Starting /dee2/code/volunteer_pipeline.sh SRR12667008 current disk space = 1540809531392 free memory = 1598904188 SRR12667008 SRAfilesize 1b95b3d2a7248c8364caeee56b96cd51 SRR12667008.sra SRR12667008.sra file validated SRR12667008 is paired end SRR12667008 is conventional basespace SRR12667008 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12667008_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.462 37.0 37.0 37.0 37.0 37.0 2 36.36325 37.0 37.0 37.0 37.0 37.0 3 36.4025 37.0 37.0 37.0 37.0 37.0 4 36.518 37.0 37.0 37.0 37.0 37.0 5 36.5345 37.0 37.0 37.0 37.0 37.0 6 36.592 37.0 37.0 37.0 37.0 37.0 7 36.455 37.0 37.0 37.0 37.0 37.0 8 36.5355 37.0 37.0 37.0 37.0 37.0 9 36.5095 37.0 37.0 37.0 37.0 37.0 10-14 36.5754 37.0 37.0 37.0 37.0 37.0 15-19 36.548 37.0 37.0 37.0 37.0 37.0 20-24 36.595600000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.5098 37.0 37.0 37.0 37.0 37.0 30-34 36.4553 37.0 37.0 37.0 37.0 37.0 35-39 36.43429999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.439800000000005 37.0 37.0 37.0 37.0 37.0 45-49 36.399899999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.436800000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.3423 37.0 37.0 37.0 37.0 37.0 60-64 36.3392 37.0 37.0 37.0 37.0 37.0 65-69 36.3471 37.0 37.0 37.0 37.0 37.0 70-74 36.32770000000001 37.0 37.0 37.0 37.0 37.0 75-79 36.26370000000001 37.0 37.0 37.0 37.0 37.0 80-84 36.175599999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.226800000000004 37.0 37.0 37.0 37.0 37.0 90-94 36.220600000000005 37.0 37.0 37.0 37.0 37.0 95-99 36.0897 37.0 37.0 37.0 37.0 37.0 100-104 36.161899999999996 37.0 37.0 37.0 37.0 37.0 105-109 36.2003 37.0 37.0 37.0 37.0 37.0 110-114 36.1444 37.0 37.0 37.0 37.0 37.0 115-119 36.045399999999994 37.0 37.0 37.0 37.0 37.0 120-124 36.044399999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.9856 37.0 37.0 37.0 37.0 37.0 130-134 35.964000000000006 37.0 37.0 37.0 37.0 37.0 135-139 35.902300000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.7346 37.0 37.0 37.0 37.0 37.0 145-149 35.6225 37.0 37.0 37.0 37.0 37.0 150-151 35.416250000000005 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 4.0 24 4.0 25 3.0 26 4.0 27 5.0 28 13.0 29 22.0 30 17.0 31 44.0 32 56.0 33 82.0 34 134.0 35 303.0 36 2831.0 37 478.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.85 14.674999999999999 7.1499999999999995 32.324999999999996 2 22.91718789091819 16.28721541155867 35.67675756817613 25.11883912934701 3 20.5 23.525 28.15 27.825 4 26.1 29.9 21.224999999999998 22.775000000000002 5 24.125 34.1 22.1 19.675 6 21.175 34.1 22.400000000000002 22.325 7 17.0 22.425 40.025 20.549999999999997 8 18.775 21.275 28.225 31.724999999999998 9 19.7 20.325 31.175000000000004 28.799999999999997 10-14 22.925 27.16 24.305 25.61 15-19 22.735 26.27 25.564999999999998 25.430000000000003 20-24 22.91 26.005 25.505 25.580000000000002 25-29 23.005 25.97 25.169999999999998 25.855 30-34 22.81 26.035000000000004 25.61 25.545 35-39 22.865 26.375 25.285000000000004 25.474999999999998 40-44 22.895 26.405 25.014999999999997 25.685000000000002 45-49 23.150000000000002 26.369999999999997 25.525 24.955 50-54 22.89 26.035000000000004 25.759999999999998 25.314999999999998 55-59 22.8 25.5 25.515 26.185000000000002 60-64 23.125 25.900000000000002 25.324999999999996 25.650000000000002 65-69 23.135 26.41 25.779999999999998 24.675 70-74 23.885 25.855 24.895 25.365 75-79 23.32 26.040000000000003 25.165 25.474999999999998 80-84 23.665 25.165 25.795 25.374999999999996 85-89 23.44 25.94 25.15 25.47 90-94 23.39 26.340000000000003 24.875 25.395 95-99 23.69 25.424999999999997 25.045 25.840000000000003 100-104 23.150000000000002 26.145000000000003 25.445 25.259999999999998 105-109 23.549999999999997 25.69 25.105 25.655 110-114 23.330000000000002 26.02 25.14 25.509999999999998 115-119 23.5 25.835 25.215 25.45 120-124 24.13 25.77 24.335 25.765 125-129 23.665 25.715 25.15 25.47 130-134 24.265 25.91 24.485 25.34 135-139 23.9 25.83 24.765 25.505 140-144 23.669999999999998 26.33 23.98 26.02 145-149 23.955000000000002 26.245 24.11 25.69 150-151 24.025 25.837500000000002 24.125 26.0125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 1.0 27 4.5 28 4.5 29 3.0 30 4.5 31 10.5 32 14.5 33 17.5 34 26.0 35 39.0 36 44.0 37 50.5 38 72.5 39 96.0 40 126.5 41 164.5 42 180.0 43 185.0 44 195.5 45 207.5 46 220.5 47 223.5 48 212.0 49 178.5 50 178.0 51 176.5 52 148.5 53 129.0 54 113.0 55 106.5 56 99.5 57 86.5 58 72.5 59 71.0 60 69.0 61 63.5 62 55.5 63 52.0 64 47.5 65 41.0 66 36.0 67 31.5 68 33.5 69 32.0 70 23.0 71 16.5 72 11.0 73 7.5 74 7.0 75 4.5 76 3.0 77 0.5 78 0.0 79 0.5 80 0.5 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.075 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 92.825 #Duplication Level Percentage of deduplicated Percentage of total 1 92.94371128467547 86.275 2 6.4368435227578775 11.95 3 0.5655803932130353 1.575 4 0.05386479935362241 0.2 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 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.32499999999999996 0.0 0.0 0.0 0.0 88-89 0.3875 0.0 0.0 0.0 0.0 90-91 0.48750000000000004 0.0 0.0 0.0 0.0 92-93 0.575 0.0 0.0 0.0 0.0 94-95 0.6875 0.0 0.0 0.0 0.0 96-97 0.925 0.0 0.0 0.0 0.0 98-99 1.0 0.0 0.0 0.0 0.0 100-101 1.0875 0.0 0.0 0.0 0.0 102-103 1.2125 0.0 0.0 0.0 0.0 104-105 1.4 0.0 0.0 0.0 0.0 106-107 1.625 0.0 0.0 0.0 0.0 108-109 1.9375 0.0 0.0 0.0 0.0 110-111 2.2625 0.0 0.0 0.0 0.0 112-113 2.575 0.0 0.0 0.0 0.0 114-115 2.9749999999999996 0.0 0.0 0.0 0.0 116-117 3.2875 0.0 0.0 0.0 0.0 118-119 3.7125 0.0 0.0 0.0 0.0 120-121 4.1 0.0 0.0 0.0 0.0 122-123 4.4375 0.0 0.0 0.0 0.0 124-125 4.975 0.0 0.0 0.0 0.0 126-127 5.449999999999999 0.0 0.0 0.0 0.0 128-129 6.0625 0.0 0.0 0.0 0.0 130-131 6.625 0.0 0.0 0.0 0.0 132-133 7.3375 0.0 0.0 0.0 0.0 134-135 7.9 0.0 0.0 0.0 0.0 136-137 8.5 0.0 0.0 0.0 0.0 138-139 8.9875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATACAAA 10 0.006830828 145.0 6 GAGCACA 35 0.0035366106 20.714287 140-144 GGAAGAG 40 0.0076550315 18.125 135-139 AGCACAC 40 0.0076550315 18.125 8 AGATCGG 50 0.0013298223 17.4 130-134 >>END_MODULE SRR12667008 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12667008_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 36.0705 37.0 37.0 37.0 37.0 37.0 2 36.1095 37.0 37.0 37.0 37.0 37.0 3 36.0825 37.0 37.0 37.0 37.0 37.0 4 36.1935 37.0 37.0 37.0 37.0 37.0 5 36.1855 37.0 37.0 37.0 37.0 37.0 6 36.1885 37.0 37.0 37.0 37.0 37.0 7 36.2075 37.0 37.0 37.0 37.0 37.0 8 36.302 37.0 37.0 37.0 37.0 37.0 9 36.2285 37.0 37.0 37.0 37.0 37.0 10-14 36.2416 37.0 37.0 37.0 37.0 37.0 15-19 36.262299999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.199799999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.1777 37.0 37.0 37.0 37.0 37.0 30-34 36.129099999999994 37.0 37.0 37.0 37.0 37.0 35-39 36.096999999999994 37.0 37.0 37.0 37.0 37.0 40-44 36.0941 37.0 37.0 37.0 37.0 37.0 45-49 35.9923 37.0 37.0 37.0 37.0 37.0 50-54 35.9726 37.0 37.0 37.0 37.0 37.0 55-59 35.9678 37.0 37.0 37.0 37.0 37.0 60-64 35.9602 37.0 37.0 37.0 37.0 37.0 65-69 35.94440000000001 37.0 37.0 37.0 37.0 37.0 70-74 35.910199999999996 37.0 37.0 37.0 37.0 37.0 75-79 35.9034 37.0 37.0 37.0 37.0 37.0 80-84 35.8409 37.0 37.0 37.0 37.0 37.0 85-89 35.858900000000006 37.0 37.0 37.0 37.0 37.0 90-94 35.8121 37.0 37.0 37.0 37.0 37.0 95-99 35.7795 37.0 37.0 37.0 37.0 37.0 100-104 35.8277 37.0 37.0 37.0 37.0 37.0 105-109 35.7952 37.0 37.0 37.0 37.0 37.0 110-114 35.6802 37.0 37.0 37.0 37.0 37.0 115-119 35.676100000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.6816 37.0 37.0 37.0 37.0 37.0 125-129 35.6269 37.0 37.0 37.0 37.0 37.0 130-134 35.5767 37.0 37.0 37.0 37.0 37.0 135-139 35.514700000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.3669 37.0 37.0 37.0 37.0 37.0 145-149 35.352700000000006 37.0 37.0 37.0 37.0 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 12 3.0 13 1.0 14 6.0 15 4.0 16 6.0 17 2.0 18 1.0 19 1.0 20 3.0 21 3.0 22 9.0 23 6.0 24 11.0 25 11.0 26 8.0 27 11.0 28 17.0 29 16.0 30 30.0 31 24.0 32 50.0 33 88.0 34 168.0 35 490.0 36 2630.0 37 401.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.85 18.125 8.7 27.325 2 29.5 20.7 27.85 21.95 3 22.1 24.7 29.7 23.5 4 26.75 32.125 19.375 21.75 5 27.224999999999998 33.650000000000006 18.175 20.95 6 23.674999999999997 34.949999999999996 18.9 22.475 7 22.325 17.1 37.4 23.175 8 21.349999999999998 20.775 23.799999999999997 34.075 9 23.275000000000002 20.549999999999997 27.075 29.099999999999998 10-14 26.095000000000002 25.155 23.51 25.240000000000002 15-19 25.6 25.44 24.745 24.215 20-24 25.35 25.005 24.279999999999998 25.365 25-29 25.365 25.790000000000003 24.325 24.52 30-34 25.97 24.765 24.474999999999998 24.79 35-39 26.045 24.805 24.47 24.68 40-44 26.07 24.925 24.565 24.44 45-49 25.665 24.845 24.610000000000003 24.88 50-54 25.935000000000002 25.535000000000004 24.265 24.265 55-59 26.305 25.415 24.595 23.685000000000002 60-64 26.279999999999998 25.485000000000003 24.52 23.715 65-69 26.375 25.525 24.64 23.46 70-74 26.215 24.709999999999997 24.94 24.135 75-79 26.185000000000002 25.21 24.490000000000002 24.115000000000002 80-84 25.905 25.44 24.52 24.135 85-89 26.645000000000003 25.119999999999997 24.529999999999998 23.705000000000002 90-94 25.4 25.775 24.62 24.205 95-99 25.705 25.259999999999998 24.86 24.175 100-104 26.05 25.740000000000002 24.515 23.695 105-109 26.57 26.085 24.525 22.82 110-114 26.340000000000003 25.419999999999998 25.045 23.195 115-119 26.47 25.319999999999997 24.51 23.7 120-124 26.974999999999998 25.605 24.715 22.705000000000002 125-129 26.3 25.31 25.040000000000003 23.35 130-134 27.485 25.324999999999996 24.7 22.49 135-139 28.015 25.785000000000004 24.34 21.86 140-144 28.525 25.94 24.215 21.32 145-149 28.53 26.105 23.674999999999997 21.69 150-151 29.475 25.124999999999996 24.3125 21.087500000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.5 10 1.0 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.5 23 2.0 24 1.5 25 0.5 26 1.5 27 1.5 28 1.0 29 2.5 30 5.0 31 4.0 32 4.0 33 8.5 34 15.5 35 30.0 36 47.0 37 56.5 38 74.5 39 92.5 40 105.0 41 120.0 42 144.0 43 178.0 44 185.0 45 181.0 46 178.0 47 188.5 48 196.0 49 177.0 50 168.0 51 166.0 52 149.0 53 141.0 54 129.5 55 102.5 56 103.0 57 102.0 58 100.0 59 93.5 60 77.0 61 70.5 62 62.5 63 55.5 64 56.0 65 56.5 66 55.5 67 58.0 68 53.0 69 44.5 70 36.5 71 27.5 72 22.0 73 16.0 74 10.0 75 6.5 76 6.0 77 6.0 78 2.5 79 1.5 80 1.5 81 0.5 82 0.0 83 0.0 84 0.5 85 0.5 86 1.0 87 1.0 88 0.5 89 0.5 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 95 0.5 96 0.0 97 1.0 98 1.5 99 1.0 100 3.0 >>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 92.65 #Duplication Level Percentage of deduplicated Percentage of total 1 92.98434970318402 86.15 2 6.314085267134377 11.700000000000001 3 0.6475984889368591 1.7999999999999998 4 0.026983270372369132 0.1 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 0.026983270372369132 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 >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.3125 0.0 0.0 0.0 0.0 88-89 0.3625 0.0 0.0 0.0 0.0 90-91 0.4625 0.0 0.0 0.0 0.0 92-93 0.55 0.0 0.0 0.0 0.0 94-95 0.6625 0.0 0.0 0.0 0.0 96-97 0.8999999999999999 0.0 0.0 0.0 0.0 98-99 0.975 0.0 0.0 0.0 0.0 100-101 1.0625 0.0 0.0 0.0 0.0 102-103 1.1875 0.0 0.0 0.0 0.0 104-105 1.375 0.0 0.0 0.0 0.0 106-107 1.6 0.0 0.0 0.0 0.0 108-109 1.9124999999999999 0.0 0.0 0.0 0.0 110-111 2.2375 0.0 0.0 0.0 0.0 112-113 2.575 0.0 0.0 0.0 0.0 114-115 3.0 0.0 0.0 0.0 0.0 116-117 3.3125 0.0 0.0 0.0 0.0 118-119 3.7375 0.0 0.0 0.0 0.0 120-121 4.137499999999999 0.0 0.0 0.0 0.0 122-123 4.487500000000001 0.0 0.0 0.0 0.0 124-125 5.025 0.0 0.0 0.0 0.0 126-127 5.5 0.0 0.0 0.0 0.0 128-129 6.1125 0.0 0.0 0.0 0.0 130-131 6.675000000000001 0.0 0.0 0.0 0.0 132-133 7.387499999999999 0.0 0.0 0.0 0.0 134-135 7.949999999999999 0.0 0.0 0.0 0.0 136-137 8.55 0.0 0.0 0.0 0.0 138-139 9.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAACTC 10 0.006830828 145.0 9 GAGCGTC 35 0.0035366106 20.714287 140-144 AGCGTCG 40 0.0076550315 18.125 1 >>END_MODULE Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671305 spots for SRR12667008.sra Written 1671305 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra Read 1671300 spots for SRR12667008.sra Written 1671300 spots for SRR12667008.sra SRR ids: ['SRR12667008.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_den_pwg_ SRR12667008.sra spots: 33426005 blocks: [[1, 1671300], [1671301, 3342600], [3342601, 5013900], [5013901, 6685200], [6685201, 8356500], [8356501, 10027800], [10027801, 11699100], [11699101, 13370400], [13370401, 15041700], [15041701, 16713000], [16713001, 18384300], [18384301, 20055600], [20055601, 21726900], [21726901, 23398200], [23398201, 25069500], [25069501, 26740800], [26740801, 28412100], [28412101, 30083400], [30083401, 31754700], [31754701, 33426005]] SRR12667008 file size 11337918 SRR12667008 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 SRR12667008 SRR12667008_1.fastq SRR12667008_2.fastq Input file: SRR12667008_1.fastq Paired file: SRR12667008_2.fastq trimmed: SRR12667008-trimmed-pair1.fastq, SRR12667008-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 18:14:48 2024 >> started Sat Dec 7 18:15:34 2024 >> done (45.864s) 33426005 read pairs processed; of these: 133 ( 0.00%) short read pairs filtered out after trimming by size control 2325 ( 0.01%) empty read pairs filtered out after trimming by size control 33423547 (99.99%) read pairs available; of these: 4286309 (12.82%) trimmed read pairs available after processing 29137238 (87.18%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 15 0.00% 20 18 0.00% 21 23 0.00% 22 16 0.00% 23 30 0.00% 24 17 0.00% 25 38 0.00% 26 33 0.00% 27 42 0.00% 28 39 0.00% 29 51 0.00% 30 48 0.00% 31 33 0.00% 32 68 0.00% 33 59 0.00% 34 62 0.00% 35 51 0.00% 36 60 0.00% 37 68 0.00% 38 86 0.00% 39 69 0.00% 40 63 0.00% 41 73 0.00% 42 75 0.00% 43 80 0.00% 44 92 0.00% 45 118 0.00% 46 121 0.00% 47 144 0.00% 48 107 0.00% 49 150 0.00% 50 156 0.00% 51 141 0.00% 52 172 0.00% 53 194 0.00% 54 235 0.00% 55 256 0.00% 56 255 0.00% 57 290 0.00% 58 325 0.00% 59 343 0.00% 60 402 0.00% 61 510 0.00% 62 518 0.00% 63 593 0.00% 64 644 0.00% 65 741 0.00% 66 791 0.00% 67 956 0.00% 68 1092 0.00% 69 1263 0.00% 70 1560 0.00% 71 1809 0.01% 72 2046 0.01% 73 2363 0.01% 74 2519 0.01% 75 2914 0.01% 76 3310 0.01% 77 3629 0.01% 78 4099 0.01% 79 4766 0.01% 80 5378 0.02% 81 6288 0.02% 82 7289 0.02% 83 8468 0.03% 84 9306 0.03% 85 9852 0.03% 86 10739 0.03% 87 11699 0.04% 88 12543 0.04% 89 13667 0.04% 90 15372 0.05% 91 17205 0.05% 92 19021 0.06% 93 21018 0.06% 94 22448 0.07% 95 24084 0.07% 96 25136 0.08% 97 26415 0.08% 98 27828 0.08% 99 29719 0.09% 100 31759 0.10% 101 33679 0.10% 102 36420 0.11% 103 39065 0.12% 104 41323 0.12% 105 43492 0.13% 106 44192 0.13% 107 45398 0.14% 108 47034 0.14% 109 48191 0.14% 110 50077 0.15% 111 53423 0.16% 112 56222 0.17% 113 58391 0.17% 114 61277 0.18% 115 62717 0.19% 116 64203 0.19% 117 65296 0.20% 118 65867 0.20% 119 67325 0.20% 120 69090 0.21% 121 71024 0.21% 122 72952 0.22% 123 76237 0.23% 124 80329 0.24% 125 82313 0.25% 126 82981 0.25% 127 83910 0.25% 128 83573 0.25% 129 84780 0.25% 130 84701 0.25% 131 86123 0.26% 132 90207 0.27% 133 92568 0.28% 134 95332 0.29% 135 97393 0.29% 136 98551 0.29% 137 98703 0.30% 138 99619 0.30% 139 98848 0.30% 140 99446 0.30% 141 100860 0.30% 142 102699 0.31% 143 104896 0.31% 144 108034 0.32% 145 109436 0.33% 146 111597 0.33% 147 111202 0.33% 148 109853 0.33% 149 109409 0.33% 150 109961 0.33% 151 29137238 87.18% 33423547 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=4.60 fanout-score-rank=23 prefix-density=0.25 prefix-fanout=3.3 sequence=GATCTCGCCGAAG criterion=fanout-score sequence-density=0.04 sequence-density-rank=28 fanout-score=149.32 fanout-score-rank=1 prefix-density=0.40 prefix-fanout=16.1 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=2.28 fanout-score-rank=33 prefix-density=0.39 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=33 fanout-score=636.56 fanout-score-rank=1 prefix-density=0.76 prefix-fanout=17.5 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGACTGTGCCGTGCTTATCATTGACTCCACGACTGGAGGTTTTGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCATGCCCTCCTTGCTTTCACTCTTGGAGTGAAGCAGATGATCTGCTGCTGCAACAAGATGGA SRR12667008 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 18:16:26 Started mapping on | Dec 07 18:16:26 Finished on | Dec 07 18:19:57 Mapping speed, Million of reads per hour | 570.26 Number of input reads | 33423547 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 31108897 Uniquely mapped reads % | 93.07% Average mapped length | 294.29 Number of splices: Total | 32800813 Number of splices: Annotated (sjdb) | 30724869 Number of splices: GT/AG | 32316883 Number of splices: GC/AG | 367430 Number of splices: AT/AC | 23416 Number of splices: Non-canonical | 93084 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.02% Deletion average length | 2.49 Insertion rate per base | 0.02% Insertion average length | 2.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 471356 % of reads mapped to multiple loci | 1.41% Number of reads mapped to too many loci | 58994 % of reads mapped to too many loci | 0.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.39% % of reads unmapped: other | 0.95% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1843294 1843294 1843294 N_multimapping 471356 471356 471356 N_noFeature 1147861 30317855 1411698 N_ambiguous 637050 5127 110862 UnstrandedReadsAssigned:29323986 PositiveStrandReadsAssigned:785915 NegativeStrandReadsAssigned:29586337 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12667008 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: SRR12667008-trimmed-pair1.fastq SRR12667008-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,423,547 reads, 30,023,179 reads pseudoaligned [quant] estimated average fragment length: 276.396 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,255 rounds 52973 SRR12667008.ke.tsv 35125 SRR12667008.se.tsv 88098 total ==> SRR12667008.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 661.534 0 0 PNS24247 1044 768.604 149.544 10.1506 PNS24249 1928 1652.6 70.6464 2.23021 PNS24246 1044 768.604 149.544 10.1506 PNS24248 1044 768.604 149.544 10.1506 PNS24244 1471 1195.6 363.723 15.8711 PNS24243 293 101.508 0 0 KQK14069 1603 1327.6 4170.28 163.878 KQK14071 474 233.506 105.089 23.4793 ==> SRR12667008.se.tsv <== BRADI_1g14170v3 4924 BRADI_1g53295v3 300 BRADI_1g59795v3 936 BRADI_1g07683v3 0 BRADI_1g00485v3 160 BRADI_1g20270v3 2029 BRADI_1g74790v3 91 BRADI_1g09890v3 0 BRADI_1g77505v3 172 BRADI_1g48960v3 0 SRR12667008 completed mapping pipeline successfully