Starting /dee2/code/volunteer_pipeline.sh SRR12670987 current disk space = 3051706908672 free memory = 1464539396 SRR12670987 SRAfilesize ff40589c891aaca90ec4e76f214962fb SRR12670987.sra SRR12670987.sra file validated SRR12670987 is paired end SRR12670987 is conventional basespace SRR12670987 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670987_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 36.38275 37.0 37.0 37.0 37.0 37.0 2 36.3265 37.0 37.0 37.0 37.0 37.0 3 36.543 37.0 37.0 37.0 37.0 37.0 4 36.527 37.0 37.0 37.0 37.0 37.0 5 36.638 37.0 37.0 37.0 37.0 37.0 6 36.5225 37.0 37.0 37.0 37.0 37.0 7 36.454 37.0 37.0 37.0 37.0 37.0 8 36.579 37.0 37.0 37.0 37.0 37.0 9 36.563 37.0 37.0 37.0 37.0 37.0 10-14 36.570100000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.56170000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.5156 37.0 37.0 37.0 37.0 37.0 25-29 36.4452 37.0 37.0 37.0 37.0 37.0 30-34 36.4344 37.0 37.0 37.0 37.0 37.0 35-39 36.443400000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.4452 37.0 37.0 37.0 37.0 37.0 45-49 36.4046 37.0 37.0 37.0 37.0 37.0 50-54 36.3842 37.0 37.0 37.0 37.0 37.0 55-59 36.36229999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.273399999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.3394 37.0 37.0 37.0 37.0 37.0 70-74 36.3212 37.0 37.0 37.0 37.0 37.0 75-79 36.2544 37.0 37.0 37.0 37.0 37.0 80-84 36.279 37.0 37.0 37.0 37.0 37.0 85-89 36.2269 37.0 37.0 37.0 37.0 37.0 90-94 36.1853 37.0 37.0 37.0 37.0 37.0 95-99 36.1522 37.0 37.0 37.0 37.0 37.0 100-104 36.189299999999996 37.0 37.0 37.0 37.0 37.0 105-109 36.0658 37.0 37.0 37.0 37.0 37.0 110-114 36.110200000000006 37.0 37.0 37.0 37.0 37.0 115-119 36.029 37.0 37.0 37.0 37.0 37.0 120-124 36.0376 37.0 37.0 37.0 37.0 37.0 125-129 36.0471 37.0 37.0 37.0 37.0 37.0 130-134 35.8281 37.0 37.0 37.0 37.0 37.0 135-139 35.8544 37.0 37.0 37.0 37.0 37.0 140-144 35.813300000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.626099999999994 37.0 37.0 37.0 37.0 37.0 150-151 35.50875 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 1.0 23 2.0 24 3.0 25 2.0 26 6.0 27 12.0 28 9.0 29 27.0 30 42.0 31 36.0 32 65.0 33 77.0 34 108.0 35 292.0 36 2669.0 37 647.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.8097024256064 11.75293823455864 5.926481620405101 43.51087771942986 2 19.5 11.450000000000001 38.65 30.4 3 17.9 15.775 26.3 40.025 4 21.9 21.6 24.474999999999998 32.025 5 23.625 29.925 23.9 22.55 6 19.6 31.8 25.924999999999997 22.675 7 14.875 24.825 42.8 17.5 8 15.85 25.05 33.2 25.900000000000002 9 17.724999999999998 23.7 35.3 23.275000000000002 10-14 19.439999999999998 29.975 28.285 22.3 15-19 19.805 27.900000000000002 28.055000000000003 24.240000000000002 20-24 19.689999999999998 28.23 27.705000000000002 24.375 25-29 19.794999999999998 28.185 27.925 24.095 30-34 19.505 27.785 28.09 24.62 35-39 19.61 28.415000000000003 28.000000000000004 23.974999999999998 40-44 20.135 28.53 27.755000000000003 23.580000000000002 45-49 20.28 28.29 27.650000000000002 23.78 50-54 20.905 28.29 27.994999999999997 22.81 55-59 19.845 27.655 28.025 24.474999999999998 60-64 19.835 28.025 27.82 24.32 65-69 20.825 27.955000000000002 28.025 23.195 70-74 20.055 28.34 27.884999999999998 23.72 75-79 20.25 28.42 27.415 23.915 80-84 20.080000000000002 28.599999999999998 27.560000000000002 23.76 85-89 20.645 27.939999999999998 27.605 23.810000000000002 90-94 20.875 27.939999999999998 27.565 23.62 95-99 20.150000000000002 28.54 27.150000000000002 24.16 100-104 20.495 28.21 27.41 23.885 105-109 21.015 27.24 28.335 23.41 110-114 20.315 28.215 27.62 23.849999999999998 115-119 20.830000000000002 28.005000000000003 27.605 23.56 120-124 20.849999999999998 27.3 28.075 23.775 125-129 21.099999999999998 27.655 27.525 23.72 130-134 20.735 28.32 27.38 23.565 135-139 20.765 27.47 27.860000000000003 23.905 140-144 21.165 28.125 27.205000000000002 23.505000000000003 145-149 21.055 28.345 27.67 22.93 150-151 20.837500000000002 28.575 26.5375 24.05 >>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 0.5 7 0.5 8 0.0 9 0.0 10 1.0 11 1.0 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 1.0 22 2.5 23 2.5 24 2.0 25 4.5 26 5.5 27 5.5 28 8.0 29 11.0 30 21.5 31 30.0 32 34.5 33 43.5 34 54.0 35 71.5 36 89.0 37 98.5 38 121.0 39 154.0 40 169.5 41 186.5 42 221.0 43 250.0 44 257.5 45 261.5 46 269.0 47 244.0 48 225.0 49 215.5 50 201.0 51 163.5 52 112.5 53 98.5 54 86.5 55 70.5 56 55.5 57 38.0 58 30.5 59 24.0 60 14.0 61 12.5 62 10.5 63 6.0 64 2.5 65 2.5 66 3.0 67 2.0 68 1.0 69 0.0 70 0.0 71 0.5 72 1.0 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 0.0 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 0.025 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 91.225 #Duplication Level Percentage of deduplicated Percentage of total 1 91.53192655522061 83.5 2 7.563716086599068 13.8 3 0.6851192107426692 1.875 4 0.1918333790079474 0.7000000000000001 5 0.027404768429706773 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 GGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0125 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.037500000000000006 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 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 0.0625 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.2375 0.0 0.0 0.0 0.0 94-95 0.25 0.0 0.0 0.0 0.0 96-97 0.25 0.0 0.0 0.0 0.0 98-99 0.275 0.0 0.0 0.0 0.0 100-101 0.3625 0.0 0.0 0.0 0.0 102-103 0.5125 0.0 0.0 0.0 0.0 104-105 0.575 0.0 0.0 0.0 0.0 106-107 0.65 0.0 0.0 0.0 0.0 108-109 0.725 0.0 0.0 0.0 0.0 110-111 0.8500000000000001 0.0 0.0 0.0 0.0 112-113 0.95 0.0 0.0 0.0 0.0 114-115 1.025 0.0 0.0 0.0 0.0 116-117 1.0625 0.0 0.0 0.0 0.0 118-119 1.2 0.0 0.0 0.0 0.0 120-121 1.3250000000000002 0.0 0.0 0.0 0.0 122-123 1.4625 0.0 0.0 0.0 0.0 124-125 1.65 0.0 0.0 0.0 0.0 126-127 1.8125 0.0 0.0 0.0 0.0 128-129 2.0 0.0 0.0 0.0 0.0 130-131 2.1500000000000004 0.0 0.0 0.0 0.0 132-133 2.4000000000000004 0.0 0.0 0.0 0.0 134-135 2.55 0.0 0.0 0.0 0.0 136-137 2.8125 0.0 0.0 0.0 0.0 138-139 3.0875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTTGAGA 10 0.006830828 145.0 1 GGCCTGA 10 0.006830828 145.0 9 >>END_MODULE SRR12670987 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670987_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 36.1815 37.0 37.0 37.0 37.0 37.0 2 36.238 37.0 37.0 37.0 37.0 37.0 3 36.221 37.0 37.0 37.0 37.0 37.0 4 36.2715 37.0 37.0 37.0 37.0 37.0 5 36.2715 37.0 37.0 37.0 37.0 37.0 6 36.226 37.0 37.0 37.0 37.0 37.0 7 36.267 37.0 37.0 37.0 37.0 37.0 8 36.3255 37.0 37.0 37.0 37.0 37.0 9 36.325 37.0 37.0 37.0 37.0 37.0 10-14 36.3365 37.0 37.0 37.0 37.0 37.0 15-19 36.32869999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.364000000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.2632 37.0 37.0 37.0 37.0 37.0 30-34 36.231300000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.19499999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.177200000000006 37.0 37.0 37.0 37.0 37.0 45-49 36.169399999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.131099999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.177499999999995 37.0 37.0 37.0 37.0 37.0 60-64 36.1355 37.0 37.0 37.0 37.0 37.0 65-69 36.0525 37.0 37.0 37.0 37.0 37.0 70-74 36.1151 37.0 37.0 37.0 37.0 37.0 75-79 36.0544 37.0 37.0 37.0 37.0 37.0 80-84 36.0266 37.0 37.0 37.0 37.0 37.0 85-89 35.9511 37.0 37.0 37.0 37.0 37.0 90-94 35.9993 37.0 37.0 37.0 37.0 37.0 95-99 35.999399999999994 37.0 37.0 37.0 37.0 37.0 100-104 35.9572 37.0 37.0 37.0 37.0 37.0 105-109 35.89149999999999 37.0 37.0 37.0 37.0 37.0 110-114 35.9216 37.0 37.0 37.0 37.0 37.0 115-119 35.854400000000005 37.0 37.0 37.0 37.0 37.0 120-124 35.76690000000001 37.0 37.0 37.0 37.0 37.0 125-129 35.727999999999994 37.0 37.0 37.0 37.0 37.0 130-134 35.7506 37.0 37.0 37.0 37.0 37.0 135-139 35.694700000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.7356 37.0 37.0 37.0 37.0 37.0 145-149 35.507 37.0 37.0 37.0 37.0 37.0 150-151 35.18625 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 3.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 2.0 22 0.0 23 4.0 24 5.0 25 5.0 26 3.0 27 14.0 28 23.0 29 21.0 30 39.0 31 49.0 32 70.0 33 83.0 34 158.0 35 420.0 36 2638.0 37 459.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.225 23.375 10.8 28.599999999999998 2 26.400000000000002 27.224999999999998 31.15 15.225 3 20.375 28.925 31.125000000000004 19.575 4 24.8 32.525 23.325000000000003 19.35 5 26.05 36.4 21.725 15.825 6 20.8 39.225 22.7 17.275 7 19.525000000000002 22.825 39.775 17.875 8 20.45 25.15 29.65 24.75 9 22.325 23.25 30.9 23.525 10-14 23.405 29.435 26.400000000000002 20.76 15-19 23.195 28.17 26.950000000000003 21.685 20-24 23.265 28.515 27.560000000000002 20.66 25-29 23.375 27.150000000000002 28.785 20.69 30-34 22.285 28.4 28.050000000000004 21.265 35-39 22.485 28.689999999999998 27.41 21.415 40-44 22.935 28.804999999999996 27.41 20.849999999999998 45-49 22.625 28.110000000000003 27.92 21.345 50-54 22.845 28.265 27.395000000000003 21.495 55-59 22.52 27.87 28.005000000000003 21.605 60-64 22.470000000000002 27.665 27.905 21.959999999999997 65-69 23.335 27.355 28.175 21.135 70-74 23.05 28.42 27.065 21.465 75-79 22.575 27.589999999999996 27.58 22.255 80-84 23.095 27.725 27.634999999999998 21.545 85-89 23.64 27.700000000000003 27.405 21.255 90-94 23.89 27.625 27.305 21.18 95-99 23.845 27.450000000000003 27.800000000000004 20.905 100-104 23.52 27.800000000000004 27.845 20.835 105-109 23.645 26.99 27.85 21.515 110-114 23.595 28.725 27.55 20.13 115-119 23.515 28.565 26.93 20.990000000000002 120-124 24.224999999999998 28.499999999999996 26.565 20.71 125-129 23.89 27.195000000000004 27.83 21.085 130-134 23.919999999999998 27.855 27.625 20.599999999999998 135-139 23.94 28.265 27.415 20.380000000000003 140-144 24.195 27.985 27.18 20.64 145-149 25.085 27.855 27.095000000000002 19.965 150-151 25.374999999999996 27.150000000000002 26.85 20.625 >>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 0.5 9 0.5 10 0.5 11 0.5 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 2.0 19 4.0 20 3.0 21 1.0 22 0.5 23 2.0 24 3.0 25 2.5 26 6.5 27 8.0 28 9.0 29 11.0 30 13.0 31 20.5 32 32.5 33 37.0 34 53.0 35 74.0 36 85.5 37 94.0 38 108.5 39 151.5 40 193.5 41 210.5 42 238.5 43 280.5 44 291.0 45 266.5 46 266.5 47 250.5 48 226.5 49 201.5 50 161.5 51 135.0 52 105.5 53 100.0 54 77.5 55 48.5 56 49.0 57 46.5 58 29.5 59 20.5 60 17.5 61 18.0 62 16.0 63 7.0 64 4.0 65 3.0 66 1.0 67 0.0 68 1.0 69 1.0 70 0.0 71 0.5 72 0.5 73 0.0 74 0.0 75 0.0 76 0.5 77 1.0 78 0.5 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 0.5 100 2.0 >>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 90.95 #Duplication Level Percentage of deduplicated Percentage of total 1 91.58878504672897 83.3 2 7.284222100054976 13.25 3 0.8521165475536009 2.325 4 0.19241341396371633 0.7000000000000001 5 0.054975261132490384 0.25 6 0.0 0.0 7 0.027487630566245192 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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit AGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 5 0.125 No Hit CAGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0125 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.037500000000000006 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 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 0.0625 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.1 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.15 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.2375 0.0 0.0 0.0 0.0 94-95 0.25 0.0 0.0 0.0 0.0 96-97 0.25 0.0 0.0 0.0 0.0 98-99 0.275 0.0 0.0 0.0 0.0 100-101 0.3625 0.0 0.0 0.0 0.0 102-103 0.5125 0.0 0.0 0.0 0.0 104-105 0.575 0.0 0.0 0.0 0.0 106-107 0.65 0.0 0.0 0.0 0.0 108-109 0.725 0.0 0.0 0.0 0.0 110-111 0.8500000000000001 0.0 0.0 0.0 0.0 112-113 0.95 0.0 0.0 0.0 0.0 114-115 1.025 0.0 0.0 0.0 0.0 116-117 1.0625 0.0 0.0 0.0 0.0 118-119 1.2 0.0 0.0 0.0 0.0 120-121 1.3250000000000002 0.0 0.0 0.0 0.0 122-123 1.4625 0.0 0.0 0.0 0.0 124-125 1.65 0.0 0.0 0.0 0.0 126-127 1.8125 0.0 0.0 0.0 0.0 128-129 2.0 0.0 0.0 0.0 0.0 130-131 2.1500000000000004 0.0 0.0 0.0 0.0 132-133 2.4000000000000004 0.0 0.0 0.0 0.0 134-135 2.5625 0.0 0.0 0.0 0.0 136-137 2.8375 0.0 0.0 0.0 0.0 138-139 3.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGTAATT 10 0.006830828 145.0 1 >>END_MODULE Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610059 spots for SRR12670987.sra Written 610059 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra Read 610058 spots for SRR12670987.sra Written 610058 spots for SRR12670987.sra SRR ids: ['SRR12670987.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_m88me4x8 SRR12670987.sra spots: 12201161 blocks: [[1, 610058], [610059, 1220116], [1220117, 1830174], [1830175, 2440232], [2440233, 3050290], [3050291, 3660348], [3660349, 4270406], [4270407, 4880464], [4880465, 5490522], [5490523, 6100580], [6100581, 6710638], [6710639, 7320696], [7320697, 7930754], [7930755, 8540812], [8540813, 9150870], [9150871, 9760928], [9760929, 10370986], [10370987, 10981044], [10981045, 11591102], [11591103, 12201161]] SRR12670987 file size 4124787 SRR12670987 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 SRR12670987 SRR12670987_1.fastq SRR12670987_2.fastq Input file: SRR12670987_1.fastq Paired file: SRR12670987_2.fastq trimmed: SRR12670987-trimmed-pair1.fastq, SRR12670987-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 Tue Feb 11 11:32:27 2025 >> started Tue Feb 11 11:32:41 2025 >> done (14.333s) 12201161 read pairs processed; of these: 44 ( 0.00%) short read pairs filtered out after trimming by size control 1502 ( 0.01%) empty read pairs filtered out after trimming by size control 12199615 (99.99%) read pairs available; of these: 625898 ( 5.13%) trimmed read pairs available after processing 11573717 (94.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 3 0.00% 20 5 0.00% 21 2 0.00% 22 3 0.00% 23 7 0.00% 24 2 0.00% 25 3 0.00% 26 6 0.00% 27 5 0.00% 28 2 0.00% 29 10 0.00% 30 7 0.00% 31 7 0.00% 32 7 0.00% 33 6 0.00% 34 4 0.00% 35 6 0.00% 36 6 0.00% 37 5 0.00% 38 15 0.00% 39 17 0.00% 40 13 0.00% 41 9 0.00% 42 10 0.00% 43 12 0.00% 44 14 0.00% 45 11 0.00% 46 15 0.00% 47 13 0.00% 48 16 0.00% 49 17 0.00% 50 24 0.00% 51 28 0.00% 52 44 0.00% 53 26 0.00% 54 20 0.00% 55 34 0.00% 56 34 0.00% 57 51 0.00% 58 54 0.00% 59 58 0.00% 60 45 0.00% 61 74 0.00% 62 82 0.00% 63 82 0.00% 64 96 0.00% 65 118 0.00% 66 139 0.00% 67 143 0.00% 68 175 0.00% 69 167 0.00% 70 209 0.00% 71 216 0.00% 72 291 0.00% 73 300 0.00% 74 351 0.00% 75 399 0.00% 76 458 0.00% 77 515 0.00% 78 554 0.00% 79 571 0.00% 80 650 0.01% 81 734 0.01% 82 797 0.01% 83 940 0.01% 84 976 0.01% 85 1128 0.01% 86 1198 0.01% 87 1350 0.01% 88 1425 0.01% 89 1606 0.01% 90 1709 0.01% 91 1846 0.02% 92 1984 0.02% 93 2274 0.02% 94 2506 0.02% 95 2654 0.02% 96 2760 0.02% 97 2944 0.02% 98 3256 0.03% 99 3387 0.03% 100 3631 0.03% 101 3709 0.03% 102 4098 0.03% 103 4091 0.03% 104 4359 0.04% 105 4693 0.04% 106 5013 0.04% 107 5161 0.04% 108 5509 0.05% 109 5718 0.05% 110 5969 0.05% 111 6158 0.05% 112 6466 0.05% 113 6685 0.05% 114 6813 0.06% 115 7399 0.06% 116 7742 0.06% 117 8025 0.07% 118 8160 0.07% 119 8597 0.07% 120 9129 0.07% 121 9107 0.07% 122 9425 0.08% 123 10354 0.08% 124 10420 0.09% 125 10899 0.09% 126 11093 0.09% 127 11663 0.10% 128 11959 0.10% 129 12387 0.10% 130 12466 0.10% 131 13074 0.11% 132 13388 0.11% 133 13770 0.11% 134 14185 0.12% 135 14579 0.12% 136 15030 0.12% 137 15229 0.12% 138 15975 0.13% 139 16779 0.14% 140 16819 0.14% 141 17779 0.15% 142 18014 0.15% 143 18503 0.15% 144 19113 0.16% 145 19573 0.16% 146 19836 0.16% 147 20244 0.17% 148 21248 0.17% 149 21618 0.18% 150 22499 0.18% 151 11573717 94.87% 12199615 reads passed initial QC criterion=sequence-density sequence-density=0.74 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=22 prefix-density=0.74 prefix-fanout=2.0 sequence=TTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=fanout-score sequence-density=0.13 sequence-density-rank=24 fanout-score=8.87 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=5.1 sequence=CCATCCACATTAGCACCATATTTGTCGACATATTGGTACAC criterion=sequence-density sequence-density=0.84 sequence-density-rank=1 fanout-score=2.27 fanout-score-rank=24 prefix-density=0.86 prefix-fanout=2.2 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=22.61 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=3.3 sequence=GGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAT SRR12670987 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 11:33:26 Started mapping on | Feb 11 11:33:27 Finished on | Feb 11 11:34:59 Mapping speed, Million of reads per hour | 477.38 Number of input reads | 12199615 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 11323504 Uniquely mapped reads % | 92.82% Average mapped length | 298.37 Number of splices: Total | 11650860 Number of splices: Annotated (sjdb) | 11423247 Number of splices: GT/AG | 11413105 Number of splices: GC/AG | 198266 Number of splices: AT/AC | 6685 Number of splices: Non-canonical | 32804 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.92 Insertion rate per base | 0.02% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 286148 % of reads mapped to multiple loci | 2.35% Number of reads mapped to too many loci | 142797 % of reads mapped to too many loci | 1.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.45% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 589963 589963 589963 N_multimapping 286148 286148 286148 N_noFeature 451650 11138241 498717 N_ambiguous 212579 748 74060 UnstrandedReadsAssigned:10659275 PositiveStrandReadsAssigned:184515 NegativeStrandReadsAssigned:10750727 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12670987 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: SRR12670987-trimmed-pair1.fastq SRR12670987-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,199,615 reads, 10,787,816 reads pseudoaligned [quant] estimated average fragment length: 280.08 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 996 rounds 52401 SRR12670987.ke.tsv 34699 SRR12670987.se.tsv 87100 total ==> SRR12670987.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1738.92 430 17.9488 Potri.005G024800.1.v4.1 1035 755.92 247 23.7174 Potri.004G059700.1.v4.1 961 682.081 7 0.744917 Potri.007G009000.2.v4.1 1416 1136.92 0 0 Potri.003G141000.2.v4.1 2943 2663.92 846.644 23.0688 Potri.016G087400.1.v4.1 270 72.0086 481.359 485.211 Potri.015G069301.1.v4.1 564 299.855 0 0 Potri.010G195200.1.v4.1 1773 1493.92 54.9583 2.67025 Potri.012G127500.1.v4.1 977 698.041 61 6.34299 ==> SRR12670987.se.tsv <== Potri.001G166300.v4.1 1 Potri.001G448400.v4.1 80 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 179 Potri.001G212900.v4.1 20 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR12670987 completed mapping pipeline successfully