Starting /dee2/code/volunteer_pipeline.sh SRR12671362 current disk space = 3053420060672 free memory = 1496639824 SRR12671362 SRAfilesize 1bd3da0578a2032d7612041344dfaf48 SRR12671362.sra SRR12671362.sra file validated SRR12671362 is paired end SRR12671362 is conventional basespace SRR12671362 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671362_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 36.5465 37.0 37.0 37.0 37.0 37.0 2 36.14625 37.0 37.0 37.0 37.0 37.0 3 36.492 37.0 37.0 37.0 37.0 37.0 4 36.4725 37.0 37.0 37.0 37.0 37.0 5 36.555 37.0 37.0 37.0 37.0 37.0 6 36.5885 37.0 37.0 37.0 37.0 37.0 7 36.453 37.0 37.0 37.0 37.0 37.0 8 36.526 37.0 37.0 37.0 37.0 37.0 9 36.5285 37.0 37.0 37.0 37.0 37.0 10-14 36.53680000000001 37.0 37.0 37.0 37.0 37.0 15-19 36.5264 37.0 37.0 37.0 37.0 37.0 20-24 36.5247 37.0 37.0 37.0 37.0 37.0 25-29 36.5115 37.0 37.0 37.0 37.0 37.0 30-34 36.426 37.0 37.0 37.0 37.0 37.0 35-39 36.40989999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.4015 37.0 37.0 37.0 37.0 37.0 45-49 36.3841 37.0 37.0 37.0 37.0 37.0 50-54 36.3728 37.0 37.0 37.0 37.0 37.0 55-59 36.3722 37.0 37.0 37.0 37.0 37.0 60-64 36.3027 37.0 37.0 37.0 37.0 37.0 65-69 36.306200000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.2758 37.0 37.0 37.0 37.0 37.0 75-79 36.2565 37.0 37.0 37.0 37.0 37.0 80-84 36.2341 37.0 37.0 37.0 37.0 37.0 85-89 36.224199999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.1813 37.0 37.0 37.0 37.0 37.0 95-99 36.161500000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.11659999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.163500000000006 37.0 37.0 37.0 37.0 37.0 110-114 36.1041 37.0 37.0 37.0 37.0 37.0 115-119 36.1008 37.0 37.0 37.0 37.0 37.0 120-124 36.0272 37.0 37.0 37.0 37.0 37.0 125-129 35.9738 37.0 37.0 37.0 37.0 37.0 130-134 35.9397 37.0 37.0 37.0 37.0 37.0 135-139 35.948899999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.8829 37.0 37.0 37.0 37.0 37.0 145-149 35.8448 37.0 37.0 37.0 37.0 37.0 150-151 35.76475 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 1.0 21 0.0 22 2.0 23 1.0 24 9.0 25 0.0 26 3.0 27 13.0 28 13.0 29 22.0 30 27.0 31 25.0 32 49.0 33 65.0 34 134.0 35 282.0 36 2920.0 37 433.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.875 10.85 5.825 32.45 2 19.06195134186105 12.590920491597693 39.60371206420868 28.74341610233258 3 17.125 17.75 29.849999999999998 35.275 4 23.3 25.124999999999996 24.325 27.250000000000004 5 22.975 33.324999999999996 23.025000000000002 20.674999999999997 6 18.075 34.875 25.324999999999996 21.725 7 14.099999999999998 25.974999999999998 43.175000000000004 16.75 8 16.0 25.025 33.275 25.7 9 17.575 22.55 35.3 24.575 10-14 20.715 29.53 27.36 22.395 15-19 20.3 27.800000000000004 28.000000000000004 23.9 20-24 20.125 28.21 27.644999999999996 24.02 25-29 20.52 28.405 27.565 23.51 30-34 20.3 27.944999999999997 27.889999999999997 23.865 35-39 20.66 27.985 27.205000000000002 24.15 40-44 20.215 28.63 27.200000000000003 23.955000000000002 45-49 20.775 27.939999999999998 27.474999999999998 23.810000000000002 50-54 20.69 28.15 27.474999999999998 23.685000000000002 55-59 19.965 28.189999999999998 28.060000000000002 23.785 60-64 20.435 28.26 27.16 24.145 65-69 19.68 28.395 27.900000000000002 24.025 70-74 19.994999999999997 28.205000000000002 28.58 23.22 75-79 20.435 27.63 27.43 24.505 80-84 20.175 27.675 27.76 24.39 85-89 20.064999999999998 28.754999999999995 27.425 23.755000000000003 90-94 20.45 28.65 27.145000000000003 23.755000000000003 95-99 20.68 28.139999999999997 27.02 24.16 100-104 20.424999999999997 27.98 27.935 23.66 105-109 21.135 27.41 27.689999999999998 23.765 110-114 21.075 28.17 27.279999999999998 23.474999999999998 115-119 20.965 27.82 27.529999999999998 23.685000000000002 120-124 20.535 27.955000000000002 26.755000000000003 24.755 125-129 21.08 28.415000000000003 26.595000000000002 23.91 130-134 21.05 27.894999999999996 27.47 23.585 135-139 21.32 28.16 26.974999999999998 23.544999999999998 140-144 21.115000000000002 27.785 27.169999999999998 23.93 145-149 21.07 27.93 27.01 23.990000000000002 150-151 20.45 27.875 27.075 24.6 >>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 0.5 6 0.5 7 0.0 8 0.0 9 0.5 10 0.5 11 0.5 12 0.5 13 1.0 14 1.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.5 20 0.5 21 3.0 22 4.0 23 3.0 24 2.5 25 3.5 26 5.5 27 6.5 28 10.5 29 15.0 30 20.0 31 24.5 32 26.0 33 33.0 34 49.5 35 64.0 36 87.5 37 119.0 38 146.0 39 150.5 40 153.0 41 191.0 42 220.0 43 238.5 44 241.0 45 242.5 46 282.5 47 267.5 48 229.0 49 211.5 50 166.0 51 151.5 52 138.5 53 109.0 54 88.0 55 64.0 56 54.0 57 43.5 58 30.5 59 29.0 60 24.5 61 13.5 62 6.5 63 4.5 64 4.5 65 2.0 66 1.5 67 3.0 68 4.0 69 2.0 70 1.0 71 1.0 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 0.325 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 84.375 #Duplication Level Percentage of deduplicated Percentage of total 1 85.27407407407406 71.95 2 11.762962962962963 19.85 3 2.3703703703703702 6.0 4 0.4148148148148148 1.4000000000000001 5 0.14814814814814814 0.625 6 0.0 0.0 7 0.02962962962962963 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 AAGAATTCCAATTGTCCGATGAACGTGAAAACTTCGGCACAGCCTATCAG 7 0.17500000000000002 No Hit ATCCTCTTCATCACTGCTATCATCATTCTCTGGTTTGGGTTTCCCATCTT 5 0.125 No Hit GTGGAGATAAGTCTCAGCCTTTTCTAATAGCTGGCCCATGCCTTTCTCTT 5 0.125 No Hit GTCCAGGGATTAGAAATGAGACACGCCAAGCAGTGGATAAAGGTAGGTCC 5 0.125 No Hit GTGAAAGAAAAGGAAGTCAAGAACGTAAAGGTGACACATTCTATTCTTTT 5 0.125 No Hit GCGCTTTCTCTTTCCCTCTTGTGGTCCCATTCACCGAGATTGAGACCAGC 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.037500000000000006 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.1875 0.0 0.0 0.0 0.0 88-89 0.2625 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 0.6125 0.0 0.0 0.0 0.0 96-97 0.6625000000000001 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.9625 0.0 0.0 0.0 0.0 102-103 1.125 0.0 0.0 0.0 0.0 104-105 1.3 0.0 0.0 0.0 0.0 106-107 1.6 0.0 0.0 0.0 0.0 108-109 1.8125 0.0 0.0 0.0 0.0 110-111 1.9 0.0 0.0 0.0 0.0 112-113 2.0375 0.0 0.0 0.0 0.0 114-115 2.2249999999999996 0.0 0.0 0.0 0.0 116-117 2.5125 0.0 0.0 0.0 0.0 118-119 2.85 0.0 0.0 0.0 0.0 120-121 3.075 0.0 0.0 0.0 0.0 122-123 3.3125 0.0 0.0 0.0 0.0 124-125 3.5625 0.0 0.0 0.0 0.0 126-127 3.7625 0.0 0.0 0.0 0.0 128-129 3.8625 0.0 0.0 0.0 0.0 130-131 4.050000000000001 0.0 0.0 0.0 0.0 132-133 4.2625 0.0 0.0 0.0 0.0 134-135 4.5125 0.0 0.0 0.0 0.0 136-137 4.9 0.0 0.0 0.0 0.0 138-139 5.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671362 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671362_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 35.9975 37.0 37.0 37.0 37.0 37.0 2 35.4975 37.0 37.0 37.0 37.0 37.0 3 35.6015 37.0 37.0 37.0 37.0 37.0 4 35.9035 37.0 37.0 37.0 37.0 37.0 5 35.9495 37.0 37.0 37.0 37.0 37.0 6 35.921 37.0 37.0 37.0 37.0 37.0 7 35.9275 37.0 37.0 37.0 37.0 37.0 8 35.9325 37.0 37.0 37.0 37.0 37.0 9 35.9245 37.0 37.0 37.0 37.0 37.0 10-14 35.9759 37.0 37.0 37.0 37.0 37.0 15-19 35.988 37.0 37.0 37.0 37.0 37.0 20-24 35.8926 37.0 37.0 37.0 37.0 37.0 25-29 35.8474 37.0 37.0 37.0 37.0 37.0 30-34 35.8428 37.0 37.0 37.0 37.0 37.0 35-39 35.854099999999995 37.0 37.0 37.0 37.0 37.0 40-44 35.8211 37.0 37.0 37.0 37.0 37.0 45-49 35.711 37.0 37.0 37.0 37.0 37.0 50-54 35.7119 37.0 37.0 37.0 37.0 37.0 55-59 35.6865 37.0 37.0 37.0 37.0 37.0 60-64 35.6934 37.0 37.0 37.0 37.0 37.0 65-69 35.6996 37.0 37.0 37.0 37.0 37.0 70-74 35.5683 37.0 37.0 37.0 37.0 37.0 75-79 35.6032 37.0 37.0 37.0 37.0 37.0 80-84 35.456 37.0 37.0 37.0 37.0 37.0 85-89 35.5908 37.0 37.0 37.0 37.0 37.0 90-94 35.520599999999995 37.0 37.0 37.0 37.0 37.0 95-99 35.488800000000005 37.0 37.0 37.0 37.0 37.0 100-104 35.446 37.0 37.0 37.0 37.0 37.0 105-109 35.3839 37.0 37.0 37.0 34.6 37.0 110-114 35.3017 37.0 37.0 37.0 32.2 37.0 115-119 35.4224 37.0 37.0 37.0 34.6 37.0 120-124 35.3488 37.0 37.0 37.0 37.0 37.0 125-129 35.2511 37.0 37.0 37.0 29.8 37.0 130-134 35.213499999999996 37.0 37.0 37.0 29.8 37.0 135-139 35.1291 37.0 37.0 37.0 25.0 37.0 140-144 35.1575 37.0 37.0 37.0 27.4 37.0 145-149 35.1921 37.0 37.0 37.0 29.8 37.0 150-151 34.851 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 3.0 13 2.0 14 4.0 15 4.0 16 3.0 17 1.0 18 1.0 19 2.0 20 5.0 21 0.0 22 8.0 23 7.0 24 9.0 25 14.0 26 17.0 27 13.0 28 14.0 29 29.0 30 37.0 31 59.0 32 74.0 33 125.0 34 271.0 35 686.0 36 2440.0 37 172.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.025 24.025 7.55 23.400000000000002 2 27.6 26.724999999999998 31.624999999999996 14.05 3 21.65 26.974999999999998 32.25 19.125 4 22.925 33.550000000000004 22.625 20.9 5 25.575 39.225 19.950000000000003 15.25 6 19.7 40.175 21.075 19.05 7 19.075 22.05 38.925 19.950000000000003 8 19.325 24.8 30.45 25.424999999999997 9 22.85 25.575 27.675 23.9 10-14 23.39 29.37 26.235000000000003 21.005 15-19 23.47 28.645 26.75 21.135 20-24 23.075000000000003 29.115000000000002 26.69 21.12 25-29 22.595000000000002 27.72 28.105000000000004 21.58 30-34 22.165000000000003 28.605000000000004 27.68 21.55 35-39 22.585 27.785 27.965 21.665 40-44 22.7 27.700000000000003 27.855 21.745 45-49 22.585 28.134999999999998 28.315 20.965 50-54 23.775 26.97 27.63 21.625 55-59 22.42 27.655 27.845 22.08 60-64 22.759999999999998 27.58 27.72 21.94 65-69 23.665 26.825 28.17 21.34 70-74 22.2 27.705000000000002 27.889999999999997 22.205 75-79 22.830000000000002 28.345 26.900000000000002 21.925 80-84 23.02 28.615000000000002 26.99 21.375 85-89 22.8 28.035 27.345000000000002 21.82 90-94 24.404999999999998 27.975 26.505000000000003 21.115000000000002 95-99 23.73 27.450000000000003 26.935 21.884999999999998 100-104 23.43 27.584999999999997 27.169999999999998 21.815 105-109 23.31 27.735 27.775 21.18 110-114 24.385 27.435 27.505000000000003 20.674999999999997 115-119 24.26 28.449999999999996 26.474999999999998 20.815 120-124 24.82 26.979999999999997 27.689999999999998 20.51 125-129 24.205 28.17 27.185 20.44 130-134 24.709999999999997 27.195000000000004 27.474999999999998 20.62 135-139 24.965 27.295 27.189999999999998 20.549999999999997 140-144 24.85 27.815 27.33 20.005 145-149 25.874999999999996 27.74 26.724999999999998 19.66 150-151 25.724999999999998 27.3625 26.7625 20.150000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 7 0.0 8 0.5 9 0.5 10 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.5 18 0.5 19 2.0 20 2.0 21 0.5 22 1.0 23 2.0 24 3.5 25 3.0 26 4.5 27 5.5 28 4.0 29 9.5 30 15.0 31 21.5 32 31.5 33 38.5 34 48.0 35 66.5 36 81.5 37 95.0 38 118.5 39 149.0 40 185.0 41 217.5 42 223.0 43 248.5 44 279.5 45 276.0 46 270.0 47 262.0 48 239.5 49 200.0 50 176.0 51 139.5 52 109.5 53 91.0 54 80.0 55 84.5 56 63.5 57 35.0 58 19.0 59 22.0 60 19.5 61 10.0 62 11.0 63 9.0 64 4.0 65 1.0 66 0.0 67 0.0 68 0.0 69 1.0 70 1.0 71 0.5 72 0.5 73 0.5 74 0.5 75 0.0 76 0.5 77 0.5 78 0.5 79 0.5 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 0.5 89 0.0 90 0.5 91 0.5 92 0.0 93 0.5 94 1.0 95 0.5 96 0.0 97 0.0 98 0.0 99 0.0 100 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 84.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 85.51540284360189 72.175 2 11.552132701421801 19.5 3 2.221563981042654 5.625 4 0.47393364928909953 1.6 5 0.1481042654028436 0.625 6 0.05924170616113744 0.3 7 0.02962085308056872 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 CTGGTATCATCTTTTCTGCAGTGTACAGCCAAATGGGGAACTTATTTGTG 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit CATTGAAAATGCAGGCAGCCATATTTCTTACACCATCAATTCTCCCTCTT 5 0.125 No Hit AATTATCTGCAAGCCTCTCTTGATTCTCGCTGCTGTTTCCTAGCTAATAG 5 0.125 No Hit CAGAGTTTATTTCTGATGGTGAAGAGGATCTCCCAGTCCCCGTTGATAAC 5 0.125 No Hit CAGCAAAAGATGAAATGCTGTCTGCCTCTGGCCTTATTAGTGGGCTAGCG 5 0.125 No Hit CTGAAACTGATATTGGCAACGCTGGCATCGCCTCCTTTGTCGGTTCCATA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 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 0.0 0.0 0.0 0.0 0.0 80-81 0.0125 0.0 0.0 0.0 0.0 82-83 0.0625 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.2375 0.0 0.0 0.0 0.0 90-91 0.4375 0.0 0.0 0.0 0.0 92-93 0.525 0.0 0.0 0.0 0.0 94-95 0.5625 0.0 0.0 0.0 0.0 96-97 0.6125 0.0 0.0 0.0 0.0 98-99 0.7125 0.0 0.0 0.0 0.0 100-101 0.9125 0.0 0.0 0.0 0.0 102-103 1.075 0.0 0.0 0.0 0.0 104-105 1.25 0.0 0.0 0.0 0.0 106-107 1.5499999999999998 0.0 0.0 0.0 0.0 108-109 1.7625 0.0 0.0 0.0 0.0 110-111 1.85 0.0 0.0 0.0 0.0 112-113 1.9874999999999998 0.0 0.0 0.0 0.0 114-115 2.1875 0.0 0.0 0.0 0.0 116-117 2.45 0.0 0.0 0.0 0.0 118-119 2.8 0.0 0.0 0.0 0.0 120-121 3.05 0.0 0.0 0.0 0.0 122-123 3.2875 0.0 0.0 0.0 0.0 124-125 3.55 0.0 0.0 0.0 0.0 126-127 3.7750000000000004 0.0 0.0 0.0 0.0 128-129 3.8875 0.0 0.0 0.0 0.0 130-131 4.074999999999999 0.0 0.0 0.0 0.0 132-133 4.2875 0.0 0.0 0.0 0.0 134-135 4.5375 0.0 0.0 0.0 0.0 136-137 4.9125 0.0 0.0 0.0 0.0 138-139 5.3125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231043 spots for SRR12671362.sra Written 1231043 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra Read 1231037 spots for SRR12671362.sra Written 1231037 spots for SRR12671362.sra SRR ids: ['SRR12671362.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9l1aogzc SRR12671362.sra spots: 24620746 blocks: [[1, 1231037], [1231038, 2462074], [2462075, 3693111], [3693112, 4924148], [4924149, 6155185], [6155186, 7386222], [7386223, 8617259], [8617260, 9848296], [9848297, 11079333], [11079334, 12310370], [12310371, 13541407], [13541408, 14772444], [14772445, 16003481], [16003482, 17234518], [17234519, 18465555], [18465556, 19696592], [19696593, 20927629], [20927630, 22158666], [22158667, 23389703], [23389704, 24620746]] SRR12671362 file size 8345506 SRR12671362 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 SRR12671362 SRR12671362_1.fastq SRR12671362_2.fastq Input file: SRR12671362_1.fastq Paired file: SRR12671362_2.fastq trimmed: SRR12671362-trimmed-pair1.fastq, SRR12671362-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 19:32:09 2025 >> started Tue Feb 11 19:32:35 2025 >> done (25.282s) 24620746 read pairs processed; of these: 170 ( 0.00%) short read pairs filtered out after trimming by size control 7764 ( 0.03%) empty read pairs filtered out after trimming by size control 24612812 (99.97%) read pairs available; of these: 1727549 ( 7.02%) trimmed read pairs available after processing 22885263 (92.98%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 22 0.00% 19 14 0.00% 20 23 0.00% 21 18 0.00% 22 26 0.00% 23 25 0.00% 24 30 0.00% 25 31 0.00% 26 34 0.00% 27 37 0.00% 28 40 0.00% 29 44 0.00% 30 33 0.00% 31 41 0.00% 32 44 0.00% 33 33 0.00% 34 45 0.00% 35 57 0.00% 36 39 0.00% 37 43 0.00% 38 64 0.00% 39 68 0.00% 40 57 0.00% 41 47 0.00% 42 67 0.00% 43 74 0.00% 44 70 0.00% 45 98 0.00% 46 83 0.00% 47 88 0.00% 48 121 0.00% 49 126 0.00% 50 132 0.00% 51 177 0.00% 52 186 0.00% 53 207 0.00% 54 217 0.00% 55 212 0.00% 56 224 0.00% 57 320 0.00% 58 328 0.00% 59 421 0.00% 60 447 0.00% 61 517 0.00% 62 586 0.00% 63 689 0.00% 64 784 0.00% 65 783 0.00% 66 857 0.00% 67 1069 0.00% 68 1147 0.00% 69 1380 0.01% 70 1502 0.01% 71 1726 0.01% 72 1926 0.01% 73 2364 0.01% 74 2545 0.01% 75 2729 0.01% 76 3020 0.01% 77 3221 0.01% 78 3442 0.01% 79 3955 0.02% 80 4188 0.02% 81 4624 0.02% 82 5048 0.02% 83 5491 0.02% 84 5931 0.02% 85 6517 0.03% 86 6982 0.03% 87 7264 0.03% 88 7658 0.03% 89 8163 0.03% 90 8745 0.04% 91 9108 0.04% 92 9379 0.04% 93 10304 0.04% 94 10752 0.04% 95 11418 0.05% 96 11625 0.05% 97 12402 0.05% 98 12486 0.05% 99 13305 0.05% 100 13914 0.06% 101 14191 0.06% 102 15041 0.06% 103 15269 0.06% 104 16077 0.07% 105 16803 0.07% 106 17075 0.07% 107 17987 0.07% 108 18181 0.07% 109 18905 0.08% 110 19011 0.08% 111 19737 0.08% 112 20603 0.08% 113 20875 0.08% 114 21611 0.09% 115 22497 0.09% 116 23095 0.09% 117 24097 0.10% 118 24690 0.10% 119 24758 0.10% 120 25946 0.11% 121 26309 0.11% 122 26578 0.11% 123 27885 0.11% 124 28733 0.12% 125 28963 0.12% 126 30034 0.12% 127 30761 0.12% 128 31490 0.13% 129 32555 0.13% 130 32846 0.13% 131 32893 0.13% 132 33814 0.14% 133 35123 0.14% 134 35085 0.14% 135 36031 0.15% 136 36721 0.15% 137 37782 0.15% 138 38470 0.16% 139 39646 0.16% 140 40320 0.16% 141 40494 0.16% 142 41378 0.17% 143 42330 0.17% 144 43018 0.17% 145 44094 0.18% 146 45167 0.18% 147 45273 0.18% 148 47619 0.19% 149 46936 0.19% 150 48693 0.20% 151 22885263 92.98% 24612812 reads passed initial QC criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=26 prefix-density=0.58 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=466.43 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=14.9 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=sequence-density sequence-density=0.76 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=28 prefix-density=0.77 prefix-fanout=2.1 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.18 sequence-density-rank=23 fanout-score=23.56 fanout-score-rank=1 prefix-density=0.85 prefix-fanout=5.1 sequence=AATGGCAGCCTCAGTTATGGCTTCACTGAACCTGAAACCATCTCCATTCACGGTTGAGAAGTCTTCAGTGAGAGGCCTCCCAACTCTTTCAAGGAGATCTTTCAAGATTGAAGCCAGTGGTGTCAAGAAGATCAAGACCGATACGCCTTATGGAACTGGTGGTGGCATGAACCT SRR12671362 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 19:33:22 Started mapping on | Feb 11 19:33:23 Finished on | Feb 11 19:36:06 Mapping speed, Million of reads per hour | 543.60 Number of input reads | 24612812 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 22604913 Uniquely mapped reads % | 91.84% Average mapped length | 296.54 Number of splices: Total | 21341665 Number of splices: Annotated (sjdb) | 20911006 Number of splices: GT/AG | 20913906 Number of splices: GC/AG | 348265 Number of splices: AT/AC | 13598 Number of splices: Non-canonical | 65896 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.03% Deletion average length | 2.88 Insertion rate per base | 0.02% Insertion average length | 2.23 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 599852 % of reads mapped to multiple loci | 2.44% Number of reads mapped to too many loci | 61994 % of reads mapped to too many loci | 0.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.28% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1408047 1408047 1408047 N_multimapping 599852 599852 599852 N_noFeature 782420 22231071 916962 N_ambiguous 383506 1760 143017 UnstrandedReadsAssigned:21438987 PositiveStrandReadsAssigned:372082 NegativeStrandReadsAssigned:21544934 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671362 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: SRR12671362-trimmed-pair1.fastq SRR12671362-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,612,812 reads, 21,645,191 reads pseudoaligned [quant] estimated average fragment length: 285.341 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,080 rounds 52401 SRR12671362.ke.tsv 34699 SRR12671362.se.tsv 87100 total ==> SRR12671362.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1733.66 590 14.3616 Potri.005G024800.1.v4.1 1035 750.659 173 9.72562 Potri.004G059700.1.v4.1 961 676.998 16 0.997347 Potri.007G009000.2.v4.1 1416 1131.66 0 0 Potri.003G141000.2.v4.1 2943 2658.66 1052 16.6981 Potri.016G087400.1.v4.1 270 79.1357 933 497.535 Potri.015G069301.1.v4.1 564 300.822 0 0 Potri.010G195200.1.v4.1 1773 1488.66 29 0.822085 Potri.012G127500.1.v4.1 977 692.847 409 24.9115 ==> SRR12671362.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 290 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 203 Potri.001G212900.v4.1 75 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 3 SRR12671362 completed mapping pipeline successfully