715 0.1 5 0.05465974309920743 0.25 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 CTCCAGGCCGATTACACCGAGGGGGATGCTCTGGACGCCCTGGGTTTGGT 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 0.025 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.07500000000000001 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1375 0.0 0.0 0.0 0.0 84-85 0.16249999999999998 0.0 0.0 0.0 0.0 86-87 0.225 0.0 0.0 0.0 0.0 88-89 0.275 0.0 0.0 0.0 0.0 90-91 0.2875 0.0 0.0 0.0 0.0 92-93 0.3125 0.0 0.0 0.0 0.0 94-95 0.375 0.0 0.0 0.0 0.0 96-97 0.45 0.0 0.0 0.0 0.0 98-99 0.5875 0.0 0.0 0.0 0.0 100-101 0.7124999999999999 0.0 0.0 0.0 0.0 102-103 0.8125 0.0 0.0 0.0 0.0 104-105 0.9125 0.0 0.0 0.0 0.0 106-107 1.15 0.0 0.0 0.0 0.0 108-109 1.3125 0.0 0.0 0.0 0.0 110-111 1.425 0.0 0.0 0.0 0.0 112-113 1.5875 0.0 0.0 0.0 0.0 114-115 1.8375 0.0 0.0 0.0 0.0 116-117 2.0125 0.0 0.0 0.0 0.0 118-119 2.325 0.0 0.0 0.0 0.0 120-121 2.6 0.0 0.0 0.0 0.0 122-123 2.8375 0.0 0.0 0.0 0.0 124-125 3.0999999999999996 0.0 0.0 0.0 0.0 126-127 3.4000000000000004 0.0 0.0 0.0 0.0 128-129 3.7750000000000004 0.0 0.0 0.0 0.0 130-131 4.075 0.0 0.0 0.0 0.0 132-133 4.6 0.0 0.0 0.0 0.0 134-135 5.0125 0.0 0.0 0.0 0.0 136-137 5.550000000000001 0.0 0.0 0.0 0.0 138-139 6.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATGGTTA 10 0.006830828 145.0 3 GATGGTT 10 0.006830828 145.0 2 >>END_MODULE Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703842 spots for SRR12666362.sra Written 1703842 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra Read 1703824 spots for SRR12666362.sra Written 1703824 spots for SRR12666362.sra SRR ids: ['SRR12666362.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yi4blj4k SRR12666362.sra spots: 34076498 blocks: [[1, 1703824], [1703825, 3407648], [3407649, 5111472], [5111473, 6815296], [6815297, 8519120], [8519121, 10222944], [10222945, 11926768], [11926769, 13630592], [13630593, 15334416], [15334417, 17038240], [17038241, 18742064], [18742065, 20445888], [20445889, 22149712], [22149713, 23853536], [23853537, 25557360], [25557361, 27261184], [27261185, 28965008], [28965009, 30668832], [30668833, 32372656], [32372657, 34076498]] SRR12666362 file size 11558984 SRR12666362 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 SRR12666362 SRR12666362_1.fastq SRR12666362_2.fastq Input file: SRR12666362_1.fastq Paired file: SRR12666362_2.fastq trimmed: SRR12666362-trimmed-pair1.fastq, SRR12666362-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 13:07:18 2024 >> started Sat Dec 7 13:08:01 2024 >> done (43.026s) 34076498 read pairs processed; of these: 87 ( 0.00%) short read pairs filtered out after trimming by size control 12500 ( 0.04%) empty read pairs filtered out after trimming by size control 34063911 (99.96%) read pairs available; of these: 2829891 ( 8.31%) trimmed read pairs available after processing 31234020 (91.69%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 10 0.00% 20 15 0.00% 21 15 0.00% 22 13 0.00% 23 26 0.00% 24 23 0.00% 25 31 0.00% 26 31 0.00% 27 33 0.00% 28 41 0.00% 29 38 0.00% 30 43 0.00% 31 51 0.00% 32 52 0.00% 33 38 0.00% 34 49 0.00% 35 53 0.00% 36 76 0.00% 37 66 0.00% 38 80 0.00% 39 71 0.00% 40 86 0.00% 41 71 0.00% 42 90 0.00% 43 74 0.00% 44 85 0.00% 45 99 0.00% 46 94 0.00% 47 91 0.00% 48 134 0.00% 49 148 0.00% 50 147 0.00% 51 148 0.00% 52 160 0.00% 53 177 0.00% 54 211 0.00% 55 190 0.00% 56 224 0.00% 57 231 0.00% 58 266 0.00% 59 290 0.00% 60 342 0.00% 61 398 0.00% 62 454 0.00% 63 458 0.00% 64 520 0.00% 65 566 0.00% 66 574 0.00% 67 644 0.00% 68 780 0.00% 69 877 0.00% 70 957 0.00% 71 1094 0.00% 72 1365 0.00% 73 1594 0.00% 74 1758 0.01% 75 1804 0.01% 76 1887 0.01% 77 2116 0.01% 78 2408 0.01% 79 2714 0.01% 80 3134 0.01% 81 3556 0.01% 82 4114 0.01% 83 4660 0.01% 84 5091 0.01% 85 5586 0.02% 86 5947 0.02% 87 6442 0.02% 88 6884 0.02% 89 7571 0.02% 90 8317 0.02% 91 9444 0.03% 92 10660 0.03% 93 11657 0.03% 94 12473 0.04% 95 13342 0.04% 96 14595 0.04% 97 14815 0.04% 98 15507 0.05% 99 16439 0.05% 100 17379 0.05% 101 18802 0.06% 102 20521 0.06% 103 22373 0.07% 104 23611 0.07% 105 24851 0.07% 106 25907 0.08% 107 26399 0.08% 108 27312 0.08% 109 28100 0.08% 110 29579 0.09% 111 31108 0.09% 112 33117 0.10% 113 34740 0.10% 114 36680 0.11% 115 38308 0.11% 116 39119 0.11% 117 39954 0.12% 118 40631 0.12% 119 41671 0.12% 120 42560 0.12% 121 44761 0.13% 122 46794 0.14% 123 48588 0.14% 124 51316 0.15% 125 52724 0.15% 126 53602 0.16% 127 54810 0.16% 128 55231 0.16% 129 55695 0.16% 130 57046 0.17% 131 57833 0.17% 132 60456 0.18% 133 62438 0.18% 134 64495 0.19% 135 66874 0.20% 136 68764 0.20% 137 69186 0.20% 138 69579 0.20% 139 70654 0.21% 140 70482 0.21% 141 72067 0.21% 142 73760 0.22% 143 75595 0.22% 144 77749 0.23% 145 80983 0.24% 146 82188 0.24% 147 84021 0.25% 148 83936 0.25% 149 83575 0.25% 150 84535 0.25% 151 31234020 91.69% 34063911 reads passed initial QC criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=4.69 fanout-score-rank=23 prefix-density=0.21 prefix-fanout=3.7 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.04 sequence-density-rank=23 fanout-score=163.84 fanout-score-rank=1 prefix-density=0.45 prefix-fanout=16.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=2.39 fanout-score-rank=28 prefix-density=0.32 prefix-fanout=2.3 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.07 sequence-density-rank=25 fanout-score=309.87 fanout-score-rank=1 prefix-density=1.01 prefix-fanout=21.4 sequence=CCGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12666362 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:08:44 Started mapping on | Dec 07 13:08:44 Finished on | Dec 07 13:12:20 Mapping speed, Million of reads per hour | 567.73 Number of input reads | 34063911 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 32170250 Uniquely mapped reads % | 94.44% Average mapped length | 296.85 Number of splices: Total | 34718122 Number of splices: Annotated (sjdb) | 32599150 Number of splices: GT/AG | 34221113 Number of splices: GC/AG | 388947 Number of splices: AT/AC | 25522 Number of splices: Non-canonical | 82540 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.53 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 524098 % of reads mapped to multiple loci | 1.54% Number of reads mapped to too many loci | 46446 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.99% % of reads unmapped: other | 0.89% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1369563 1369563 1369563 N_multimapping 524098 524098 524098 N_noFeature 1033551 31435866 1280119 N_ambiguous 581474 4215 94837 UnstrandedReadsAssigned:30555225 PositiveStrandReadsAssigned:730169 NegativeStrandReadsAssigned:30795294 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666362 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: SRR12666362-trimmed-pair1.fastq SRR12666362-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 34,063,911 reads, 31,147,237 reads pseudoaligned [quant] estimated average fragment length: 291.003 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,212 rounds 52973 SRR12666362.ke.tsv 35125 SRR12666362.se.tsv 88098 total ==> SRR12666362.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 646.929 0 0 PNS24247 1044 753.997 153.399 9.93733 PNS24249 1928 1638 216.512 6.45633 PNS24246 1044 753.997 153.399 9.93733 PNS24248 1044 753.997 153.399 9.93733 PNS24244 1471 1181 218.29 9.02823 PNS24243 293 90.7988 1 0.537943 KQK14069 1603 1313 4170.92 155.162 KQK14071 474 219.813 51.3556 11.4117 ==> SRR12666362.se.tsv <== BRADI_1g14170v3 4370 BRADI_1g53295v3 1716 BRADI_1g59795v3 166 BRADI_1g07683v3 0 BRADI_1g00485v3 102 BRADI_1g20270v3 3212 BRADI_1g74790v3 158 BRADI_1g09890v3 0 BRADI_1g77505v3 238 BRADI_1g48960v3 0 SRR12666362 completed mapping pipeline successfully