Starting /dee2/code/volunteer_pipeline.sh SRR12919362 current disk space = 3050941636608 free memory = 1461137564 SRR12919362 SRAfilesize c0f40196225f59e1d4e708a5e43124a5 SRR12919362.sra SRR12919362.sra file validated SRR12919362 is paired end SRR12919362 is conventional basespace SRR12919362 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919362_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.464 37.0 37.0 37.0 37.0 37.0 2 36.1005 37.0 37.0 37.0 37.0 37.0 3 36.5295 37.0 37.0 37.0 37.0 37.0 4 36.608 37.0 37.0 37.0 37.0 37.0 5 36.6345 37.0 37.0 37.0 37.0 37.0 6 36.5115 37.0 37.0 37.0 37.0 37.0 7 36.6095 37.0 37.0 37.0 37.0 37.0 8 36.625 37.0 37.0 37.0 37.0 37.0 9 36.623 37.0 37.0 37.0 37.0 37.0 10-14 36.6582 37.0 37.0 37.0 37.0 37.0 15-19 36.6332 37.0 37.0 37.0 37.0 37.0 20-24 36.638 37.0 37.0 37.0 37.0 37.0 25-29 36.5355 37.0 37.0 37.0 37.0 37.0 30-34 36.535799999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.562599999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.497 37.0 37.0 37.0 37.0 37.0 45-49 36.5112 37.0 37.0 37.0 37.0 37.0 50-54 36.4498 37.0 37.0 37.0 37.0 37.0 55-59 36.463800000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.3952 37.0 37.0 37.0 37.0 37.0 65-69 36.3335 37.0 37.0 37.0 37.0 37.0 70-74 36.374100000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.3192 37.0 37.0 37.0 37.0 37.0 80-84 36.335699999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.24929999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.2145 37.0 37.0 37.0 37.0 37.0 95-99 36.243100000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.1576 37.0 37.0 37.0 37.0 37.0 105-109 36.091699999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.0418 37.0 37.0 37.0 37.0 37.0 115-119 36.0786 37.0 37.0 37.0 37.0 37.0 120-124 36.0636 37.0 37.0 37.0 37.0 37.0 125-129 36.0205 37.0 37.0 37.0 37.0 37.0 130-134 35.911199999999994 37.0 37.0 37.0 37.0 37.0 135-139 35.8991 37.0 37.0 37.0 37.0 37.0 140-144 35.7657 37.0 37.0 37.0 37.0 37.0 145-149 35.767 37.0 37.0 37.0 37.0 37.0 150-151 35.62025 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 0.0 25 1.0 26 3.0 27 6.0 28 10.0 29 11.0 30 24.0 31 36.0 32 60.0 33 49.0 34 123.0 35 340.0 36 2976.0 37 360.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.1 12.625 8.825 46.45 2 18.13131313131313 12.904040404040403 38.86363636363636 30.1010101010101 3 16.950000000000003 17.325 28.15 37.574999999999996 4 20.325 25.224999999999998 25.974999999999998 28.475 5 22.475 31.125000000000004 24.975 21.425 6 20.599999999999998 35.449999999999996 23.599999999999998 20.349999999999998 7 15.6 26.400000000000002 41.85 16.150000000000002 8 17.575 25.575 30.95 25.900000000000002 9 15.75 24.175 35.0 25.074999999999996 10-14 18.970000000000002 29.580000000000002 28.050000000000004 23.400000000000002 15-19 19.38 28.71 27.24 24.67 20-24 19.075 28.749999999999996 28.32 23.855 25-29 18.83 28.849999999999998 28.294999999999998 24.025 30-34 19.42 28.660000000000004 27.860000000000003 24.060000000000002 35-39 19.265 29.160000000000004 27.615000000000002 23.96 40-44 19.7 28.205000000000002 27.815 24.279999999999998 45-49 20.055 28.405 27.839999999999996 23.7 50-54 19.79 28.42 28.144999999999996 23.645 55-59 19.509999999999998 28.425 28.13 23.935000000000002 60-64 19.855 28.77 28.035 23.34 65-69 19.965 28.749999999999996 27.584999999999997 23.7 70-74 19.220000000000002 28.64 28.015 24.125 75-79 20.244999999999997 28.365000000000002 27.295 24.095 80-84 19.73 28.810000000000002 27.555000000000003 23.905 85-89 20.080000000000002 28.634999999999998 27.605 23.68 90-94 19.82 29.325000000000003 27.33 23.525 95-99 19.725 27.87 28.4 24.005000000000003 100-104 20.25 27.944999999999997 28.144999999999996 23.66 105-109 20.055 28.63 27.615000000000002 23.7 110-114 20.305 27.900000000000002 28.185 23.61 115-119 20.645 28.384999999999998 27.1 23.87 120-124 20.169999999999998 28.37 27.355 24.104999999999997 125-129 20.09 28.275 27.400000000000002 24.235 130-134 20.23 28.449999999999996 27.61 23.71 135-139 20.43 28.535 26.995 24.04 140-144 21.105 27.810000000000002 27.16 23.925 145-149 20.64 28.555000000000003 26.76 24.044999999999998 150-151 21.212500000000002 28.7 26.0 24.087500000000002 >>END_MODULE >>Per sequence GC content pass #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 0.5 16 0.5 17 1.0 18 1.0 19 0.5 20 0.5 21 0.5 22 1.0 23 1.0 24 1.5 25 3.0 26 4.0 27 7.5 28 15.5 29 19.0 30 15.5 31 19.5 32 38.0 33 50.0 34 55.0 35 64.0 36 98.5 37 125.0 38 123.5 39 151.5 40 199.5 41 235.0 42 255.0 43 256.0 44 274.5 45 277.0 46 261.0 47 249.5 48 231.5 49 191.5 50 153.5 51 142.5 52 110.5 53 92.0 54 76.5 55 51.0 56 40.5 57 34.0 58 21.0 59 11.0 60 10.5 61 9.0 62 5.0 63 2.0 64 2.0 65 3.5 66 3.0 67 2.0 68 0.5 69 0.0 70 0.5 71 0.5 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 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 1.0 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 92.05 #Duplication Level Percentage of deduplicated Percentage of total 1 92.42259641499186 85.075 2 6.653992395437262 12.25 3 0.7876154263986964 2.175 4 0.13579576317218903 0.5 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 0.0125 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.175 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.225 0.0 0.0 0.0 0.0 94-95 0.275 0.0 0.0 0.0 0.0 96-97 0.3125 0.0 0.0 0.0 0.0 98-99 0.3875 0.0 0.0 0.0 0.0 100-101 0.525 0.0 0.0 0.0 0.0 102-103 0.625 0.0 0.0 0.0 0.0 104-105 0.8 0.0 0.0 0.0 0.0 106-107 1.0125 0.0 0.0 0.0 0.0 108-109 1.275 0.0 0.0 0.0 0.0 110-111 1.5 0.0 0.0 0.0 0.0 112-113 1.8 0.0 0.0 0.0 0.0 114-115 2.0875 0.0 0.0 0.0 0.0 116-117 2.4124999999999996 0.0 0.0 0.0 0.0 118-119 2.7125 0.0 0.0 0.0 0.0 120-121 3.0125 0.0 0.0 0.0 0.0 122-123 3.375 0.0 0.0 0.0 0.0 124-125 3.6375 0.0 0.0 0.0 0.0 126-127 4.0625 0.0 0.0 0.0 0.0 128-129 4.3875 0.0 0.0 0.0 0.0 130-131 4.7875 0.0 0.0 0.0 0.0 132-133 5.1 0.0 0.0 0.0 0.0 134-135 5.375 0.0 0.0 0.0 0.0 136-137 5.7375 0.0 0.0 0.0 0.0 138-139 6.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12919362 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12919362_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.156 37.0 37.0 37.0 37.0 37.0 2 36.137 37.0 37.0 37.0 37.0 37.0 3 36.18 37.0 37.0 37.0 37.0 37.0 4 36.2335 37.0 37.0 37.0 37.0 37.0 5 36.2715 37.0 37.0 37.0 37.0 37.0 6 36.3045 37.0 37.0 37.0 37.0 37.0 7 36.155 37.0 37.0 37.0 37.0 37.0 8 36.277 37.0 37.0 37.0 37.0 37.0 9 36.203 37.0 37.0 37.0 37.0 37.0 10-14 36.2475 37.0 37.0 37.0 37.0 37.0 15-19 36.2164 37.0 37.0 37.0 37.0 37.0 20-24 36.1766 37.0 37.0 37.0 37.0 37.0 25-29 36.131 37.0 37.0 37.0 37.0 37.0 30-34 36.0803 37.0 37.0 37.0 37.0 37.0 35-39 36.0658 37.0 37.0 37.0 37.0 37.0 40-44 36.012299999999996 37.0 37.0 37.0 37.0 37.0 45-49 35.9943 37.0 37.0 37.0 37.0 37.0 50-54 35.9573 37.0 37.0 37.0 37.0 37.0 55-59 35.9753 37.0 37.0 37.0 37.0 37.0 60-64 35.91760000000001 37.0 37.0 37.0 37.0 37.0 65-69 35.922399999999996 37.0 37.0 37.0 37.0 37.0 70-74 35.8642 37.0 37.0 37.0 37.0 37.0 75-79 35.7784 37.0 37.0 37.0 37.0 37.0 80-84 35.8121 37.0 37.0 37.0 37.0 37.0 85-89 35.799 37.0 37.0 37.0 37.0 37.0 90-94 35.7326 37.0 37.0 37.0 37.0 37.0 95-99 35.6756 37.0 37.0 37.0 37.0 37.0 100-104 35.726099999999995 37.0 37.0 37.0 37.0 37.0 105-109 35.6165 37.0 37.0 37.0 37.0 37.0 110-114 35.6077 37.0 37.0 37.0 37.0 37.0 115-119 35.668899999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.5261 37.0 37.0 37.0 37.0 37.0 125-129 35.5197 37.0 37.0 37.0 37.0 37.0 130-134 35.4428 37.0 37.0 37.0 37.0 37.0 135-139 35.343799999999995 37.0 37.0 37.0 34.6 37.0 140-144 35.3292 37.0 37.0 37.0 32.2 37.0 145-149 35.178000000000004 37.0 37.0 37.0 25.0 37.0 150-151 34.951499999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 2.0 15 1.0 16 0.0 17 1.0 18 1.0 19 2.0 20 2.0 21 0.0 22 9.0 23 4.0 24 4.0 25 12.0 26 12.0 27 14.0 28 14.0 29 27.0 30 25.0 31 58.0 32 59.0 33 102.0 34 241.0 35 556.0 36 2607.0 37 244.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 32.425 23.525 13.225000000000001 30.825000000000003 2 29.375 25.174999999999997 31.574999999999996 13.875000000000002 3 19.1 28.15 32.324999999999996 20.424999999999997 4 22.2 34.8 24.175 18.825 5 23.425 37.875 21.475 17.224999999999998 6 21.275 37.525 23.3 17.9 7 19.325 22.6 39.900000000000006 18.175 8 20.825 25.45 29.025000000000002 24.7 9 19.7 25.324999999999996 31.1 23.875 10-14 22.74 28.79 27.245 21.224999999999998 15-19 23.49 28.005000000000003 27.57 20.935000000000002 20-24 22.615 28.794999999999998 28.24 20.349999999999998 25-29 23.064999999999998 28.050000000000004 28.249999999999996 20.635 30-34 23.285 28.23 27.725 20.76 35-39 23.57 28.645 26.965 20.82 40-44 23.215 28.395 28.050000000000004 20.34 45-49 22.825 28.749999999999996 28.060000000000002 20.365 50-54 22.919999999999998 29.154999999999998 27.894999999999996 20.03 55-59 23.395 28.125 27.755000000000003 20.724999999999998 60-64 23.27 28.095 28.115000000000002 20.52 65-69 23.355 28.4 27.565 20.68 70-74 23.865 28.499999999999996 27.74 19.895 75-79 23.125 28.095 28.27 20.51 80-84 23.45 28.435 27.615000000000002 20.5 85-89 24.02 27.925 27.76 20.294999999999998 90-94 23.57 28.355000000000004 27.744999999999997 20.330000000000002 95-99 23.625 28.24 27.534999999999997 20.599999999999998 100-104 23.845 28.185 27.46 20.51 105-109 24.169999999999998 28.689999999999998 26.61 20.53 110-114 23.705000000000002 28.945 27.18 20.169999999999998 115-119 24.025 28.005000000000003 27.644999999999996 20.325 120-124 24.32 28.02 27.655 20.005 125-129 24.7 28.315 26.69 20.294999999999998 130-134 24.265 28.655 27.095000000000002 19.985 135-139 24.97 28.144999999999996 27.485 19.400000000000002 140-144 25.705 28.76 26.474999999999998 19.06 145-149 25.490000000000002 28.560000000000002 26.645000000000003 19.305 150-151 26.087500000000002 27.975 26.900000000000002 19.037499999999998 >>END_MODULE >>Per sequence GC content pass #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 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.5 16 1.0 17 1.5 18 1.5 19 1.0 20 1.0 21 0.5 22 1.5 23 2.0 24 2.5 25 4.5 26 5.5 27 5.5 28 10.5 29 18.0 30 21.5 31 23.5 32 28.5 33 40.0 34 47.0 35 61.0 36 94.5 37 121.0 38 137.0 39 174.0 40 214.5 41 239.0 42 252.0 43 261.0 44 279.5 45 264.0 46 256.0 47 265.0 48 241.5 49 203.5 50 153.0 51 119.5 52 90.5 53 76.5 54 66.0 55 46.5 56 37.5 57 31.0 58 25.0 59 16.0 60 12.0 61 7.0 62 7.5 63 8.0 64 5.0 65 3.0 66 2.0 67 2.5 68 2.0 69 0.5 70 0.0 71 0.0 72 0.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 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 1.5 >>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 92.175 #Duplication Level Percentage of deduplicated Percentage of total 1 92.45999457553566 85.225 2 6.6992134526715486 12.35 3 0.7323026851098454 2.025 4 0.10848928668294007 0.4 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 0.0125 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.175 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.225 0.0 0.0 0.0 0.0 94-95 0.275 0.0 0.0 0.0 0.0 96-97 0.3125 0.0 0.0 0.0 0.0 98-99 0.3875 0.0 0.0 0.0 0.0 100-101 0.525 0.0 0.0 0.0 0.0 102-103 0.625 0.0 0.0 0.0 0.0 104-105 0.8 0.0 0.0 0.0 0.0 106-107 1.0125 0.0 0.0 0.0 0.0 108-109 1.275 0.0 0.0 0.0 0.0 110-111 1.5 0.0 0.0 0.0 0.0 112-113 1.7875 0.0 0.0 0.0 0.0 114-115 2.0625 0.0 0.0 0.0 0.0 116-117 2.3875 0.0 0.0 0.0 0.0 118-119 2.6875 0.0 0.0 0.0 0.0 120-121 2.9875 0.0 0.0 0.0 0.0 122-123 3.3499999999999996 0.0 0.0 0.0 0.0 124-125 3.6125 0.0 0.0 0.0 0.0 126-127 4.0375 0.0 0.0 0.0 0.0 128-129 4.3625 0.0 0.0 0.0 0.0 130-131 4.7375 0.0 0.0 0.0 0.0 132-133 5.05 0.0 0.0 0.0 0.0 134-135 5.324999999999999 0.0 0.0 0.0 0.0 136-137 5.7 0.0 0.0 0.0 0.0 138-139 6.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114944 spots for SRR12919362.sra Written 1114944 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra Read 1114931 spots for SRR12919362.sra Written 1114931 spots for SRR12919362.sra SRR ids: ['SRR12919362.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_c1lakh9j SRR12919362.sra spots: 22298633 blocks: [[1, 1114931], [1114932, 2229862], [2229863, 3344793], [3344794, 4459724], [4459725, 5574655], [5574656, 6689586], [6689587, 7804517], [7804518, 8919448], [8919449, 10034379], [10034380, 11149310], [11149311, 12264241], [12264242, 13379172], [13379173, 14494103], [14494104, 15609034], [15609035, 16723965], [16723966, 17838896], [17838897, 18953827], [18953828, 20068758], [20068759, 21183689], [21183690, 22298633]] SRR12919362 file size 7556350 SRR12919362 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 SRR12919362 SRR12919362_1.fastq SRR12919362_2.fastq Input file: SRR12919362_1.fastq Paired file: SRR12919362_2.fastq trimmed: SRR12919362-trimmed-pair1.fastq, SRR12919362-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 Wed Feb 12 20:40:01 2025 >> started Wed Feb 12 20:40:42 2025 >> done (41.159s) 22298633 read pairs processed; of these: 50 ( 0.00%) short read pairs filtered out after trimming by size control 235 ( 0.00%) empty read pairs filtered out after trimming by size control 22298348 (100.00%) read pairs available; of these: 2082092 ( 9.34%) trimmed read pairs available after processing 20216256 (90.66%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 7 0.00% 20 5 0.00% 21 7 0.00% 22 7 0.00% 23 6 0.00% 24 7 0.00% 25 7 0.00% 26 6 0.00% 27 10 0.00% 28 9 0.00% 29 10 0.00% 30 16 0.00% 31 13 0.00% 32 19 0.00% 33 23 0.00% 34 17 0.00% 35 14 0.00% 36 22 0.00% 37 23 0.00% 38 22 0.00% 39 21 0.00% 40 30 0.00% 41 26 0.00% 42 29 0.00% 43 24 0.00% 44 23 0.00% 45 36 0.00% 46 24 0.00% 47 38 0.00% 48 40 0.00% 49 54 0.00% 50 71 0.00% 51 71 0.00% 52 83 0.00% 53 73 0.00% 54 75 0.00% 55 93 0.00% 56 82 0.00% 57 126 0.00% 58 157 0.00% 59 163 0.00% 60 197 0.00% 61 230 0.00% 62 256 0.00% 63 296 0.00% 64 330 0.00% 65 362 0.00% 66 391 0.00% 67 444 0.00% 68 501 0.00% 69 544 0.00% 70 773 0.00% 71 872 0.00% 72 1033 0.00% 73 1204 0.01% 74 1274 0.01% 75 1376 0.01% 76 1540 0.01% 77 1699 0.01% 78 2048 0.01% 79 2223 0.01% 80 2544 0.01% 81 2979 0.01% 82 3422 0.02% 83 3806 0.02% 84 4269 0.02% 85 4641 0.02% 86 4933 0.02% 87 5248 0.02% 88 5914 0.03% 89 6296 0.03% 90 7255 0.03% 91 7857 0.04% 92 8459 0.04% 93 9798 0.04% 94 10626 0.05% 95 11400 0.05% 96 11922 0.05% 97 12581 0.06% 98 12866 0.06% 99 13649 0.06% 100 14635 0.07% 101 15717 0.07% 102 16715 0.07% 103 18187 0.08% 104 18997 0.09% 105 19817 0.09% 106 20813 0.09% 107 21371 0.10% 108 21670 0.10% 109 22723 0.10% 110 23241 0.10% 111 24700 0.11% 112 25940 0.12% 113 26552 0.12% 114 28372 0.13% 115 29239 0.13% 116 30624 0.14% 117 31095 0.14% 118 31565 0.14% 119 32339 0.15% 120 32719 0.15% 121 33884 0.15% 122 34691 0.16% 123 36318 0.16% 124 37602 0.17% 125 38611 0.17% 126 40270 0.18% 127 40550 0.18% 128 40878 0.18% 129 41848 0.19% 130 41742 0.19% 131 42089 0.19% 132 43993 0.20% 133 45271 0.20% 134 45419 0.20% 135 46929 0.21% 136 48466 0.22% 137 49011 0.22% 138 49119 0.22% 139 49872 0.22% 140 50315 0.23% 141 50913 0.23% 142 51463 0.23% 143 53012 0.24% 144 53899 0.24% 145 54818 0.25% 146 55989 0.25% 147 56364 0.25% 148 57020 0.26% 149 57607 0.26% 150 57445 0.26% 151 20216256 90.66% 22298348 reads passed initial QC criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=4.35 fanout-score-rank=29 prefix-density=0.15 prefix-fanout=3.8 sequence=TTAGCATTCTCAGGCAACACAAACTTCCTCATAAACTTACCAACCCTCCTTTCCATTCTCACATACTTGGCCCCTTCTTTCTCCTCTCCGCGCTTCCTCTCTCCACTGATAACCAGCACATTGTCATCCTCCACTTGAACCTTGATGTCCCCTGATTTCAGTCCCGGCATGTCAATGACGAACGCATAAGAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=284.22 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=17.2 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTG criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=6.85 fanout-score-rank=22 prefix-density=0.26 prefix-fanout=4.1 sequence=TCTTTGATCCTTTCTCTCTTGACATCTGGGACCCTTTCCAGGACTTTCCCTTCAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=476.04 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=17.6 sequence=AAGAGAAGAAACACTAAAAAAATCACACAAGCGAAATCTCCAGCGAGAAGAGAAAGATGGATTTCAGAATCATGGGTCTTGACGCGCCACTCTTCAACACCCTCCAGCACATGATGGATGCAAGTGATCATGAGGCAGACAAGTCCTTCAATGCGCCAACACGCACTTACGTACGTGATGCCAAGGCAATGGCATCAACACCAGCTGATGTGAAAGAGTATCCAA SRR12919362 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 20:41:55 Started mapping on | Feb 12 20:41:55 Finished on | Feb 12 20:48:46 Mapping speed, Million of reads per hour | 195.31 Number of input reads | 22298348 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 20650426 Uniquely mapped reads % | 92.61% Average mapped length | 295.99 Number of splices: Total | 19138082 Number of splices: Annotated (sjdb) | 18677294 Number of splices: GT/AG | 18773584 Number of splices: GC/AG | 278558 Number of splices: AT/AC | 17671 Number of splices: Non-canonical | 68269 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 3.02 Insertion rate per base | 0.03% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 580318 % of reads mapped to multiple loci | 2.60% Number of reads mapped to too many loci | 93051 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.21% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1067604 1067604 1067604 N_multimapping 580318 580318 580318 N_noFeature 811431 20399991 929273 N_ambiguous 266523 1327 133432 UnstrandedReadsAssigned:19572472 PositiveStrandReadsAssigned:249108 NegativeStrandReadsAssigned:19587721 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12919362 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR12919362-trimmed-pair1.fastq SRR12919362-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,298,348 reads, 19,638,666 reads pseudoaligned [quant] estimated average fragment length: 279.173 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,118 rounds 52401 SRR12919362.ke.tsv 34699 SRR12919362.se.tsv 87100 total ==> SRR12919362.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1739.83 978 31.8817 Potri.005G024800.1.v4.1 1035 756.827 201 15.0629 Potri.004G059700.1.v4.1 961 683.16 62 5.14728 Potri.007G009000.2.v4.1 1416 1137.83 0 0 Potri.003G141000.2.v4.1 2943 2664.83 827 17.6013 Potri.016G087400.1.v4.1 270 83.8174 1492.28 1009.77 Potri.015G069301.1.v4.1 564 306.502 0 0 Potri.010G195200.1.v4.1 1773 1494.83 97 3.68035 Potri.012G127500.1.v4.1 977 699.004 5376 436.203 ==> SRR12919362.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 63 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 224 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 1 SRR12919362 completed mapping pipeline successfully