Starting /dee2/code/volunteer_pipeline.sh SRR12949786 current disk space = 1543983792128 free memory = 1601860824 SRR12949786 SRAfilesize c54902639affa1a632fff9036952ca0c SRR12949786.sra SRR12949786.sra file validated SRR12949786 is paired end SRR12949786 is conventional basespace SRR12949786 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12949786_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 36.509 37.0 37.0 37.0 37.0 37.0 2 36.12075 37.0 37.0 37.0 37.0 37.0 3 36.6075 37.0 37.0 37.0 37.0 37.0 4 36.674 37.0 37.0 37.0 37.0 37.0 5 36.6235 37.0 37.0 37.0 37.0 37.0 6 36.691 37.0 37.0 37.0 37.0 37.0 7 36.6085 37.0 37.0 37.0 37.0 37.0 8 36.731 37.0 37.0 37.0 37.0 37.0 9 36.6735 37.0 37.0 37.0 37.0 37.0 10-14 36.6539 37.0 37.0 37.0 37.0 37.0 15-19 36.658 37.0 37.0 37.0 37.0 37.0 20-24 36.6234 37.0 37.0 37.0 37.0 37.0 25-29 36.6009 37.0 37.0 37.0 37.0 37.0 30-34 36.5903 37.0 37.0 37.0 37.0 37.0 35-39 36.5844 37.0 37.0 37.0 37.0 37.0 40-44 36.5601 37.0 37.0 37.0 37.0 37.0 45-49 36.5476 37.0 37.0 37.0 37.0 37.0 50-54 36.5001 37.0 37.0 37.0 37.0 37.0 55-59 36.49980000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.4599 37.0 37.0 37.0 37.0 37.0 65-69 36.5037 37.0 37.0 37.0 37.0 37.0 70-74 36.436899999999994 37.0 37.0 37.0 37.0 37.0 75-79 36.4075 37.0 37.0 37.0 37.0 37.0 80-84 36.3489 37.0 37.0 37.0 37.0 37.0 85-89 36.38100000000001 37.0 37.0 37.0 37.0 37.0 90-94 36.3771 37.0 37.0 37.0 37.0 37.0 95-99 36.2977 37.0 37.0 37.0 37.0 37.0 100-104 36.3647 37.0 37.0 37.0 37.0 37.0 105-109 36.2702 37.0 37.0 37.0 37.0 37.0 110-114 36.2488 37.0 37.0 37.0 37.0 37.0 115-119 36.205000000000005 37.0 37.0 37.0 37.0 37.0 120-124 36.144099999999995 37.0 37.0 37.0 37.0 37.0 125-129 36.0856 37.0 37.0 37.0 37.0 37.0 130-134 36.0283 37.0 37.0 37.0 37.0 37.0 135-139 36.0518 37.0 37.0 37.0 37.0 37.0 140-144 35.902 37.0 37.0 37.0 37.0 37.0 145-149 35.9989 37.0 37.0 37.0 37.0 37.0 150-151 35.712500000000006 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 0.0 23 3.0 24 0.0 25 0.0 26 5.0 27 7.0 28 4.0 29 20.0 30 17.0 31 27.0 32 38.0 33 52.0 34 104.0 35 289.0 36 2850.0 37 583.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.8 9.325 7.000000000000001 35.875 2 22.79281558310144 9.891221856817607 32.4816594991146 34.834303060966356 3 22.5 14.85 23.275000000000002 39.375 4 26.974999999999998 20.5 22.1 30.425 5 28.925 26.0 21.875 23.200000000000003 6 23.325000000000003 29.9 22.225 24.55 7 19.0 24.05 38.6 18.35 8 20.25 23.599999999999998 28.825 27.325 9 21.475 22.5 32.175 23.849999999999998 10-14 23.075000000000003 26.450000000000003 24.935 25.540000000000003 15-19 23.375 25.275 25.669999999999998 25.679999999999996 20-24 23.23 25.16 25.259999999999998 26.35 25-29 23.605 24.875 25.31 26.21 30-34 22.825 25.490000000000002 25.55 26.135 35-39 23.155 25.52 25.415 25.91 40-44 23.485 24.965 25.505 26.045 45-49 23.515 25.074999999999996 24.92 26.490000000000002 50-54 23.82 25.009999999999998 25.124999999999996 26.045 55-59 23.74 24.58 25.915 25.765 60-64 24.23 24.8 24.69 26.279999999999998 65-69 23.799999999999997 24.705 24.91 26.584999999999997 70-74 24.2 25.295 24.455 26.05 75-79 23.94 25.645 24.68 25.735000000000003 80-84 23.7 25.255 25.455 25.590000000000003 85-89 23.77 25.215 24.795 26.22 90-94 24.740000000000002 24.895 24.895 25.47 95-99 24.27 24.665 24.759999999999998 26.305 100-104 23.825 25.040000000000003 24.995 26.14 105-109 24.755 24.095 24.735 26.415 110-114 24.279999999999998 24.895 24.705 26.119999999999997 115-119 23.990000000000002 25.245 24.22 26.545 120-124 24.525 24.83 24.23 26.415 125-129 24.474999999999998 25.06 23.94 26.525 130-134 24.15 25.035 24.725 26.090000000000003 135-139 24.205 24.45 24.985 26.36 140-144 24.48 24.595 24.09 26.834999999999997 145-149 24.43 24.37 24.85 26.35 150-151 24.55 25.674999999999997 23.7 26.075 >>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 0.5 7 0.5 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 0.5 23 0.5 24 0.0 25 0.5 26 1.0 27 1.5 28 1.5 29 2.5 30 5.5 31 7.5 32 13.0 33 16.0 34 17.0 35 27.5 36 39.5 37 56.5 38 72.0 39 86.0 40 105.0 41 132.0 42 169.0 43 175.5 44 176.5 45 199.0 46 204.0 47 198.5 48 197.0 49 183.0 50 171.0 51 154.0 52 140.5 53 124.5 54 103.5 55 112.5 56 104.5 57 83.5 58 91.0 59 92.0 60 74.0 61 61.0 62 58.5 63 62.5 64 62.0 65 64.5 66 61.0 67 46.5 68 44.0 69 48.5 70 42.0 71 32.0 72 24.0 73 20.0 74 14.0 75 5.5 76 4.5 77 2.5 78 1.5 79 2.5 80 1.0 81 0.0 82 0.0 83 0.5 84 0.5 85 0.5 86 0.5 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 1.175 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 91.55 #Duplication Level Percentage of deduplicated Percentage of total 1 91.83506280720918 84.075 2 7.2637902785363195 13.3 3 0.7373020207536866 2.025 4 0.1638448935008192 0.6 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.05 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 0.075 0.0 0.0 0.0 0.0 68-69 0.1 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 0.225 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.2875 0.0 0.0 0.0 0.0 82-83 0.4125 0.0 0.0 0.0 0.0 84-85 0.44999999999999996 0.0 0.0 0.0 0.0 86-87 0.5375 0.0 0.0 0.0 0.0 88-89 0.75 0.0 0.0 0.0 0.0 90-91 0.825 0.0 0.0 0.0 0.0 92-93 0.95 0.0 0.0 0.0 0.0 94-95 1.1124999999999998 0.0 0.0 0.0 0.0 96-97 1.2125 0.0 0.0 0.0 0.0 98-99 1.3250000000000002 0.0 0.0 0.0 0.0 100-101 1.525 0.0 0.0 0.0 0.0 102-103 1.6875 0.0 0.0 0.0 0.0 104-105 1.85 0.0 0.0 0.0 0.0 106-107 1.975 0.0 0.0 0.0 0.0 108-109 2.125 0.0 0.0 0.0 0.0 110-111 2.3625 0.0 0.0 0.0 0.0 112-113 2.5375 0.0 0.0 0.0 0.0 114-115 2.7875 0.0 0.0 0.0 0.0 116-117 3.2625 0.0 0.0 0.0 0.0 118-119 3.65 0.0 0.0 0.0 0.0 120-121 3.8875 0.0 0.0 0.0 0.0 122-123 4.2875 0.0 0.0 0.0 0.0 124-125 4.65 0.0 0.0 0.0 0.0 126-127 4.9625 0.0 0.0 0.0 0.0 128-129 5.2 0.0 0.0 0.0 0.0 130-131 5.7375 0.0 0.0 0.0 0.0 132-133 6.2875 0.0 0.0 0.0 0.0 134-135 6.675000000000001 0.0 0.0 0.0 0.0 136-137 7.0625 0.0 0.0 0.0 0.0 138-139 7.5875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAGTTT 10 0.006830828 145.0 9 >>END_MODULE SRR12949786 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12949786_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 36.363 37.0 37.0 37.0 37.0 37.0 2 36.224 37.0 37.0 37.0 37.0 37.0 3 36.3135 37.0 37.0 37.0 37.0 37.0 4 36.2365 37.0 37.0 37.0 37.0 37.0 5 36.375 37.0 37.0 37.0 37.0 37.0 6 36.2065 37.0 37.0 37.0 37.0 37.0 7 36.283 37.0 37.0 37.0 37.0 37.0 8 36.383 37.0 37.0 37.0 37.0 37.0 9 36.189 37.0 37.0 37.0 37.0 37.0 10-14 36.2894 37.0 37.0 37.0 37.0 37.0 15-19 36.257 37.0 37.0 37.0 37.0 37.0 20-24 36.2228 37.0 37.0 37.0 37.0 37.0 25-29 36.234399999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.107000000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.135299999999994 37.0 37.0 37.0 37.0 37.0 40-44 36.1139 37.0 37.0 37.0 37.0 37.0 45-49 36.0991 37.0 37.0 37.0 37.0 37.0 50-54 36.0646 37.0 37.0 37.0 37.0 37.0 55-59 36.0705 37.0 37.0 37.0 37.0 37.0 60-64 36.009499999999996 37.0 37.0 37.0 37.0 37.0 65-69 35.945499999999996 37.0 37.0 37.0 37.0 37.0 70-74 35.95 37.0 37.0 37.0 37.0 37.0 75-79 35.9445 37.0 37.0 37.0 37.0 37.0 80-84 35.943599999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.910199999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.873000000000005 37.0 37.0 37.0 37.0 37.0 95-99 35.846900000000005 37.0 37.0 37.0 37.0 37.0 100-104 35.8394 37.0 37.0 37.0 37.0 37.0 105-109 35.846199999999996 37.0 37.0 37.0 37.0 37.0 110-114 35.79299999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.7709 37.0 37.0 37.0 37.0 37.0 120-124 35.602199999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.5714 37.0 37.0 37.0 37.0 37.0 130-134 35.4651 37.0 37.0 37.0 37.0 37.0 135-139 35.3892 37.0 37.0 37.0 37.0 37.0 140-144 35.3545 37.0 37.0 37.0 34.6 37.0 145-149 35.293600000000005 37.0 37.0 37.0 37.0 37.0 150-151 35.04375 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 3.0 14 7.0 15 2.0 16 1.0 17 1.0 18 1.0 19 3.0 20 2.0 21 9.0 22 1.0 23 9.0 24 9.0 25 12.0 26 8.0 27 8.0 28 16.0 29 17.0 30 27.0 31 34.0 32 50.0 33 100.0 34 180.0 35 437.0 36 2651.0 37 410.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.525 17.299999999999997 10.225 30.95 2 30.975 22.225 24.975 21.825 3 24.125 23.95 28.325 23.599999999999998 4 28.675 28.375 19.625 23.325000000000003 5 30.775000000000002 30.049999999999997 18.975 20.200000000000003 6 22.85 35.125 20.200000000000003 21.825 7 24.775 18.05 34.55 22.625 8 24.65 21.925 22.5 30.925000000000004 9 24.25 21.25 28.050000000000004 26.450000000000003 10-14 26.13 25.14 22.925 25.805 15-19 25.919999999999998 24.69 23.82 25.569999999999997 20-24 25.724999999999998 25.345000000000002 23.24 25.69 25-29 26.584999999999997 24.7 22.88 25.835 30-34 25.77 24.905 23.745 25.580000000000002 35-39 26.275 24.81 23.745 25.169999999999998 40-44 26.634999999999998 24.845 23.44 25.080000000000002 45-49 26.279999999999998 25.255 23.630000000000003 24.834999999999997 50-54 26.32 24.855 23.59 25.235000000000003 55-59 25.985000000000003 25.35 23.44 25.224999999999998 60-64 26.32 25.15 24.075 24.455 65-69 27.005000000000003 25.005 23.630000000000003 24.36 70-74 26.884999999999998 25.275 23.36 24.48 75-79 26.56 25.505 23.87 24.065 80-84 26.365 24.14 24.595 24.9 85-89 26.640000000000004 23.985 24.265 25.11 90-94 26.655 24.945 24.22 24.18 95-99 26.88 24.67 24.035 24.415 100-104 27.145000000000003 24.955 23.79 24.11 105-109 26.765 25.025 24.099999999999998 24.11 110-114 26.6 24.975 23.9 24.525 115-119 27.445000000000004 25.19 23.715 23.65 120-124 27.650000000000002 25.45 23.425 23.474999999999998 125-129 27.62 25.230000000000004 22.79 24.36 130-134 27.755000000000003 25.405 23.125 23.715 135-139 27.98 25.145 23.655 23.22 140-144 28.810000000000002 25.019999999999996 23.535 22.634999999999998 145-149 28.925 24.815 23.49 22.770000000000003 150-151 27.9125 24.95 24.087500000000002 23.05 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.5 6 0.5 7 0.0 8 1.5 9 1.5 10 0.5 11 1.5 12 1.0 13 0.0 14 0.5 15 0.5 16 0.5 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 1.5 24 1.0 25 0.5 26 1.5 27 2.0 28 2.0 29 3.5 30 5.5 31 6.5 32 6.5 33 9.0 34 14.0 35 20.0 36 34.5 37 47.0 38 68.5 39 95.0 40 103.5 41 118.0 42 153.0 43 179.5 44 173.0 45 172.5 46 164.0 47 153.0 48 149.0 49 148.5 50 154.0 51 147.5 52 134.5 53 126.5 54 119.5 55 105.5 56 92.5 57 93.0 58 108.0 59 103.5 60 96.0 61 83.0 62 72.0 63 73.5 64 73.0 65 74.0 66 80.0 67 76.5 68 63.5 69 50.5 70 43.0 71 44.0 72 40.0 73 31.5 74 20.5 75 13.0 76 8.5 77 5.5 78 6.0 79 4.5 80 1.0 81 1.0 82 1.0 83 1.0 84 1.0 85 0.0 86 0.0 87 0.5 88 0.5 89 0.0 90 0.5 91 0.5 92 0.0 93 0.5 94 0.5 95 0.0 96 0.0 97 0.5 98 0.5 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 91.55 #Duplication Level Percentage of deduplicated Percentage of total 1 91.88967777170944 84.125 2 7.209175314036045 13.200000000000001 3 0.70999453850355 1.95 4 0.1638448935008192 0.6 5 0.027307482250136534 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 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 0.025 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 0.05 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 0.075 0.0 0.0 0.0 0.0 68-69 0.1 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 0.225 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.4375 0.0 0.0 0.0 0.0 84-85 0.475 0.0 0.0 0.0 0.0 86-87 0.5625 0.0 0.0 0.0 0.0 88-89 0.775 0.0 0.0 0.0 0.0 90-91 0.85 0.0 0.0 0.0 0.0 92-93 0.975 0.0 0.0 0.0 0.0 94-95 1.1375000000000002 0.0 0.0 0.0 0.0 96-97 1.2374999999999998 0.0 0.0 0.0 0.0 98-99 1.35 0.0 0.0 0.0 0.0 100-101 1.5499999999999998 0.0 0.0 0.0 0.0 102-103 1.7125 0.0 0.0 0.0 0.0 104-105 1.875 0.0 0.0 0.0 0.0 106-107 2.0250000000000004 0.0 0.0 0.0 0.0 108-109 2.175 0.0 0.0 0.0 0.0 110-111 2.4125 0.0 0.0 0.0 0.0 112-113 2.5875 0.0 0.0 0.0 0.0 114-115 2.8375 0.0 0.0 0.0 0.0 116-117 3.3125 0.0 0.0 0.0 0.0 118-119 3.7 0.0 0.0 0.0 0.0 120-121 3.9375 0.0 0.0 0.0 0.0 122-123 4.3375 0.0 0.0 0.0 0.0 124-125 4.7 0.0 0.0 0.0 0.0 126-127 5.012499999999999 0.0 0.0 0.0 0.0 128-129 5.25 0.0 0.0 0.0 0.0 130-131 5.7875 0.0 0.0 0.0 0.0 132-133 6.3625 0.0 0.0 0.0 0.0 134-135 6.775 0.0 0.0 0.0 0.0 136-137 7.1625 0.0 0.0 0.0 0.0 138-139 7.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGAAGA 10 0.006830828 145.0 4 GAAGACC 10 0.006830828 145.0 6 GAGCAAA 10 0.006830828 145.0 1 CTGGAGT 10 0.006830828 145.0 145 AGACCAC 10 0.006830828 145.0 8 >>END_MODULE Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182230 spots for SRR12949786.sra Written 2182230 spots for SRR12949786.sra Read 2182234 spots for SRR12949786.sra Written 2182234 spots for SRR12949786.sra SRR ids: ['SRR12949786.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_6qylh1cm SRR12949786.sra spots: 43644604 blocks: [[1, 2182230], [2182231, 4364460], [4364461, 6546690], [6546691, 8728920], [8728921, 10911150], [10911151, 13093380], [13093381, 15275610], [15275611, 17457840], [17457841, 19640070], [19640071, 21822300], [21822301, 24004530], [24004531, 26186760], [26186761, 28368990], [28368991, 30551220], [30551221, 32733450], [32733451, 34915680], [34915681, 37097910], [37097911, 39280140], [39280141, 41462370], [41462371, 43644604]] SRR12949786 file size 14810645 SRR12949786 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 SRR12949786 SRR12949786_1.fastq SRR12949786_2.fastq Input file: SRR12949786_1.fastq Paired file: SRR12949786_2.fastq trimmed: SRR12949786-trimmed-pair1.fastq, SRR12949786-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 10:01:45 2024 >> started Sat Dec 7 10:02:35 2024 >> done (49.819s) 43644604 read pairs processed; of these: 261 ( 0.00%) short read pairs filtered out after trimming by size control 32976 ( 0.08%) empty read pairs filtered out after trimming by size control 43611367 (99.92%) read pairs available; of these: 5118035 (11.74%) trimmed read pairs available after processing 38493332 (88.26%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 20 0.00% 19 25 0.00% 20 29 0.00% 21 12 0.00% 22 22 0.00% 23 36 0.00% 24 45 0.00% 25 42 0.00% 26 42 0.00% 27 66 0.00% 28 68 0.00% 29 70 0.00% 30 66 0.00% 31 62 0.00% 32 78 0.00% 33 81 0.00% 34 69 0.00% 35 81 0.00% 36 86 0.00% 37 107 0.00% 38 128 0.00% 39 136 0.00% 40 150 0.00% 41 173 0.00% 42 165 0.00% 43 175 0.00% 44 181 0.00% 45 209 0.00% 46 236 0.00% 47 272 0.00% 48 283 0.00% 49 334 0.00% 50 419 0.00% 51 548 0.00% 52 597 0.00% 53 616 0.00% 54 647 0.00% 55 737 0.00% 56 826 0.00% 57 965 0.00% 58 1120 0.00% 59 1317 0.00% 60 1570 0.00% 61 1794 0.00% 62 2025 0.00% 63 2246 0.01% 64 2569 0.01% 65 2687 0.01% 66 3049 0.01% 67 3611 0.01% 68 3703 0.01% 69 4347 0.01% 70 4957 0.01% 71 5645 0.01% 72 6410 0.01% 73 7192 0.02% 74 7972 0.02% 75 8738 0.02% 76 9501 0.02% 77 10525 0.02% 78 11012 0.03% 79 12462 0.03% 80 13413 0.03% 81 14489 0.03% 82 15885 0.04% 83 16893 0.04% 84 18556 0.04% 85 19983 0.05% 86 21347 0.05% 87 22197 0.05% 88 24102 0.06% 89 24677 0.06% 90 26151 0.06% 91 27543 0.06% 92 28322 0.06% 93 30452 0.07% 94 32302 0.07% 95 33556 0.08% 96 35350 0.08% 97 36952 0.08% 98 37949 0.09% 99 39620 0.09% 100 41732 0.10% 101 41884 0.10% 102 43791 0.10% 103 45586 0.10% 104 47201 0.11% 105 48548 0.11% 106 50591 0.12% 107 52623 0.12% 108 54849 0.13% 109 56436 0.13% 110 57362 0.13% 111 58943 0.14% 112 61142 0.14% 113 62706 0.14% 114 65170 0.15% 115 67663 0.16% 116 68501 0.16% 117 70621 0.16% 118 73275 0.17% 119 75533 0.17% 120 77225 0.18% 121 79533 0.18% 122 80345 0.18% 123 82330 0.19% 124 85121 0.20% 125 86713 0.20% 126 89057 0.20% 127 91419 0.21% 128 93043 0.21% 129 96532 0.22% 130 97884 0.22% 131 98812 0.23% 132 101121 0.23% 133 103887 0.24% 134 104788 0.24% 135 106863 0.25% 136 110056 0.25% 137 111001 0.25% 138 113231 0.26% 139 116022 0.27% 140 118909 0.27% 141 120005 0.28% 142 123449 0.28% 143 122930 0.28% 144 126132 0.29% 145 128399 0.29% 146 128600 0.29% 147 131364 0.30% 148 133255 0.31% 149 134744 0.31% 150 138013 0.32% 151 38493332 88.26% 43611367 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=4.33 fanout-score-rank=27 prefix-density=0.25 prefix-fanout=3.6 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.05 sequence-density-rank=28 fanout-score=218.81 fanout-score-rank=1 prefix-density=0.58 prefix-fanout=17.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=2.27 fanout-score-rank=36 prefix-density=0.46 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=25 fanout-score=313.16 fanout-score-rank=1 prefix-density=1.13 prefix-fanout=20.8 sequence=CCGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12949786 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:03:51 Started mapping on | Dec 07 10:03:51 Finished on | Dec 07 10:07:13 Mapping speed, Million of reads per hour | 777.23 Number of input reads | 43611367 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 41310965 Uniquely mapped reads % | 94.73% Average mapped length | 294.89 Number of splices: Total | 42541983 Number of splices: Annotated (sjdb) | 39758021 Number of splices: GT/AG | 41996464 Number of splices: GC/AG | 469137 Number of splices: AT/AC | 30718 Number of splices: Non-canonical | 45664 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.58 Insertion rate per base | 0.00% Insertion average length | 1.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 484680 % of reads mapped to multiple loci | 1.11% Number of reads mapped to too many loci | 144847 % of reads mapped to too many loci | 0.33% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.36% % of reads unmapped: other | 1.47% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1815722 1815722 1815722 N_multimapping 484680 484680 484680 N_noFeature 1291553 40358218 1614982 N_ambiguous 723819 5394 94946 UnstrandedReadsAssigned:39295593 PositiveStrandReadsAssigned:947353 NegativeStrandReadsAssigned:39601037 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12949786 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: SRR12949786-trimmed-pair1.fastq SRR12949786-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 43,611,367 reads, 40,292,227 reads pseudoaligned [quant] estimated average fragment length: 275.376 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,130 rounds 52973 SRR12949786.ke.tsv 35125 SRR12949786.se.tsv 88098 total ==> SRR12949786.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 662.471 0 0 PNS24247 1044 769.624 154.018 7.50478 PNS24249 1928 1653.62 277.919 6.30273 PNS24246 1044 769.624 154.018 7.50478 PNS24248 1044 769.624 154.018 7.50478 PNS24244 1471 1196.62 247.028 7.74168 PNS24243 293 98.6677 0 0 KQK14069 1603 1328.62 8811.73 248.717 KQK14071 474 232.067 100.979 16.3179 ==> SRR12949786.se.tsv <== BRADI_1g14170v3 9300 BRADI_1g53295v3 165 BRADI_1g59795v3 728 BRADI_1g07683v3 0 BRADI_1g00485v3 113 BRADI_1g20270v3 3000 BRADI_1g74790v3 93 BRADI_1g09890v3 0 BRADI_1g77505v3 266 BRADI_1g48960v3 0 SRR12949786 completed mapping pipeline successfully