Starting /dee2/code/volunteer_pipeline.sh SRR12951297 current disk space = 1543337689088 free memory = 1601868872 SRR12951297 SRAfilesize f415a76bd8954df6894d55a4dd042661 SRR12951297.sra SRR12951297.sra file validated SRR12951297 is paired end SRR12951297 is conventional basespace SRR12951297 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951297_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.539 37.0 37.0 37.0 37.0 37.0 2 36.30625 37.0 37.0 37.0 37.0 37.0 3 36.505 37.0 37.0 37.0 37.0 37.0 4 36.6475 37.0 37.0 37.0 37.0 37.0 5 36.6285 37.0 37.0 37.0 37.0 37.0 6 36.6235 37.0 37.0 37.0 37.0 37.0 7 36.521 37.0 37.0 37.0 37.0 37.0 8 36.6035 37.0 37.0 37.0 37.0 37.0 9 36.6635 37.0 37.0 37.0 37.0 37.0 10-14 36.618399999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.5921 37.0 37.0 37.0 37.0 37.0 20-24 36.55499999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.52120000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.470600000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.4385 37.0 37.0 37.0 37.0 37.0 40-44 36.470600000000005 37.0 37.0 37.0 37.0 37.0 45-49 36.4521 37.0 37.0 37.0 37.0 37.0 50-54 36.436699999999995 37.0 37.0 37.0 37.0 37.0 55-59 36.395300000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.4088 37.0 37.0 37.0 37.0 37.0 65-69 36.373599999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.3102 37.0 37.0 37.0 37.0 37.0 75-79 36.2663 37.0 37.0 37.0 37.0 37.0 80-84 36.2418 37.0 37.0 37.0 37.0 37.0 85-89 36.234 37.0 37.0 37.0 37.0 37.0 90-94 36.239700000000006 37.0 37.0 37.0 37.0 37.0 95-99 36.2219 37.0 37.0 37.0 37.0 37.0 100-104 36.2772 37.0 37.0 37.0 37.0 37.0 105-109 36.217600000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.1428 37.0 37.0 37.0 37.0 37.0 115-119 36.1567 37.0 37.0 37.0 37.0 37.0 120-124 36.096700000000006 37.0 37.0 37.0 37.0 37.0 125-129 36.097300000000004 37.0 37.0 37.0 37.0 37.0 130-134 36.0052 37.0 37.0 37.0 37.0 37.0 135-139 35.9653 37.0 37.0 37.0 37.0 37.0 140-144 35.8371 37.0 37.0 37.0 37.0 37.0 145-149 35.7128 37.0 37.0 37.0 37.0 37.0 150-151 35.62375 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 2.0 22 3.0 23 0.0 24 1.0 25 2.0 26 8.0 27 6.0 28 10.0 29 13.0 30 24.0 31 33.0 32 47.0 33 70.0 34 149.0 35 273.0 36 2818.0 37 540.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.675 11.55 4.1000000000000005 37.675 2 20.382005529027396 10.605679819050012 37.04448353857753 31.967831113345063 3 18.375 14.299999999999999 25.474999999999998 41.85 4 25.025 20.25 23.674999999999997 31.05 5 27.625 25.924999999999997 22.875 23.575 6 24.825 30.925000000000004 22.075 22.175 7 20.474999999999998 25.2 35.275 19.05 8 19.875 23.974999999999998 30.049999999999997 26.1 9 22.3 20.05 32.074999999999996 25.575 10-14 23.9 26.029999999999998 25.61 24.46 15-19 24.505 24.345 24.990000000000002 26.16 20-24 24.195 25.240000000000002 24.765 25.8 25-29 24.11 24.8 24.495 26.595000000000002 30-34 24.675 24.44 24.48 26.405 35-39 24.325 24.09 25.285000000000004 26.3 40-44 24.6 24.465 25.430000000000003 25.505 45-49 23.76 24.68 25.005 26.555 50-54 24.325 24.575 24.67 26.43 55-59 25.03 24.625 24.165 26.179999999999996 60-64 24.91 24.6 24.07 26.419999999999998 65-69 24.48 24.779999999999998 24.94 25.8 70-74 24.805 24.29 24.265 26.640000000000004 75-79 24.545 25.014999999999997 24.64 25.8 80-84 25.095 24.67 24.27 25.965 85-89 25.009999999999998 24.755 24.560000000000002 25.674999999999997 90-94 24.560000000000002 23.990000000000002 24.834999999999997 26.615 95-99 24.895 23.990000000000002 24.515 26.6 100-104 25.47 24.759999999999998 24.22 25.55 105-109 25.135 24.545 24.415 25.905 110-114 25.34 24.915000000000003 24.44 25.305 115-119 25.36 24.52 24.135 25.985000000000003 120-124 24.945 24.555 24.46 26.040000000000003 125-129 24.9 24.645 24.19 26.265 130-134 25.16 25.055 23.115 26.669999999999998 135-139 24.945 25.074999999999996 23.51 26.47 140-144 25.074999999999996 24.725 23.465 26.735 145-149 25.955000000000002 24.154999999999998 23.724999999999998 26.165 150-151 25.7625 24.025 23.8625 26.35 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 0.5 25 0.5 26 1.0 27 2.0 28 2.0 29 1.0 30 2.5 31 6.5 32 10.5 33 18.0 34 26.5 35 28.5 36 39.0 37 63.0 38 76.0 39 92.0 40 105.5 41 126.5 42 148.5 43 161.5 44 185.0 45 184.5 46 173.5 47 187.0 48 180.5 49 169.5 50 178.5 51 156.0 52 125.0 53 105.0 54 107.5 55 109.0 56 103.0 57 88.0 58 72.0 59 76.5 60 79.0 61 64.5 62 53.5 63 68.0 64 71.0 65 66.0 66 60.0 67 55.0 68 56.0 69 56.5 70 55.0 71 44.0 72 34.0 73 35.0 74 27.5 75 17.0 76 16.5 77 12.0 78 7.0 79 5.5 80 3.0 81 0.5 82 0.0 83 0.5 84 0.5 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 0.525 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 81.825 #Duplication Level Percentage of deduplicated Percentage of total 1 82.61533761075466 67.60000000000001 2 13.62664222425909 22.3 3 2.9636419187289946 7.2749999999999995 4 0.6110601894286587 2.0 5 0.12221203788573175 0.5 6 0.030553009471432937 0.15 7 0.030553009471432937 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 ACTGGAATTAGTCCGGTTGAGATCCCATATCTTCAAGGTATTGTCAGTTG 7 0.17500000000000002 No Hit GGCCTTCACCTTGTCGAAGTCCGAGTTGACGCACCTCAGGAAATGATCCG 6 0.15 No Hit GCCACGATGGATCGATCGGTTGAATATGTCCTTTAAACGCTATAAGACCT 5 0.125 No Hit GTCCTTGTTTCCAGTGGTGGTCACAAAGATGTCAGCCTCTGAGACAACAT 5 0.125 No Hit ATCTGGACGAGCAAGAGCGAGAATCATGGGCTTTCGAGGGTTTGAGAAGA 5 0.125 No Hit GCCTCAAGTAAGGCAGCATTTCTGAAATGGTTTCCTTCTCTTTGCCTACA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.05 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.16249999999999998 0.0 0.0 0.0 0.0 70-71 0.21250000000000002 0.0 0.0 0.0 0.0 72-73 0.2625 0.0 0.0 0.0 0.0 74-75 0.325 0.0 0.0 0.0 0.0 76-77 0.525 0.0 0.0 0.0 0.0 78-79 0.625 0.0 0.0 0.0 0.0 80-81 0.6875 0.0 0.0 0.0 0.0 82-83 0.825 0.0 0.0 0.0 0.0 84-85 0.925 0.0 0.0 0.0 0.0 86-87 1.05 0.0 0.0 0.0 0.0 88-89 1.3375 0.0 0.0 0.0 0.0 90-91 1.6124999999999998 0.0 0.0 0.0 0.0 92-93 1.875 0.0 0.0 0.0 0.0 94-95 2.2125000000000004 0.0 0.0 0.0 0.0 96-97 2.525 0.0 0.0 0.0 0.0 98-99 2.7 0.0 0.0 0.0 0.0 100-101 3.0 0.0 0.0 0.0 0.0 102-103 3.45 0.0 0.0 0.0 0.0 104-105 3.9875 0.0 0.0 0.0 0.0 106-107 4.6 0.0 0.0 0.0 0.0 108-109 5.1625 0.0 0.0 0.0 0.0 110-111 5.7625 0.0 0.0 0.0 0.0 112-113 6.2375 0.0 0.0 0.0 0.0 114-115 6.6875 0.0 0.0 0.0 0.0 116-117 7.25 0.0 0.0 0.0 0.0 118-119 7.737500000000001 0.0 0.0 0.0 0.0 120-121 8.3375 0.0 0.0 0.0 0.0 122-123 8.95 0.0 0.0 0.0 0.0 124-125 9.7 0.0 0.0 0.0 0.0 126-127 11.0 0.0 0.0 0.0 0.0 128-129 11.6875 0.0 0.0 0.0 0.0 130-131 12.55 0.0 0.0 0.0 0.0 132-133 13.425 0.0 0.0 0.0 0.0 134-135 14.1375 0.0 0.0 0.0 0.0 136-137 14.95 0.0 0.0 0.0 0.0 138-139 15.7 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12951297 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951297_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 36.304 37.0 37.0 37.0 37.0 37.0 2 36.1015 37.0 37.0 37.0 37.0 37.0 3 36.134 37.0 37.0 37.0 37.0 37.0 4 36.303 37.0 37.0 37.0 37.0 37.0 5 36.2625 37.0 37.0 37.0 37.0 37.0 6 36.2925 37.0 37.0 37.0 37.0 37.0 7 36.2885 37.0 37.0 37.0 37.0 37.0 8 36.324 37.0 37.0 37.0 37.0 37.0 9 36.304 37.0 37.0 37.0 37.0 37.0 10-14 36.33069999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.273199999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.251099999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.2067 37.0 37.0 37.0 37.0 37.0 30-34 36.1837 37.0 37.0 37.0 37.0 37.0 35-39 36.1246 37.0 37.0 37.0 37.0 37.0 40-44 36.1808 37.0 37.0 37.0 37.0 37.0 45-49 36.1323 37.0 37.0 37.0 37.0 37.0 50-54 36.131299999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.0654 37.0 37.0 37.0 37.0 37.0 60-64 36.0766 37.0 37.0 37.0 37.0 37.0 65-69 36.0299 37.0 37.0 37.0 37.0 37.0 70-74 35.964099999999995 37.0 37.0 37.0 37.0 37.0 75-79 35.996300000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.974199999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.904700000000005 37.0 37.0 37.0 37.0 37.0 90-94 35.9342 37.0 37.0 37.0 37.0 37.0 95-99 35.9154 37.0 37.0 37.0 37.0 37.0 100-104 35.8221 37.0 37.0 37.0 37.0 37.0 105-109 35.804500000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.698600000000006 37.0 37.0 37.0 37.0 37.0 115-119 35.7786 37.0 37.0 37.0 37.0 37.0 120-124 35.594 37.0 37.0 37.0 37.0 37.0 125-129 35.55329999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.325599999999994 37.0 37.0 37.0 34.6 37.0 135-139 35.332300000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.1872 37.0 37.0 37.0 34.6 37.0 145-149 35.043899999999994 37.0 37.0 37.0 25.0 37.0 150-151 34.596000000000004 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 6.0 14 1.0 15 2.0 16 2.0 17 1.0 18 1.0 19 2.0 20 3.0 21 2.0 22 4.0 23 6.0 24 6.0 25 3.0 26 10.0 27 12.0 28 13.0 29 17.0 30 18.0 31 37.0 32 51.0 33 102.0 34 200.0 35 601.0 36 2624.0 37 276.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.0 22.3 5.45 31.25 2 30.3 21.025 26.700000000000003 21.975 3 22.675 24.224999999999998 28.7 24.4 4 24.2 31.775 20.125 23.9 5 28.625 30.875000000000004 18.6 21.9 6 23.549999999999997 35.625 17.95 22.875 7 23.45 19.400000000000002 33.300000000000004 23.849999999999998 8 22.6 22.85 24.45 30.099999999999998 9 23.875 20.825 26.825 28.475 10-14 26.035000000000004 24.445 23.400000000000002 26.119999999999997 15-19 25.985000000000003 25.055 23.064999999999998 25.895000000000003 20-24 25.915 25.11 23.835 25.14 25-29 27.060000000000002 24.3 23.375 25.264999999999997 30-34 26.334999999999997 24.82 23.669999999999998 25.174999999999997 35-39 26.279999999999998 25.35 22.975 25.395 40-44 26.369999999999997 24.865000000000002 22.705000000000002 26.06 45-49 26.52 24.77 23.1 25.61 50-54 26.61 24.36 23.7 25.330000000000002 55-59 27.125 24.240000000000002 23.62 25.014999999999997 60-64 26.795 24.740000000000002 23.5 24.965 65-69 26.395000000000003 24.104999999999997 23.385 26.115 70-74 26.375 24.385 23.56 25.679999999999996 75-79 26.825 24.610000000000003 23.31 25.255 80-84 27.025 24.255 23.34 25.380000000000003 85-89 27.52 24.875 22.625 24.98 90-94 27.384999999999998 24.42 23.16 25.035 95-99 26.88 24.275 23.41 25.435000000000002 100-104 27.229999999999997 24.64 23.13 25.0 105-109 27.615000000000002 24.295 22.775000000000002 25.314999999999998 110-114 27.465 24.12 23.73 24.685000000000002 115-119 28.560000000000002 24.97 22.78 23.69 120-124 28.74 25.0 23.165 23.095 125-129 28.660000000000004 25.255 22.775000000000002 23.31 130-134 29.659999999999997 25.195 22.55 22.595000000000002 135-139 29.435 24.2 23.294999999999998 23.07 140-144 30.31 24.89 22.29 22.509999999999998 145-149 31.674999999999997 24.085 22.695 21.545 150-151 31.15 24.9375 22.537499999999998 21.375 >>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 0.5 17 1.0 18 0.5 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 0.5 25 0.5 26 0.0 27 0.0 28 1.0 29 4.0 30 6.0 31 6.5 32 8.0 33 12.0 34 22.0 35 30.0 36 38.0 37 46.5 38 66.0 39 86.0 40 91.0 41 115.5 42 150.0 43 144.0 44 149.5 45 174.5 46 172.0 47 171.0 48 168.0 49 158.5 50 137.0 51 134.5 52 124.5 53 118.0 54 128.0 55 116.5 56 108.5 57 98.0 58 83.0 59 82.0 60 79.5 61 79.5 62 83.5 63 77.0 64 69.0 65 65.5 66 68.5 67 77.0 68 78.5 69 71.5 70 60.0 71 48.0 72 43.0 73 32.5 74 28.5 75 25.0 76 17.0 77 8.0 78 6.0 79 6.5 80 3.5 81 1.5 82 1.0 83 1.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.5 93 1.5 94 1.5 95 0.5 96 1.0 97 1.0 98 1.0 99 1.5 100 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 82.15 #Duplication Level Percentage of deduplicated Percentage of total 1 83.2318928788801 68.375 2 13.20754716981132 21.7 3 2.6171637248934876 6.45 4 0.699939135727328 2.3 5 0.12172854534388314 0.5 6 0.06086427267194157 0.3 7 0.030432136335970784 0.17500000000000002 8 0.030432136335970784 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 GAGTATTAACCAGAAAAATTGTGTTGATACAATCAGAAATGTCGCCAACG 7 0.17500000000000002 No Hit CCTTGAGATACATTGGCAGCATGGTTGCTGATGTCCACCGCACCTTGCTA 6 0.15 No Hit CCTTCTTCGTGACGCAGACGCTACGGGGCCTGGCCAGGGACGGCAGGACA 6 0.15 No Hit GTGATGTTGGCAAGGGCTGTGCTTCTGCGCTCAAGCAGGCTGGTGCCCGT 5 0.125 No Hit CTCCTCGCCTAGATCCAATCCCCAACAAACTTCTCCCCACTCCAGCCGCC 5 0.125 No Hit AGGATCCTCAATACCAAGAAAAGAGAATGGTTGCTCAAAGAAACGGAAAA 5 0.125 No Hit GGAGTTTGGACATATAGTGCCCCATGATGTTGATCTGGATGGTGAAGAAG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.05 0.0 0.0 0.0 0.0 58-59 0.0625 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.16249999999999998 0.0 0.0 0.0 0.0 70-71 0.21250000000000002 0.0 0.0 0.0 0.0 72-73 0.2625 0.0 0.0 0.0 0.0 74-75 0.325 0.0 0.0 0.0 0.0 76-77 0.525 0.0 0.0 0.0 0.0 78-79 0.625 0.0 0.0 0.0 0.0 80-81 0.6875 0.0 0.0 0.0 0.0 82-83 0.825 0.0 0.0 0.0 0.0 84-85 0.9 0.0 0.0 0.0 0.0 86-87 1.025 0.0 0.0 0.0 0.0 88-89 1.3125 0.0 0.0 0.0 0.0 90-91 1.5875 0.0 0.0 0.0 0.0 92-93 1.85 0.0 0.0 0.0 0.0 94-95 2.1875 0.0 0.0 0.0 0.0 96-97 2.475 0.0 0.0 0.0 0.0 98-99 2.675 0.0 0.0 0.0 0.0 100-101 2.975 0.0 0.0 0.0 0.0 102-103 3.425 0.0 0.0 0.0 0.0 104-105 3.9625 0.0 0.0 0.0 0.0 106-107 4.575 0.0 0.0 0.0 0.0 108-109 5.137499999999999 0.0 0.0 0.0 0.0 110-111 5.7375 0.0 0.0 0.0 0.0 112-113 6.225 0.0 0.0 0.0 0.0 114-115 6.6875 0.0 0.0 0.0 0.0 116-117 7.2625 0.0 0.0 0.0 0.0 118-119 7.762499999999999 0.0 0.0 0.0 0.0 120-121 8.3625 0.0 0.0 0.0 0.0 122-123 8.975000000000001 0.0 0.0 0.0 0.0 124-125 9.75 0.0 0.0 0.0 0.0 126-127 11.0375 0.0 0.0 0.0 0.0 128-129 11.7375 0.0 0.0 0.0 0.0 130-131 12.6125 0.0 0.0 0.0 0.0 132-133 13.5 0.0 0.0 0.0 0.0 134-135 14.2125 0.0 0.0 0.0 0.0 136-137 15.0 0.0 0.0 0.0 0.0 138-139 15.662500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTAGC 10 0.006830828 145.0 4 >>END_MODULE Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775195 spots for SRR12951297.sra Written 1775195 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra Read 1775182 spots for SRR12951297.sra Written 1775182 spots for SRR12951297.sra SRR ids: ['SRR12951297.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hpu3kz39 SRR12951297.sra spots: 35503653 blocks: [[1, 1775182], [1775183, 3550364], [3550365, 5325546], [5325547, 7100728], [7100729, 8875910], [8875911, 10651092], [10651093, 12426274], [12426275, 14201456], [14201457, 15976638], [15976639, 17751820], [17751821, 19527002], [19527003, 21302184], [21302185, 23077366], [23077367, 24852548], [24852549, 26627730], [26627731, 28402912], [28402913, 30178094], [30178095, 31953276], [31953277, 33728458], [33728459, 35503653]] SRR12951297 file size 12043994 SRR12951297 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 SRR12951297 SRR12951297_1.fastq SRR12951297_2.fastq Input file: SRR12951297_1.fastq Paired file: SRR12951297_2.fastq trimmed: SRR12951297-trimmed-pair1.fastq, SRR12951297-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 10:58:38 2024 >> started Sat Dec 7 10:59:16 2024 >> done (38.431s) 35503653 read pairs processed; of these: 396 ( 0.00%) short read pairs filtered out after trimming by size control 52797 ( 0.15%) empty read pairs filtered out after trimming by size control 35450460 (99.85%) read pairs available; of these: 7374423 (20.80%) trimmed read pairs available after processing 28076037 (79.20%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 26 0.00% 20 30 0.00% 21 39 0.00% 22 49 0.00% 23 50 0.00% 24 46 0.00% 25 64 0.00% 26 73 0.00% 27 63 0.00% 28 61 0.00% 29 77 0.00% 30 114 0.00% 31 101 0.00% 32 97 0.00% 33 132 0.00% 34 122 0.00% 35 114 0.00% 36 150 0.00% 37 145 0.00% 38 156 0.00% 39 155 0.00% 40 192 0.00% 41 181 0.00% 42 181 0.00% 43 203 0.00% 44 222 0.00% 45 248 0.00% 46 229 0.00% 47 277 0.00% 48 330 0.00% 49 411 0.00% 50 406 0.00% 51 465 0.00% 52 563 0.00% 53 634 0.00% 54 606 0.00% 55 678 0.00% 56 777 0.00% 57 876 0.00% 58 1087 0.00% 59 1356 0.00% 60 1588 0.00% 61 1941 0.01% 62 2051 0.01% 63 2475 0.01% 64 2641 0.01% 65 2805 0.01% 66 3350 0.01% 67 3626 0.01% 68 4262 0.01% 69 4978 0.01% 70 5816 0.02% 71 6616 0.02% 72 7583 0.02% 73 8536 0.02% 74 9808 0.03% 75 10935 0.03% 76 12087 0.03% 77 13028 0.04% 78 13985 0.04% 79 15939 0.04% 80 17914 0.05% 81 19736 0.06% 82 22981 0.06% 83 25034 0.07% 84 27854 0.08% 85 29978 0.08% 86 32240 0.09% 87 33874 0.10% 88 35861 0.10% 89 37863 0.11% 90 41408 0.12% 91 43906 0.12% 92 47670 0.13% 93 50450 0.14% 94 54582 0.15% 95 57520 0.16% 96 60497 0.17% 97 62904 0.18% 98 64740 0.18% 99 67132 0.19% 100 70599 0.20% 101 72572 0.20% 102 76011 0.21% 103 80399 0.23% 104 82599 0.23% 105 86445 0.24% 106 89336 0.25% 107 90791 0.26% 108 93510 0.26% 109 96219 0.27% 110 96120 0.27% 111 99555 0.28% 112 103437 0.29% 113 105209 0.30% 114 109485 0.31% 115 112981 0.32% 116 114516 0.32% 117 117074 0.33% 118 118654 0.33% 119 119028 0.34% 120 122101 0.34% 121 123058 0.35% 122 124102 0.35% 123 127749 0.36% 124 131768 0.37% 125 132753 0.37% 126 134859 0.38% 127 137495 0.39% 128 137395 0.39% 129 139363 0.39% 130 139288 0.39% 131 139198 0.39% 132 141662 0.40% 133 142980 0.40% 134 144244 0.41% 135 147205 0.42% 136 149138 0.42% 137 147535 0.42% 138 149494 0.42% 139 151998 0.43% 140 150401 0.42% 141 151081 0.43% 142 153366 0.43% 143 152199 0.43% 144 153789 0.43% 145 155774 0.44% 146 153531 0.43% 147 157480 0.44% 148 156605 0.44% 149 156118 0.44% 150 156153 0.44% 151 28076037 79.20% 35450460 reads passed initial QC criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=36 prefix-density=0.24 prefix-fanout=1.9 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.03 sequence-density-rank=32 fanout-score=520.21 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=20.7 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=4.33 fanout-score-rank=26 prefix-density=0.25 prefix-fanout=3.7 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=1248.46 fanout-score-rank=1 prefix-density=1.01 prefix-fanout=20.5 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGA SRR12951297 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:59:59 Started mapping on | Dec 07 10:59:59 Finished on | Dec 07 11:02:54 Mapping speed, Million of reads per hour | 729.27 Number of input reads | 35450460 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 33915768 Uniquely mapped reads % | 95.67% Average mapped length | 289.14 Number of splices: Total | 34377630 Number of splices: Annotated (sjdb) | 32132766 Number of splices: GT/AG | 33921284 Number of splices: GC/AG | 375864 Number of splices: AT/AC | 23093 Number of splices: Non-canonical | 57389 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.74 Insertion rate per base | 0.01% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 358068 % of reads mapped to multiple loci | 1.01% Number of reads mapped to too many loci | 52037 % of reads mapped to too many loci | 0.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.55% % of reads unmapped: other | 0.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1176624 1176624 1176624 N_multimapping 358068 358068 358068 N_noFeature 1097380 33069207 1376198 N_ambiguous 663256 5027 96228 UnstrandedReadsAssigned:32155132 PositiveStrandReadsAssigned:841534 NegativeStrandReadsAssigned:32443342 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=147 echo kmer=143 SRR12951297 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: SRR12951297-trimmed-pair1.fastq SRR12951297-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,450,460 reads, 32,848,590 reads pseudoaligned [quant] estimated average fragment length: 235.161 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,323 rounds 52973 SRR12951297.ke.tsv 35125 SRR12951297.se.tsv 88098 total ==> SRR12951297.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 702.309 0 0 PNS24247 1044 809.839 87.3424 4.97853 PNS24249 1928 1693.84 321.49 8.76131 PNS24246 1044 809.839 87.3424 4.97853 PNS24248 1044 809.839 87.3424 4.97853 PNS24244 1471 1236.84 112.483 4.19807 PNS24243 293 113.683 0 0 KQK14069 1603 1368.84 1933.92 65.217 KQK14071 474 259.653 55.1256 9.80019 ==> SRR12951297.se.tsv <== BRADI_1g14170v3 2092 BRADI_1g53295v3 64 BRADI_1g59795v3 608 BRADI_1g07683v3 0 BRADI_1g00485v3 160 BRADI_1g20270v3 5431 BRADI_1g74790v3 191 BRADI_1g09890v3 30 BRADI_1g77505v3 547 BRADI_1g48960v3 2 SRR12951297 completed mapping pipeline successfully