Starting /dee2/code/volunteer_pipeline.sh SRR12670153 current disk space = 3054879404032 free memory = 1508664832 SRR12670153 SRAfilesize abf0eb19719289472d2059cd3b252860 SRR12670153.sra SRR12670153.sra file validated SRR12670153 is paired end SRR12670153 is conventional basespace SRR12670153 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670153_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6255 37.0 37.0 37.0 37.0 37.0 2 36.47825 37.0 37.0 37.0 37.0 37.0 3 36.596 37.0 37.0 37.0 37.0 37.0 4 36.6565 37.0 37.0 37.0 37.0 37.0 5 36.6465 37.0 37.0 37.0 37.0 37.0 6 36.6775 37.0 37.0 37.0 37.0 37.0 7 36.538 37.0 37.0 37.0 37.0 37.0 8 36.603 37.0 37.0 37.0 37.0 37.0 9 36.4845 37.0 37.0 37.0 37.0 37.0 10-14 36.583600000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.55930000000001 37.0 37.0 37.0 37.0 37.0 20-24 36.548700000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.5308 37.0 37.0 37.0 37.0 37.0 30-34 36.47670000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.4928 37.0 37.0 37.0 37.0 37.0 40-44 36.4695 37.0 37.0 37.0 37.0 37.0 45-49 36.4366 37.0 37.0 37.0 37.0 37.0 50-54 36.4467 37.0 37.0 37.0 37.0 37.0 55-59 36.3794 37.0 37.0 37.0 37.0 37.0 60-64 36.3908 37.0 37.0 37.0 37.0 37.0 65-69 36.357600000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.2697 37.0 37.0 37.0 37.0 37.0 75-79 36.2934 37.0 37.0 37.0 37.0 37.0 80-84 36.264300000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.2287 37.0 37.0 37.0 37.0 37.0 90-94 36.2379 37.0 37.0 37.0 37.0 37.0 95-99 36.195 37.0 37.0 37.0 37.0 37.0 100-104 36.2239 37.0 37.0 37.0 37.0 37.0 105-109 36.1827 37.0 37.0 37.0 37.0 37.0 110-114 36.1613 37.0 37.0 37.0 37.0 37.0 115-119 36.1708 37.0 37.0 37.0 37.0 37.0 120-124 36.052800000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.9976 37.0 37.0 37.0 37.0 37.0 130-134 35.8846 37.0 37.0 37.0 37.0 37.0 135-139 35.687 37.0 37.0 37.0 37.0 37.0 140-144 35.388400000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.2866 37.0 37.0 37.0 37.0 37.0 150-151 35.037 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 2.0 24 0.0 25 3.0 26 2.0 27 15.0 28 10.0 29 15.0 30 26.0 31 34.0 32 61.0 33 76.0 34 153.0 35 304.0 36 2882.0 37 415.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.775 11.075 5.975 41.175 2 19.53965474105579 13.034776082061548 37.60320240180135 29.82236677508131 3 17.8 15.1 28.725 38.375 4 21.9 23.724999999999998 25.5 28.875 5 23.925 31.3 22.725 22.05 6 21.55 31.85 24.675 21.925 7 16.925 26.075 39.65 17.349999999999998 8 18.025 25.525 32.550000000000004 23.9 9 20.075000000000003 23.125 34.0 22.8 10-14 20.285 29.095 27.555000000000003 23.064999999999998 15-19 20.4 27.955000000000002 28.16 23.485 20-24 20.515 27.639999999999997 28.115000000000002 23.73 25-29 20.655 27.91 28.110000000000003 23.325000000000003 30-34 20.665 27.375 27.96 24.0 35-39 21.224999999999998 26.895000000000003 27.905 23.974999999999998 40-44 20.45 28.005000000000003 27.88 23.665 45-49 20.61 27.415 28.110000000000003 23.865 50-54 20.31 27.284999999999997 28.549999999999997 23.855 55-59 20.615 27.644999999999996 27.92 23.82 60-64 21.005 27.375 27.935 23.685000000000002 65-69 20.95 27.93 27.575 23.544999999999998 70-74 21.279999999999998 27.694999999999997 27.534999999999997 23.49 75-79 21.005 27.92 27.189999999999998 23.885 80-84 21.04 27.575 27.825 23.56 85-89 21.57 27.485 27.250000000000004 23.695 90-94 21.8 28.494999999999997 26.85 22.855 95-99 22.27 27.255000000000003 27.37 23.105 100-104 21.77 27.41 27.005000000000003 23.815 105-109 21.965 27.47 27.46 23.105 110-114 21.425 28.29 26.779999999999998 23.505000000000003 115-119 21.795 29.235 25.735000000000003 23.235 120-124 22.35 28.244999999999997 25.645 23.76 125-129 21.490000000000002 28.455000000000002 25.740000000000002 24.315 130-134 22.02 27.834999999999997 25.230000000000004 24.915000000000003 135-139 21.759999999999998 28.075 25.445 24.72 140-144 21.08 27.47 26.155 25.295 145-149 21.465 26.900000000000002 25.89 25.745 150-151 21.224999999999998 27.537499999999998 25.8625 25.374999999999996 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 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 1.5 23 1.5 24 0.0 25 0.0 26 3.0 27 4.5 28 8.5 29 10.5 30 12.5 31 20.5 32 23.0 33 34.5 34 49.0 35 55.0 36 63.0 37 83.0 38 120.0 39 151.5 40 174.5 41 193.5 42 215.5 43 246.0 44 256.5 45 254.5 46 253.0 47 252.5 48 234.0 49 233.0 50 235.0 51 186.5 52 132.0 53 105.0 54 89.5 55 73.5 56 65.0 57 49.5 58 33.5 59 28.0 60 20.5 61 10.5 62 5.5 63 3.5 64 2.0 65 0.5 66 1.0 67 1.0 68 0.5 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 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 0.0 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 79.425 #Duplication Level Percentage of deduplicated Percentage of total 1 80.51621026125275 63.949999999999996 2 14.730878186968837 23.400000000000002 3 3.4623858986465215 8.25 4 0.9757632987094743 3.1 5 0.28328611898017 1.125 6 0.0 0.0 7 0.03147623544224111 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 GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGT 7 0.17500000000000002 No Hit GTCTGGCATTCTTGTACTGCAAGTAGTATGCATGCTCCCAAACATCAATT 5 0.125 No Hit CTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCT 5 0.125 No Hit GCTCCTCATCACCCCGGATTGCTAGCTGCAGATGCCTTGGTGTTATACGT 5 0.125 No Hit GTGAAAGTATGTTAGAAATGGAGGGACGGGACCATATCTGAAAGCAAAGG 5 0.125 No Hit CTATCAACAAATTCGAGTAAGCCATCAGGGGGTCTCCGGTAAAAGAATCT 5 0.125 No Hit ATCATATTCAATTTCAAGCTCATCAAGAAATCTATGAGCTGGTTTACGCA 5 0.125 No Hit CTCGGAGCTATGGTGTTTATGTGGCCTGTCTATGATATTTTCCAGTACCG 5 0.125 No Hit GCCAACATGTGAAAGCCCCTCGTCACTTATGTTTAGGCAAATTCCTAATT 5 0.125 No Hit CGTTAAGAAAACTGATCCCTCCGCCGCTAAAGATGGCATCGGGATCTCTA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 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 0.05 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 0.075 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.42500000000000004 0.0 0.0 0.0 0.0 76-77 0.6125 0.0 0.0 0.0 0.0 78-79 0.775 0.0 0.0 0.0 0.0 80-81 0.8625 0.0 0.0 0.0 0.0 82-83 1.0875 0.0 0.0 0.0 0.0 84-85 1.4375 0.0 0.0 0.0 0.0 86-87 1.775 0.0 0.0 0.0 0.0 88-89 2.2375 0.0 0.0 0.0 0.0 90-91 2.725 0.0 0.0 0.0 0.0 92-93 3.3 0.0 0.0 0.0 0.0 94-95 3.6625 0.0 0.0 0.0 0.0 96-97 4.125 0.0 0.0 0.0 0.0 98-99 4.5875 0.0 0.0 0.0 0.0 100-101 5.15 0.0 0.0 0.0 0.0 102-103 5.75 0.0 0.0 0.0 0.0 104-105 6.425 0.0 0.0 0.0 0.0 106-107 7.2125 0.0 0.0 0.0 0.0 108-109 8.3875 0.0 0.0 0.0 0.0 110-111 9.1875 0.0 0.0 0.0 0.0 112-113 9.8625 0.0 0.0 0.0 0.0 114-115 10.85 0.0 0.0 0.0 0.0 116-117 11.7375 0.0 0.0 0.0 0.0 118-119 12.7 0.0 0.0 0.0 0.0 120-121 13.7375 0.0 0.0 0.0 0.0 122-123 15.3125 0.0 0.0 0.0 0.0 124-125 16.262500000000003 0.0 0.0 0.0 0.0 126-127 17.6375 0.0 0.0 0.0 0.0 128-129 18.9625 0.0 0.0 0.0 0.0 130-131 19.612499999999997 0.0 0.0 0.0 0.0 132-133 20.862499999999997 0.0 0.0 0.0 0.0 134-135 21.8625 0.0 0.0 0.0 0.0 136-137 23.075000000000003 0.0 0.0 0.0 0.0 138-139 23.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTTTA 10 0.006830828 145.0 5 ACACTCC 55 0.0025160722 15.818182 140-144 CAGTCAC 60 0.004491891 14.500001 135-139 >>END_MODULE SRR12670153 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670153_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3975 37.0 37.0 37.0 37.0 37.0 2 36.3625 37.0 37.0 37.0 37.0 37.0 3 36.3135 37.0 37.0 37.0 37.0 37.0 4 36.242 37.0 37.0 37.0 37.0 37.0 5 36.316 37.0 37.0 37.0 37.0 37.0 6 36.2245 37.0 37.0 37.0 37.0 37.0 7 36.2725 37.0 37.0 37.0 37.0 37.0 8 36.3395 37.0 37.0 37.0 37.0 37.0 9 36.321 37.0 37.0 37.0 37.0 37.0 10-14 36.3823 37.0 37.0 37.0 37.0 37.0 15-19 36.376999999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.28 37.0 37.0 37.0 37.0 37.0 25-29 36.3065 37.0 37.0 37.0 37.0 37.0 30-34 36.269 37.0 37.0 37.0 37.0 37.0 35-39 36.2278 37.0 37.0 37.0 37.0 37.0 40-44 36.188900000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.1981 37.0 37.0 37.0 37.0 37.0 50-54 36.129 37.0 37.0 37.0 37.0 37.0 55-59 36.158699999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.1374 37.0 37.0 37.0 37.0 37.0 65-69 36.0997 37.0 37.0 37.0 37.0 37.0 70-74 36.1107 37.0 37.0 37.0 37.0 37.0 75-79 36.0864 37.0 37.0 37.0 37.0 37.0 80-84 36.0341 37.0 37.0 37.0 37.0 37.0 85-89 36.0085 37.0 37.0 37.0 37.0 37.0 90-94 36.073600000000006 37.0 37.0 37.0 37.0 37.0 95-99 35.9508 37.0 37.0 37.0 37.0 37.0 100-104 35.858399999999996 37.0 37.0 37.0 37.0 37.0 105-109 35.880700000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.7541 37.0 37.0 37.0 37.0 37.0 115-119 35.837 37.0 37.0 37.0 37.0 37.0 120-124 35.6609 37.0 37.0 37.0 37.0 37.0 125-129 35.547399999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.4077 37.0 37.0 37.0 34.6 37.0 135-139 35.2485 37.0 37.0 37.0 34.6 37.0 140-144 34.9785 37.0 37.0 37.0 25.0 37.0 145-149 34.692499999999995 37.0 37.0 37.0 25.0 37.0 150-151 34.51175 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 2.0 15 1.0 16 1.0 17 0.0 18 3.0 19 3.0 20 1.0 21 4.0 22 2.0 23 6.0 24 3.0 25 5.0 26 6.0 27 8.0 28 10.0 29 15.0 30 47.0 31 36.0 32 61.0 33 85.0 34 204.0 35 545.0 36 2656.0 37 294.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.0 25.85 9.025 27.125 2 27.025 28.225 28.875 15.875 3 20.200000000000003 28.349999999999998 31.2 20.25 4 23.9 34.949999999999996 22.225 18.925 5 23.974999999999998 37.025000000000006 21.7 17.299999999999997 6 20.424999999999997 39.825 21.075 18.675 7 19.3 23.35 36.775000000000006 20.575 8 20.95 26.0 27.6 25.45 9 22.5 25.025 28.15 24.325 10-14 22.71 29.685 25.525 22.08 15-19 22.585 27.525 28.37 21.52 20-24 23.22 29.205 26.35 21.224999999999998 25-29 22.720000000000002 28.455000000000002 27.685 21.14 30-34 22.8 28.405 27.095000000000002 21.7 35-39 22.465 28.465 27.295 21.775 40-44 22.665 27.834999999999997 28.349999999999998 21.15 45-49 21.83 28.310000000000002 27.900000000000002 21.959999999999997 50-54 22.915 28.449999999999996 27.62 21.015 55-59 22.869999999999997 27.765 27.05 22.314999999999998 60-64 22.85 28.110000000000003 27.465 21.575 65-69 22.935 27.779999999999998 27.534999999999997 21.75 70-74 23.32 27.6 27.73 21.349999999999998 75-79 23.585 28.09 26.46 21.865000000000002 80-84 24.104999999999997 28.32 25.97 21.605 85-89 23.919999999999998 28.205000000000002 26.865 21.01 90-94 23.849999999999998 28.455000000000002 26.255 21.44 95-99 24.169999999999998 28.449999999999996 26.009999999999998 21.37 100-104 24.425 29.025000000000002 26.61 19.939999999999998 105-109 24.625 28.465 25.91 21.0 110-114 25.490000000000002 28.095 25.97 20.445 115-119 25.955000000000002 28.634999999999998 25.69 19.72 120-124 25.624999999999996 28.17 26.21 19.994999999999997 125-129 26.075 28.29 24.785 20.849999999999998 130-134 28.09 27.35 25.069999999999997 19.49 135-139 29.220000000000002 26.615 25.0 19.165 140-144 28.925 27.095000000000002 24.79 19.189999999999998 145-149 30.5 26.555 24.025 18.92 150-151 30.9375 25.974999999999998 24.1875 18.9 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 1.0 6 0.5 7 0.5 8 1.0 9 1.0 10 1.0 11 1.5 12 1.5 13 0.5 14 0.5 15 0.5 16 0.0 17 0.5 18 0.5 19 1.0 20 1.0 21 1.0 22 1.5 23 0.5 24 0.5 25 1.5 26 2.0 27 4.0 28 4.5 29 5.5 30 9.5 31 13.0 32 20.5 33 25.0 34 37.0 35 59.5 36 86.5 37 117.5 38 144.0 39 153.0 40 177.0 41 213.5 42 237.0 43 258.0 44 259.0 45 269.5 46 270.0 47 255.0 48 245.5 49 217.0 50 173.5 51 133.0 52 119.0 53 105.0 54 87.5 55 70.0 56 49.5 57 43.5 58 33.0 59 24.5 60 20.0 61 13.0 62 8.5 63 4.5 64 1.5 65 0.5 66 1.0 67 1.5 68 2.0 69 1.5 70 1.0 71 0.5 72 0.0 73 0.5 74 0.5 75 0.5 76 0.5 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 0.5 98 1.0 99 0.5 100 0.5 >>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 79.07499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 80.87258931394246 63.949999999999996 2 13.97407524502055 22.1 3 3.477711033828643 8.25 4 1.327853303825482 4.2 5 0.284539993676889 1.125 6 0.03161555485298767 0.15 7 0.0 0.0 8 0.0 0.0 9 0.03161555485298767 0.22499999999999998 >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 9 0.22499999999999998 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 6 0.15 No Hit CTGAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCA 5 0.125 No Hit TCTGGCTGGTCAATTTAATCCAGCTAATGGTATTGGTCTGGCAAACACTA 5 0.125 No Hit GCTCTACAGGGCTCTGGATGGGTGTGGTTTGGCCTGGACAAAGAATCAAA 5 0.125 No Hit CAAAAACAACTCGTGTATCATATGGAGGAAACTCATAACACCGCAACCGC 5 0.125 No Hit AGGAGAAAAAACTCTTTCTCCACTCCTGCCTCCTTGCCTTCCCGTTCCCA 5 0.125 No Hit AACTACTACACGTTTCACTCCCATAAAATCCACCTCTCCTGCCATTTCCA 5 0.125 No Hit TAACAGATAATGAGATTGATGATGAAGGTCTGAAGTCCATTTCTAGATGT 5 0.125 No Hit TTTATTCCGATTAACTAACCGATCAATCTGACGGACTCCGCTTCTCCTCC 5 0.125 No Hit CAAGAAAAAACCCACCTCTCGTTCCTCTCGTGCTGGTCTTCAGTTTCCTG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 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 0.05 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 0.075 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.225 0.0 0.0 0.0 0.0 72-73 0.35 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.5875 0.0 0.0 0.0 0.0 78-79 0.75 0.0 0.0 0.0 0.0 80-81 0.8375 0.0 0.0 0.0 0.0 82-83 1.0625 0.0 0.0 0.0 0.0 84-85 1.4375 0.0 0.0 0.0 0.0 86-87 1.8 0.0 0.0 0.0 0.0 88-89 2.2375 0.0 0.0 0.0 0.0 90-91 2.75 0.0 0.0 0.0 0.0 92-93 3.325 0.0 0.0 0.0 0.0 94-95 3.7 0.0 0.0 0.0 0.0 96-97 4.175000000000001 0.0 0.0 0.0 0.0 98-99 4.637499999999999 0.0 0.0 0.0 0.0 100-101 5.2 0.0 0.0 0.0 0.0 102-103 5.762499999999999 0.0 0.0 0.0 0.0 104-105 6.4875 0.0 0.0 0.0 0.0 106-107 7.3 0.0 0.0 0.0 0.0 108-109 8.4875 0.0 0.0 0.0 0.0 110-111 9.287500000000001 0.0 0.0 0.0 0.0 112-113 9.9625 0.0 0.0 0.0 0.0 114-115 10.962499999999999 0.0 0.0 0.0 0.0 116-117 11.8625 0.0 0.0 0.0 0.0 118-119 12.825 0.0 0.0 0.0 0.0 120-121 13.8625 0.0 0.0 0.0 0.0 122-123 15.4375 0.0 0.0 0.0 0.0 124-125 16.387500000000003 0.0 0.0 0.0 0.0 126-127 17.7875 0.0 0.0 0.0 0.0 128-129 19.1125 0.0 0.0 0.0 0.0 130-131 19.7875 0.0 0.0 0.0 0.0 132-133 21.0375 0.0 0.0 0.0 0.0 134-135 22.0125 0.0 0.0 0.0 0.0 136-137 23.15 0.0 0.0 0.0 0.0 138-139 23.9625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTAGACT 10 0.006830828 145.0 9 >>END_MODULE Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324114 spots for SRR12670153.sra Written 324114 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra Read 324102 spots for SRR12670153.sra Written 324102 spots for SRR12670153.sra SRR ids: ['SRR12670153.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_i3_r11vm SRR12670153.sra spots: 6482052 blocks: [[1, 324102], [324103, 648204], [648205, 972306], [972307, 1296408], [1296409, 1620510], [1620511, 1944612], [1944613, 2268714], [2268715, 2592816], [2592817, 2916918], [2916919, 3241020], [3241021, 3565122], [3565123, 3889224], [3889225, 4213326], [4213327, 4537428], [4537429, 4861530], [4861531, 5185632], [5185633, 5509734], [5509735, 5833836], [5833837, 6157938], [6157939, 6482052]] SRR12670153 file size 2188055 SRR12670153 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 SRR12670153 SRR12670153_1.fastq SRR12670153_2.fastq Input file: SRR12670153_1.fastq Paired file: SRR12670153_2.fastq trimmed: SRR12670153-trimmed-pair1.fastq, SRR12670153-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 05:41:14 2025 >> started Tue Feb 11 05:47:36 2025 >> done (381.545s) 6482052 read pairs processed; of these: 24 ( 0.00%) short read pairs filtered out after trimming by size control 3130 ( 0.05%) empty read pairs filtered out after trimming by size control 6478898 (99.95%) read pairs available; of these: 1786640 (27.58%) trimmed read pairs available after processing 4692258 (72.42%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 2 0.00% 20 4 0.00% 21 8 0.00% 22 13 0.00% 23 18 0.00% 24 14 0.00% 25 17 0.00% 26 26 0.00% 27 23 0.00% 28 27 0.00% 29 32 0.00% 30 46 0.00% 31 37 0.00% 32 40 0.00% 33 40 0.00% 34 44 0.00% 35 62 0.00% 36 51 0.00% 37 60 0.00% 38 54 0.00% 39 69 0.00% 40 102 0.00% 41 119 0.00% 42 104 0.00% 43 97 0.00% 44 96 0.00% 45 94 0.00% 46 149 0.00% 47 132 0.00% 48 187 0.00% 49 200 0.00% 50 260 0.00% 51 323 0.00% 52 312 0.00% 53 333 0.01% 54 343 0.01% 55 372 0.01% 56 432 0.01% 57 455 0.01% 58 551 0.01% 59 634 0.01% 60 854 0.01% 61 855 0.01% 62 1053 0.02% 63 1128 0.02% 64 1192 0.02% 65 1289 0.02% 66 1349 0.02% 67 1542 0.02% 68 1813 0.03% 69 2063 0.03% 70 2363 0.04% 71 2515 0.04% 72 3217 0.05% 73 3555 0.05% 74 3829 0.06% 75 4116 0.06% 76 4464 0.07% 77 4714 0.07% 78 5127 0.08% 79 5803 0.09% 80 6302 0.10% 81 7028 0.11% 82 7871 0.12% 83 8634 0.13% 84 9430 0.15% 85 10114 0.16% 86 10757 0.17% 87 11342 0.18% 88 11569 0.18% 89 12176 0.19% 90 13382 0.21% 91 13792 0.21% 92 14842 0.23% 93 16293 0.25% 94 17361 0.27% 95 18477 0.29% 96 18758 0.29% 97 19523 0.30% 98 19333 0.30% 99 20149 0.31% 100 21063 0.33% 101 21163 0.33% 102 22014 0.34% 103 22977 0.35% 104 24099 0.37% 105 24540 0.38% 106 25130 0.39% 107 25065 0.39% 108 25320 0.39% 109 25558 0.39% 110 25555 0.39% 111 25484 0.39% 112 26407 0.41% 113 26806 0.41% 114 28001 0.43% 115 28658 0.44% 116 28616 0.44% 117 29070 0.45% 118 29366 0.45% 119 28436 0.44% 120 28972 0.45% 121 29059 0.45% 122 28910 0.45% 123 29695 0.46% 124 30313 0.47% 125 30513 0.47% 126 31018 0.48% 127 30931 0.48% 128 30696 0.47% 129 30450 0.47% 130 30501 0.47% 131 29800 0.46% 132 30058 0.46% 133 30667 0.47% 134 30716 0.47% 135 30976 0.48% 136 31208 0.48% 137 30828 0.48% 138 31137 0.48% 139 31095 0.48% 140 30660 0.47% 141 30518 0.47% 142 30654 0.47% 143 30705 0.47% 144 31158 0.48% 145 31177 0.48% 146 31078 0.48% 147 30966 0.48% 148 31114 0.48% 149 31068 0.48% 150 30710 0.47% 151 4692258 72.42% 6478898 reads passed initial QC criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=33 prefix-density=0.53 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTAG criterion=fanout-score sequence-density=0.03 sequence-density-rank=35 fanout-score=108.57 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=12.9 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTC criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=35 prefix-density=0.61 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=49.86 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=6.8 sequence=AAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12670153 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 05:59:51 Started mapping on | Feb 11 06:00:24 Finished on | Feb 11 06:21:47 Mapping speed, Million of reads per hour | 18.18 Number of input reads | 6478898 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 6049227 Uniquely mapped reads % | 93.37% Average mapped length | 283.18 Number of splices: Total | 5954836 Number of splices: Annotated (sjdb) | 5830653 Number of splices: GT/AG | 5830458 Number of splices: GC/AG | 100219 Number of splices: AT/AC | 3368 Number of splices: Non-canonical | 20791 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.91 Insertion rate per base | 0.02% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 152466 % of reads mapped to multiple loci | 2.35% Number of reads mapped to too many loci | 50106 % of reads mapped to too many loci | 0.77% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.30% % of reads unmapped: other | 0.20% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 277205 277205 277205 N_multimapping 152466 152466 152466 N_noFeature 194267 5951906 233969 N_ambiguous 94174 439 36298 UnstrandedReadsAssigned:5760786 PositiveStrandReadsAssigned:96882 NegativeStrandReadsAssigned:5778960 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=134 echo kmer=129 SRR12670153 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: SRR12670153-trimmed-pair1.fastq SRR12670153-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,478,898 reads, 5,806,868 reads pseudoaligned [quant] estimated average fragment length: 208.577 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,006 rounds 52401 SRR12670153.ke.tsv 34699 SRR12670153.se.tsv 87100 total ==> SRR12670153.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1810.42 217 18.9784 Potri.005G024800.1.v4.1 1035 827.423 86 16.457 Potri.004G059700.1.v4.1 961 753.448 1 0.210149 Potri.007G009000.2.v4.1 1416 1208.42 0 0 Potri.003G141000.2.v4.1 2943 2735.42 368 21.3012 Potri.016G087400.1.v4.1 270 109.22 229 331.982 Potri.015G069301.1.v4.1 564 364.251 0 0 Potri.010G195200.1.v4.1 1773 1565.42 16 1.61834 Potri.012G127500.1.v4.1 977 769.423 39 8.02565 ==> SRR12670153.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 98 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 76 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 4 SRR12670153 completed mapping pipeline successfully