Starting /dee2/code/volunteer_pipeline.sh SRR12951313 current disk space = 1543045218304 free memory = 1601823532 SRR12951313 SRAfilesize bd63ec9a04885a59249a74dd97b7ceab SRR12951313.sra SRR12951313.sra file validated SRR12951313 is paired end SRR12951313 is conventional basespace SRR12951313 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951313_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 36.5225 37.0 37.0 37.0 37.0 37.0 2 36.24575 37.0 37.0 37.0 37.0 37.0 3 36.5045 37.0 37.0 37.0 37.0 37.0 4 36.5665 37.0 37.0 37.0 37.0 37.0 5 36.6535 37.0 37.0 37.0 37.0 37.0 6 36.581 37.0 37.0 37.0 37.0 37.0 7 36.5405 37.0 37.0 37.0 37.0 37.0 8 36.5815 37.0 37.0 37.0 37.0 37.0 9 36.55 37.0 37.0 37.0 37.0 37.0 10-14 36.603 37.0 37.0 37.0 37.0 37.0 15-19 36.5612 37.0 37.0 37.0 37.0 37.0 20-24 36.5449 37.0 37.0 37.0 37.0 37.0 25-29 36.4944 37.0 37.0 37.0 37.0 37.0 30-34 36.4593 37.0 37.0 37.0 37.0 37.0 35-39 36.458600000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.458999999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.41969999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.36409999999999 37.0 37.0 37.0 37.0 37.0 55-59 36.37339999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.3444 37.0 37.0 37.0 37.0 37.0 65-69 36.306799999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.284800000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.3105 37.0 37.0 37.0 37.0 37.0 80-84 36.3052 37.0 37.0 37.0 37.0 37.0 85-89 36.2832 37.0 37.0 37.0 37.0 37.0 90-94 36.266200000000005 37.0 37.0 37.0 37.0 37.0 95-99 36.1796 37.0 37.0 37.0 37.0 37.0 100-104 36.236599999999996 37.0 37.0 37.0 37.0 37.0 105-109 36.266000000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.1256 37.0 37.0 37.0 37.0 37.0 115-119 36.1613 37.0 37.0 37.0 37.0 37.0 120-124 36.0737 37.0 37.0 37.0 37.0 37.0 125-129 36.0506 37.0 37.0 37.0 37.0 37.0 130-134 36.04729999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.98479999999999 37.0 37.0 37.0 37.0 37.0 140-144 35.847500000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.7857 37.0 37.0 37.0 37.0 37.0 150-151 35.59325 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 3.0 24 3.0 25 1.0 26 3.0 27 5.0 28 18.0 29 13.0 30 26.0 31 22.0 32 51.0 33 84.0 34 122.0 35 298.0 36 2888.0 37 462.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.925 12.725 4.324999999999999 39.025 2 20.090520492833793 10.736736233341714 35.9316067387478 33.24113653507669 3 17.724999999999998 13.425 27.35 41.5 4 24.349999999999998 19.625 22.45 33.575 5 28.349999999999998 26.200000000000003 22.075 23.375 6 24.8 28.599999999999998 22.375 24.224999999999998 7 18.325 25.6 37.675 18.4 8 20.075000000000003 23.549999999999997 29.925 26.450000000000003 9 20.424999999999997 22.675 32.875 24.025 10-14 23.48 26.33 24.915000000000003 25.275 15-19 22.845 26.095000000000002 25.05 26.009999999999998 20-24 23.155 26.165 24.945 25.735000000000003 25-29 23.28 25.285000000000004 25.045 26.39 30-34 22.86 25.230000000000004 25.445 26.465 35-39 23.945 24.4 25.88 25.775 40-44 23.785 25.230000000000004 24.925 26.06 45-49 23.599999999999998 25.275 24.38 26.745 50-54 23.73 25.419999999999998 25.36 25.490000000000002 55-59 23.405 24.88 25.240000000000002 26.474999999999998 60-64 23.86 25.795 24.64 25.705 65-69 23.755000000000003 25.974999999999998 24.310000000000002 25.96 70-74 24.169999999999998 24.55 25.115 26.165 75-79 24.135 24.465 25.264999999999997 26.135 80-84 23.915 25.395 25.124999999999996 25.564999999999998 85-89 23.86 25.295 24.94 25.905 90-94 23.945 25.365 24.654999999999998 26.035000000000004 95-99 24.25 24.82 25.455 25.474999999999998 100-104 24.455 25.605 24.14 25.8 105-109 24.310000000000002 24.779999999999998 24.26 26.650000000000002 110-114 24.68 25.555 24.195 25.569999999999997 115-119 24.445 26.150000000000002 23.885 25.52 120-124 24.834999999999997 25.305 23.895 25.965 125-129 24.505 25.66 23.775 26.06 130-134 24.779999999999998 25.66 23.990000000000002 25.569999999999997 135-139 24.27 25.669999999999998 23.935000000000002 26.125 140-144 24.605 26.1 23.46 25.835 145-149 24.990000000000002 25.605 23.52 25.885 150-151 24.3125 25.45 23.775 26.4625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 0.5 27 1.0 28 2.5 29 5.5 30 7.0 31 10.0 32 13.5 33 20.5 34 30.5 35 38.0 36 51.0 37 61.5 38 77.5 39 92.0 40 106.5 41 136.0 42 168.5 43 178.5 44 189.5 45 207.5 46 217.0 47 210.0 48 177.0 49 166.5 50 169.5 51 139.0 52 130.0 53 131.5 54 106.5 55 87.5 56 78.0 57 75.5 58 78.5 59 71.0 60 54.0 61 52.0 62 63.5 63 69.5 64 67.0 65 62.5 66 56.5 67 50.0 68 39.0 69 32.5 70 30.0 71 27.0 72 26.0 73 28.0 74 27.0 75 25.0 76 16.0 77 8.0 78 8.5 79 7.0 80 3.5 81 2.0 82 3.5 83 3.0 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 0.575 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 86.2 #Duplication Level Percentage of deduplicated Percentage of total 1 87.03596287703016 75.02499999999999 2 10.527842227378189 18.15 3 2.0011600928074245 5.175 4 0.3190255220417633 1.0999999999999999 5 0.08700696055684454 0.375 6 0.0 0.0 7 0.029002320185614848 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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTGAGCCATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 25 (97% over 38bp) AAGAAACTGGGCAAGAGTCAACTGGTCAGCGAGAAGCAAGTACTACCTCC 5 0.125 No Hit GTACAATGTAAGGTAATGTGAAAACTACACACTTGGCTACGAGTCCTACT 5 0.125 No Hit GCCTGTTCAAGATAGGGCAAGAGATATTCCTCGACACTTCTTGGACCAAT 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 62-63 0.1 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 0.1125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.35 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.45 0.0 0.0 0.0 0.0 86-87 0.55 0.0 0.0 0.0 0.0 88-89 0.6625000000000001 0.0 0.0 0.0 0.0 90-91 0.925 0.0 0.0 0.0 0.0 92-93 1.075 0.0 0.0 0.0 0.0 94-95 1.2625000000000002 0.0 0.0 0.0 0.0 96-97 1.4 0.0 0.0 0.0 0.0 98-99 1.65 0.0 0.0 0.0 0.0 100-101 2.0375 0.0 0.0 0.0 0.0 102-103 2.5 0.0 0.0 0.0 0.0 104-105 3.0625 0.0 0.0 0.0 0.0 106-107 3.4000000000000004 0.0 0.0 0.0 0.0 108-109 3.7375 0.0 0.0 0.0 0.0 110-111 4.225 0.0 0.0 0.0 0.0 112-113 4.7375 0.0 0.0 0.0 0.0 114-115 5.1875 0.0 0.0 0.0 0.0 116-117 5.762499999999999 0.0 0.0 0.0 0.0 118-119 6.25 0.0 0.0 0.0 0.0 120-121 6.775 0.0 0.0 0.0 0.0 122-123 7.4375 0.0 0.0 0.0 0.0 124-125 8.2 0.0 0.0 0.0 0.0 126-127 8.875 0.0 0.0 0.0 0.0 128-129 9.4875 0.0 0.0 0.0 0.0 130-131 10.2125 0.0 0.0 0.0 0.0 132-133 10.8625 0.0 0.0 0.0 0.0 134-135 11.575 0.0 0.0 0.0 0.0 136-137 12.162500000000001 0.0 0.0 0.0 0.0 138-139 13.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAAAAT 10 0.006830828 145.0 7 AGCAGAT 10 0.006830828 145.0 6 GACAAAA 10 0.006830828 145.0 6 >>END_MODULE SRR12951313 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951313_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1825 37.0 37.0 37.0 37.0 37.0 2 36.119 37.0 37.0 37.0 37.0 37.0 3 36.1225 37.0 37.0 37.0 37.0 37.0 4 36.2885 37.0 37.0 37.0 37.0 37.0 5 36.2515 37.0 37.0 37.0 37.0 37.0 6 36.301 37.0 37.0 37.0 37.0 37.0 7 36.1975 37.0 37.0 37.0 37.0 37.0 8 36.276 37.0 37.0 37.0 37.0 37.0 9 36.2965 37.0 37.0 37.0 37.0 37.0 10-14 36.2768 37.0 37.0 37.0 37.0 37.0 15-19 36.2599 37.0 37.0 37.0 37.0 37.0 20-24 36.1925 37.0 37.0 37.0 37.0 37.0 25-29 36.1574 37.0 37.0 37.0 37.0 37.0 30-34 36.0966 37.0 37.0 37.0 37.0 37.0 35-39 36.11409999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.0673 37.0 37.0 37.0 37.0 37.0 45-49 36.0661 37.0 37.0 37.0 37.0 37.0 50-54 36.0133 37.0 37.0 37.0 37.0 37.0 55-59 36.0007 37.0 37.0 37.0 37.0 37.0 60-64 35.96990000000001 37.0 37.0 37.0 37.0 37.0 65-69 35.951800000000006 37.0 37.0 37.0 37.0 37.0 70-74 35.888799999999996 37.0 37.0 37.0 37.0 37.0 75-79 35.920500000000004 37.0 37.0 37.0 37.0 37.0 80-84 35.8897 37.0 37.0 37.0 37.0 37.0 85-89 35.8135 37.0 37.0 37.0 37.0 37.0 90-94 35.8813 37.0 37.0 37.0 37.0 37.0 95-99 35.786500000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.7886 37.0 37.0 37.0 37.0 37.0 105-109 35.7273 37.0 37.0 37.0 37.0 37.0 110-114 35.7826 37.0 37.0 37.0 37.0 37.0 115-119 35.8277 37.0 37.0 37.0 37.0 37.0 120-124 35.6474 37.0 37.0 37.0 37.0 37.0 125-129 35.614 37.0 37.0 37.0 37.0 37.0 130-134 35.5609 37.0 37.0 37.0 37.0 37.0 135-139 35.5081 37.0 37.0 37.0 37.0 37.0 140-144 35.416700000000006 37.0 37.0 37.0 37.0 37.0 145-149 35.2236 37.0 37.0 37.0 32.2 37.0 150-151 35.0135 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 5.0 15 2.0 16 2.0 17 1.0 18 1.0 19 4.0 20 6.0 21 6.0 22 5.0 23 5.0 24 8.0 25 6.0 26 14.0 27 8.0 28 7.0 29 20.0 30 23.0 31 40.0 32 46.0 33 79.0 34 192.0 35 547.0 36 2677.0 37 294.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.95 24.65 7.8 28.599999999999998 2 27.825 24.474999999999998 27.750000000000004 19.950000000000003 3 22.1 24.525 29.75 23.625 4 25.2 31.225 21.05 22.525000000000002 5 27.575 31.4 21.25 19.775000000000002 6 24.325 33.475 20.45 21.75 7 23.275000000000002 20.825 33.324999999999996 22.575 8 22.15 22.375 25.624999999999996 29.849999999999998 9 23.474999999999998 22.45 26.150000000000002 27.925 10-14 25.755 25.740000000000002 23.125 25.380000000000003 15-19 26.3 24.675 23.84 25.185000000000002 20-24 26.240000000000002 25.564999999999998 23.98 24.215 25-29 26.055 24.97 23.97 25.005 30-34 26.119999999999997 24.965 24.245 24.67 35-39 26.145000000000003 24.91 23.875 25.069999999999997 40-44 26.145000000000003 25.165 23.674999999999997 25.014999999999997 45-49 26.105 25.6 24.095 24.2 50-54 26.35 25.505 24.065 24.08 55-59 26.265 24.84 24.255 24.64 60-64 27.005000000000003 25.319999999999997 23.86 23.815 65-69 26.405 24.41 24.605 24.58 70-74 26.83 25.124999999999996 23.880000000000003 24.165 75-79 26.695 25.324999999999996 24.07 23.91 80-84 26.924999999999997 25.82 23.755000000000003 23.5 85-89 26.51 24.825 24.295 24.37 90-94 26.040000000000003 24.62 24.474999999999998 24.865000000000002 95-99 26.479999999999997 25.09 23.96 24.47 100-104 27.16 25.480000000000004 23.54 23.82 105-109 27.57 25.27 23.535 23.625 110-114 27.43 25.61 24.095 22.865 115-119 27.765 25.095 23.830000000000002 23.31 120-124 28.22 25.405 23.9 22.475 125-129 28.194999999999997 24.66 24.145 23.0 130-134 28.565 25.525 23.51 22.400000000000002 135-139 29.049999999999997 24.884999999999998 23.830000000000002 22.235 140-144 29.425 25.064999999999998 23.11 22.400000000000002 145-149 29.75 25.555 23.45 21.245 150-151 30.8125 24.462500000000002 22.662499999999998 22.0625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.5 9 0.5 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 1.0 18 0.5 19 0.5 20 0.5 21 0.5 22 0.0 23 0.0 24 0.0 25 1.0 26 2.0 27 2.5 28 2.5 29 2.0 30 3.5 31 6.5 32 8.5 33 13.0 34 18.0 35 29.0 36 53.0 37 75.0 38 83.0 39 100.0 40 125.5 41 125.0 42 151.0 43 182.5 44 185.5 45 183.5 46 187.5 47 190.5 48 165.0 49 145.0 50 148.0 51 138.0 52 125.5 53 123.0 54 108.5 55 95.5 56 94.0 57 86.0 58 78.5 59 74.0 60 63.0 61 63.5 62 61.0 63 65.5 64 73.5 65 70.0 66 61.0 67 59.0 68 58.0 69 50.0 70 47.0 71 42.0 72 29.5 73 26.5 74 28.5 75 20.5 76 15.5 77 11.0 78 4.0 79 1.5 80 2.5 81 3.0 82 2.0 83 0.5 84 0.0 85 1.0 86 1.5 87 0.5 88 0.5 89 0.5 90 0.0 91 0.5 92 1.0 93 0.5 94 0.5 95 1.5 96 2.5 97 2.5 98 1.0 99 1.0 100 4.0 >>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 86.275 #Duplication Level Percentage of deduplicated Percentage of total 1 87.53984352361634 75.52499999999999 2 10.026079397276153 17.299999999999997 3 1.8255578093306288 4.725 4 0.4056795131845842 1.4000000000000001 5 0.11590843233845263 0.5 6 0.057954216169226316 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.028977108084613158 0.25 >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 10 0.25 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 6 0.15 No Hit CCCACGTTGGAGCAGCAGCAGAGAGCCGGAGCGCCACCAGCCATCCGATC 6 0.15 No Hit TAATACTCCCTCCGATCCATAATAAGTGTCTCAGATTTTGTACTAACTTG 5 0.125 No Hit CAAGAGATAACCATAAATCAGCTGAAAGAAAGAGATATGCTTGCCTCGAA 5 0.125 No Hit GTCCAAAACCTCGGCAGTCTTCATCCCTCACGGGCCAGGTGCTGTCAAAG 5 0.125 No Hit GTTGGTAATGGGACCAAAGCAGACACCTAATGTCCGCAGAGCTCTATTGC 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 0.0125 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 0.0625 0.0 0.0 0.0 0.0 62-63 0.1 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 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.225 0.0 0.0 0.0 0.0 78-79 0.2625 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.35 0.0 0.0 0.0 0.0 84-85 0.425 0.0 0.0 0.0 0.0 86-87 0.525 0.0 0.0 0.0 0.0 88-89 0.6375 0.0 0.0 0.0 0.0 90-91 0.9 0.0 0.0 0.0 0.0 92-93 1.05 0.0 0.0 0.0 0.0 94-95 1.2374999999999998 0.0 0.0 0.0 0.0 96-97 1.375 0.0 0.0 0.0 0.0 98-99 1.625 0.0 0.0 0.0 0.0 100-101 2.0125 0.0 0.0 0.0 0.0 102-103 2.5 0.0 0.0 0.0 0.0 104-105 3.0875000000000004 0.0 0.0 0.0 0.0 106-107 3.425 0.0 0.0 0.0 0.0 108-109 3.775 0.0 0.0 0.0 0.0 110-111 4.275 0.0 0.0 0.0 0.0 112-113 4.8375 0.0 0.0 0.0 0.0 114-115 5.2875 0.0 0.0 0.0 0.0 116-117 5.862500000000001 0.0 0.0 0.0 0.0 118-119 6.35 0.0 0.0 0.0 0.0 120-121 6.875 0.0 0.0 0.0 0.0 122-123 7.5375 0.0 0.0 0.0 0.0 124-125 8.3 0.0 0.0 0.0 0.0 126-127 8.975 0.0 0.0 0.0 0.0 128-129 9.5875 0.0 0.0 0.0 0.0 130-131 10.3375 0.0 0.0 0.0 0.0 132-133 11.0125 0.0 0.0 0.0 0.0 134-135 11.7125 0.0 0.0 0.0 0.0 136-137 12.3125 0.0 0.0 0.0 0.0 138-139 13.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCCCCC 40 0.0076550315 18.125 60-64 >>END_MODULE Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081174 spots for SRR12951313.sra Written 2081174 spots for SRR12951313.sra Read 2081176 spots for SRR12951313.sra Written 2081176 spots for SRR12951313.sra SRR ids: ['SRR12951313.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_psuhl50a SRR12951313.sra spots: 41623482 blocks: [[1, 2081174], [2081175, 4162348], [4162349, 6243522], [6243523, 8324696], [8324697, 10405870], [10405871, 12487044], [12487045, 14568218], [14568219, 16649392], [16649393, 18730566], [18730567, 20811740], [20811741, 22892914], [22892915, 24974088], [24974089, 27055262], [27055263, 29136436], [29136437, 31217610], [31217611, 33298784], [33298785, 35379958], [35379959, 37461132], [37461133, 39542306], [39542307, 41623482]] SRR12951313 file size 14123779 SRR12951313 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 SRR12951313 SRR12951313_1.fastq SRR12951313_2.fastq Input file: SRR12951313_1.fastq Paired file: SRR12951313_2.fastq trimmed: SRR12951313-trimmed-pair1.fastq, SRR12951313-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 11:33:52 2024 >> started Sat Dec 7 11:34:44 2024 >> done (52.150s) 41623482 read pairs processed; of these: 294 ( 0.00%) short read pairs filtered out after trimming by size control 55516 ( 0.13%) empty read pairs filtered out after trimming by size control 41567672 (99.87%) read pairs available; of these: 7038474 (16.93%) trimmed read pairs available after processing 34529198 (83.07%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 18 0.00% 20 17 0.00% 21 37 0.00% 22 27 0.00% 23 52 0.00% 24 57 0.00% 25 62 0.00% 26 84 0.00% 27 89 0.00% 28 104 0.00% 29 108 0.00% 30 99 0.00% 31 116 0.00% 32 95 0.00% 33 149 0.00% 34 137 0.00% 35 126 0.00% 36 118 0.00% 37 128 0.00% 38 139 0.00% 39 149 0.00% 40 169 0.00% 41 143 0.00% 42 183 0.00% 43 168 0.00% 44 150 0.00% 45 176 0.00% 46 186 0.00% 47 277 0.00% 48 255 0.00% 49 304 0.00% 50 356 0.00% 51 332 0.00% 52 416 0.00% 53 477 0.00% 54 488 0.00% 55 494 0.00% 56 594 0.00% 57 613 0.00% 58 793 0.00% 59 883 0.00% 60 1029 0.00% 61 1260 0.00% 62 1465 0.00% 63 1534 0.00% 64 1736 0.00% 65 1818 0.00% 66 2017 0.00% 67 2208 0.01% 68 2402 0.01% 69 2984 0.01% 70 3421 0.01% 71 3965 0.01% 72 4564 0.01% 73 5418 0.01% 74 5972 0.01% 75 6590 0.02% 76 7250 0.02% 77 7896 0.02% 78 8960 0.02% 79 10045 0.02% 80 11054 0.03% 81 12685 0.03% 82 14546 0.03% 83 16291 0.04% 84 18182 0.04% 85 20442 0.05% 86 22089 0.05% 87 23588 0.06% 88 25452 0.06% 89 27311 0.07% 90 29708 0.07% 91 33002 0.08% 92 35435 0.09% 93 38890 0.09% 94 42692 0.10% 95 45289 0.11% 96 48611 0.12% 97 50953 0.12% 98 53447 0.13% 99 55290 0.13% 100 58021 0.14% 101 61418 0.15% 102 64082 0.15% 103 68864 0.17% 104 72133 0.17% 105 75404 0.18% 106 79204 0.19% 107 81288 0.20% 108 83272 0.20% 109 86454 0.21% 110 89114 0.21% 111 91681 0.22% 112 95061 0.23% 113 98942 0.24% 114 102458 0.25% 115 106123 0.26% 116 109092 0.26% 117 111491 0.27% 118 114150 0.27% 119 115628 0.28% 120 117547 0.28% 121 119165 0.29% 122 122393 0.29% 123 124409 0.30% 124 129140 0.31% 125 129670 0.31% 126 133754 0.32% 127 136450 0.33% 128 137098 0.33% 129 138410 0.33% 130 139816 0.34% 131 140921 0.34% 132 143920 0.35% 133 145017 0.35% 134 147831 0.36% 135 151646 0.36% 136 153255 0.37% 137 153825 0.37% 138 155132 0.37% 139 155878 0.37% 140 156800 0.38% 141 157527 0.38% 142 160472 0.39% 143 159691 0.38% 144 161044 0.39% 145 163434 0.39% 146 162958 0.39% 147 163664 0.39% 148 166830 0.40% 149 165255 0.40% 150 164762 0.40% 151 34529198 83.07% 41567672 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=3.16 fanout-score-rank=36 prefix-density=0.29 prefix-fanout=2.5 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.04 sequence-density-rank=29 fanout-score=273.46 fanout-score-rank=1 prefix-density=0.69 prefix-fanout=16.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=35 prefix-density=0.91 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.09 sequence-density-rank=20 fanout-score=251.20 fanout-score-rank=1 prefix-density=1.05 prefix-fanout=21.2 sequence=CGCCGCCGCCGA SRR12951313 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:35:41 Started mapping on | Dec 07 11:35:41 Finished on | Dec 07 11:40:06 Mapping speed, Million of reads per hour | 564.69 Number of input reads | 41567672 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 39401705 Uniquely mapped reads % | 94.79% Average mapped length | 292.24 Number of splices: Total | 37492198 Number of splices: Annotated (sjdb) | 34732590 Number of splices: GT/AG | 36981818 Number of splices: GC/AG | 426528 Number of splices: AT/AC | 25003 Number of splices: Non-canonical | 58849 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.24 Insertion rate per base | 0.01% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 433565 % of reads mapped to multiple loci | 1.04% Number of reads mapped to too many loci | 99502 % of reads mapped to too many loci | 0.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.74% % of reads unmapped: other | 1.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1732402 1732402 1732402 N_multimapping 433565 433565 433565 N_noFeature 1639555 38361004 1978001 N_ambiguous 831668 5380 129421 UnstrandedReadsAssigned:36930482 PositiveStrandReadsAssigned:1035321 NegativeStrandReadsAssigned:37294283 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951313 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: SRR12951313-trimmed-pair1.fastq SRR12951313-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 41,567,672 reads, 37,700,606 reads pseudoaligned [quant] estimated average fragment length: 251.199 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,196 rounds 52973 SRR12951313.ke.tsv 35125 SRR12951313.se.tsv 88098 total ==> SRR12951313.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 686.467 0 0 PNS24247 1044 793.801 216.802 10.6867 PNS24249 1928 1677.8 522.383 12.1826 PNS24246 1044 793.801 216.802 10.6867 PNS24248 1044 793.801 216.802 10.6867 PNS24244 1471 1220.8 274.211 8.78887 PNS24243 293 108.784 0 0 KQK14069 1603 1352.8 41637.3 1204.32 KQK14071 474 250.003 168.644 26.3949 ==> SRR12951313.se.tsv <== BRADI_1g14170v3 42428 BRADI_1g53295v3 320 BRADI_1g59795v3 1036 BRADI_1g07683v3 0 BRADI_1g00485v3 35 BRADI_1g20270v3 1396 BRADI_1g74790v3 3008 BRADI_1g09890v3 1 BRADI_1g77505v3 457 BRADI_1g48960v3 0 SRR12951313 completed mapping pipeline successfully