Starting /dee2/code/volunteer_pipeline.sh SRR12670165 current disk space = 3055556149248 free memory = 1580288224 SRR12670165 SRAfilesize 86291f5e900e2189b977b932bc00b107 SRR12670165.sra SRR12670165.sra file validated SRR12670165 is paired end SRR12670165 is conventional basespace SRR12670165 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670165_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 36.273 37.0 37.0 37.0 37.0 37.0 2 36.23825 37.0 37.0 37.0 37.0 37.0 3 36.4575 37.0 37.0 37.0 37.0 37.0 4 36.518 37.0 37.0 37.0 37.0 37.0 5 36.56 37.0 37.0 37.0 37.0 37.0 6 36.5855 37.0 37.0 37.0 37.0 37.0 7 36.4705 37.0 37.0 37.0 37.0 37.0 8 36.562 37.0 37.0 37.0 37.0 37.0 9 36.5145 37.0 37.0 37.0 37.0 37.0 10-14 36.554899999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.508300000000006 37.0 37.0 37.0 37.0 37.0 20-24 36.4685 37.0 37.0 37.0 37.0 37.0 25-29 36.4708 37.0 37.0 37.0 37.0 37.0 30-34 36.4385 37.0 37.0 37.0 37.0 37.0 35-39 36.4022 37.0 37.0 37.0 37.0 37.0 40-44 36.373599999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.312200000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.2625 37.0 37.0 37.0 37.0 37.0 55-59 36.250600000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.211999999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.1788 37.0 37.0 37.0 37.0 37.0 70-74 36.1579 37.0 37.0 37.0 37.0 37.0 75-79 36.196600000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.2207 37.0 37.0 37.0 37.0 37.0 85-89 36.118 37.0 37.0 37.0 37.0 37.0 90-94 36.1195 37.0 37.0 37.0 37.0 37.0 95-99 36.0903 37.0 37.0 37.0 37.0 37.0 100-104 36.092699999999994 37.0 37.0 37.0 37.0 37.0 105-109 36.0314 37.0 37.0 37.0 37.0 37.0 110-114 35.8267 37.0 37.0 37.0 37.0 37.0 115-119 35.769999999999996 37.0 37.0 37.0 37.0 37.0 120-124 35.46810000000001 37.0 37.0 37.0 37.0 37.0 125-129 35.167899999999996 37.0 37.0 37.0 32.2 37.0 130-134 34.8361 37.0 37.0 37.0 25.0 37.0 135-139 34.4539 37.0 37.0 37.0 25.0 37.0 140-144 34.010799999999996 37.0 37.0 37.0 25.0 37.0 145-149 33.724000000000004 37.0 37.0 37.0 22.2 37.0 150-151 33.3305 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 1.0 23 1.0 24 5.0 25 1.0 26 4.0 27 7.0 28 13.0 29 21.0 30 29.0 31 40.0 32 96.0 33 240.0 34 260.0 35 495.0 36 2528.0 37 258.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.074999999999996 10.9 11.175 39.85 2 21.051314142678347 14.44305381727159 33.26658322903629 31.23904881101377 3 19.025 20.7 27.825 32.45 4 24.25 27.35 23.175 25.224999999999998 5 23.1 33.725 23.05 20.125 6 21.224999999999998 33.95 23.825 21.0 7 15.45 23.35 43.0 18.2 8 19.0 23.95 31.775 25.275 9 18.775 24.224999999999998 33.1 23.9 10-14 21.21 28.660000000000004 26.950000000000003 23.18 15-19 20.630000000000003 27.725 27.83 23.815 20-24 20.855 27.705000000000002 27.334999999999997 24.104999999999997 25-29 20.71 28.310000000000002 27.33 23.65 30-34 20.49 28.335 27.765 23.41 35-39 20.43 28.060000000000002 27.48 24.03 40-44 20.87 28.17 27.065 23.895 45-49 20.64 28.84 27.42 23.1 50-54 20.415 28.34 27.525 23.72 55-59 20.72 28.144999999999996 27.55 23.585 60-64 20.745 28.525 27.395000000000003 23.335 65-69 20.560000000000002 28.315 27.46 23.665 70-74 21.015 28.299999999999997 27.395000000000003 23.29 75-79 21.245 28.050000000000004 27.365000000000002 23.34 80-84 21.505 28.694999999999997 26.69 23.11 85-89 21.65 28.68 26.200000000000003 23.47 90-94 21.745 28.994999999999997 25.900000000000002 23.36 95-99 21.78 28.52 26.179999999999996 23.52 100-104 21.9 29.125 25.245 23.73 105-109 21.975 28.799999999999997 25.2 24.025 110-114 22.115000000000002 28.134999999999998 25.779999999999998 23.97 115-119 22.18 28.405 25.679999999999996 23.735 120-124 22.15 28.060000000000002 26.22 23.57 125-129 23.02 27.265 25.665 24.05 130-134 22.865 27.134999999999998 26.055 23.945 135-139 23.630000000000003 26.02 26.155 24.195 140-144 24.22 25.679999999999996 26.150000000000002 23.95 145-149 24.975 25.8 25.655 23.57 150-151 24.4875 25.662499999999998 25.7 24.15 >>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 0.5 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 0.5 20 1.5 21 1.5 22 2.0 23 3.0 24 2.0 25 2.0 26 4.0 27 4.5 28 9.5 29 15.0 30 15.5 31 18.5 32 22.5 33 33.5 34 46.0 35 70.0 36 86.5 37 86.0 38 116.0 39 145.5 40 159.5 41 195.5 42 235.0 43 241.0 44 244.0 45 245.5 46 247.0 47 260.5 48 249.0 49 222.5 50 200.5 51 178.0 52 142.5 53 108.0 54 96.5 55 72.5 56 51.0 57 47.0 58 34.0 59 26.5 60 19.0 61 12.0 62 6.5 63 1.5 64 3.0 65 5.0 66 3.5 67 2.5 68 2.0 69 1.0 70 0.5 71 0.5 72 0.5 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 0.125 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 82.85 #Duplication Level Percentage of deduplicated Percentage of total 1 84.30899215449608 69.85 2 12.190706095353047 20.200000000000003 3 2.3838261919130956 5.925 4 0.8449004224502112 2.8000000000000003 5 0.18105009052504525 0.75 6 0.06035003017501509 0.3 7 0.030175015087507546 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 AACCCATAAACCACAGCTAAAGCCCCTGGTATCATTCTTGCTGCCACGGC 7 0.17500000000000002 No Hit GTCCGACTCCGGTCACGAGACCTTGCACAAAGTAACCCAAGATGGCCAAC 6 0.15 No Hit AAATATCTATCAGAACCCAACAATTGTAGATGATCTGATGCAACATTGAT 6 0.15 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTGACAGGATCTCGTTT 5 0.125 TruSeq Adapter, Index 19 (97% over 37bp) GCCTGGTTATGCAAGCCCAATCACATACCGCTCAGGGAACTGGAAACCAG 5 0.125 No Hit CCAGATACCAGTAGCGCTTGCCCGCTTAAGCTCTGCGGCACACATCACCA 5 0.125 No Hit GCCAGAGAGCTCAAATTTGCCAAGCAAATTGTTGTCCCTTGTCCGTGTCC 5 0.125 No Hit CCATCATCCTCAAAAACATAACATCATCCAAACACCACAAACATACCCAG 5 0.125 No Hit CCTCCCTTTGTCTTCGCATTCGAGCTGCCCATGACATGCTCCCACCAGCA 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 0.0 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 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.2 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.3125 0.0 0.0 0.0 0.0 60-61 0.5 0.0 0.0 0.0 0.0 62-63 0.6875 0.0 0.0 0.0 0.0 64-65 0.8500000000000001 0.0 0.0 0.0 0.0 66-67 1.0375 0.0 0.0 0.0 0.0 68-69 1.15 0.0 0.0 0.0 0.0 70-71 1.4874999999999998 0.0 0.0 0.0 0.0 72-73 2.0375 0.0 0.0 0.0 0.0 74-75 2.5375 0.0 0.0 0.0 0.0 76-77 3.0374999999999996 0.0 0.0 0.0 0.0 78-79 3.7375 0.0 0.0 0.0 0.0 80-81 4.425000000000001 0.0 0.0 0.0 0.0 82-83 5.324999999999999 0.0 0.0 0.0 0.0 84-85 6.275 0.0 0.0 0.0 0.0 86-87 6.95 0.0 0.0 0.0 0.0 88-89 7.7125 0.0 0.0 0.0 0.0 90-91 8.7125 0.0 0.0 0.0 0.0 92-93 9.8125 0.0 0.0 0.0 0.0 94-95 11.05 0.0 0.0 0.0 0.0 96-97 12.125 0.0 0.0 0.0 0.0 98-99 13.0375 0.0 0.0 0.0 0.0 100-101 14.1375 0.0 0.0 0.0 0.0 102-103 15.412500000000001 0.0 0.0 0.0 0.0 104-105 16.4625 0.0 0.0 0.0 0.0 106-107 17.575000000000003 0.0 0.0 0.0 0.0 108-109 18.8125 0.0 0.0 0.0 0.0 110-111 19.625 0.0 0.0 0.0 0.0 112-113 20.575 0.0 0.0 0.0 0.0 114-115 21.5375 0.0 0.0 0.0 0.0 116-117 22.725 0.0 0.0 0.0 0.0 118-119 23.700000000000003 0.0 0.0 0.0 0.0 120-121 24.9125 0.0 0.0 0.0 0.0 122-123 25.7375 0.0 0.0 0.0 0.0 124-125 26.7625 0.0 0.0 0.0 0.0 126-127 27.6875 0.0 0.0 0.0 0.0 128-129 28.8125 0.0 0.0 0.0 0.0 130-131 29.7625 0.0 0.0 0.0 0.0 132-133 30.6875 0.0 0.0 0.0 0.0 134-135 31.65 0.0 0.0 0.0 0.0 136-137 32.375 0.0 0.0 0.0 0.0 138-139 33.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670165 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670165_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1135 37.0 37.0 37.0 37.0 37.0 2 36.182 37.0 37.0 37.0 37.0 37.0 3 36.162 37.0 37.0 37.0 37.0 37.0 4 36.095 37.0 37.0 37.0 37.0 37.0 5 36.229 37.0 37.0 37.0 37.0 37.0 6 36.1685 37.0 37.0 37.0 37.0 37.0 7 36.111 37.0 37.0 37.0 37.0 37.0 8 36.1675 37.0 37.0 37.0 37.0 37.0 9 36.1115 37.0 37.0 37.0 37.0 37.0 10-14 36.153200000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.173500000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.1072 37.0 37.0 37.0 37.0 37.0 25-29 36.037400000000005 37.0 37.0 37.0 37.0 37.0 30-34 35.980000000000004 37.0 37.0 37.0 37.0 37.0 35-39 35.9306 37.0 37.0 37.0 37.0 37.0 40-44 36.0057 37.0 37.0 37.0 37.0 37.0 45-49 35.9459 37.0 37.0 37.0 37.0 37.0 50-54 35.8866 37.0 37.0 37.0 37.0 37.0 55-59 35.8717 37.0 37.0 37.0 37.0 37.0 60-64 35.8629 37.0 37.0 37.0 37.0 37.0 65-69 35.7978 37.0 37.0 37.0 37.0 37.0 70-74 35.7605 37.0 37.0 37.0 37.0 37.0 75-79 35.795399999999994 37.0 37.0 37.0 37.0 37.0 80-84 35.769 37.0 37.0 37.0 37.0 37.0 85-89 35.684999999999995 37.0 37.0 37.0 37.0 37.0 90-94 35.7031 37.0 37.0 37.0 37.0 37.0 95-99 35.6191 37.0 37.0 37.0 37.0 37.0 100-104 35.4756 37.0 37.0 37.0 37.0 37.0 105-109 35.33 37.0 37.0 37.0 32.2 37.0 110-114 35.2548 37.0 37.0 37.0 29.8 37.0 115-119 35.1564 37.0 37.0 37.0 27.4 37.0 120-124 34.759100000000004 37.0 37.0 37.0 25.0 37.0 125-129 34.5015 37.0 37.0 37.0 25.0 37.0 130-134 34.185500000000005 37.0 37.0 37.0 25.0 37.0 135-139 33.9491 37.0 37.0 37.0 25.0 37.0 140-144 33.506299999999996 37.0 37.0 37.0 13.8 37.0 145-149 33.0747 37.0 37.0 37.0 11.0 37.0 150-151 32.672250000000005 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 6.0 14 4.0 15 5.0 16 1.0 17 0.0 18 5.0 19 0.0 20 0.0 21 7.0 22 6.0 23 5.0 24 8.0 25 10.0 26 7.0 27 17.0 28 15.0 29 28.0 30 40.0 31 82.0 32 140.0 33 196.0 34 350.0 35 671.0 36 2231.0 37 165.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.625 20.175 14.475 25.724999999999998 2 28.875 22.8 30.65 17.675 3 22.275 27.575 29.075 21.075 4 23.825 36.15 20.9 19.125 5 23.9 37.275000000000006 21.6 17.224999999999998 6 23.225 36.95 21.7 18.125 7 19.475 20.775 38.625 21.125 8 22.35 24.4 26.974999999999998 26.275 9 22.125 26.35 29.025000000000002 22.5 10-14 23.35 28.775000000000002 26.435 21.44 15-19 23.085 28.849999999999998 26.75 21.315 20-24 23.22 27.785 27.700000000000003 21.295 25-29 23.880000000000003 28.535 26.735 20.849999999999998 30-34 22.71 28.360000000000003 27.93 21.0 35-39 22.835 28.4 27.36 21.404999999999998 40-44 23.335 27.505000000000003 27.79 21.37 45-49 23.35 27.675 27.889999999999997 21.085 50-54 23.27 28.15 27.36 21.22 55-59 22.895 27.26 28.155 21.69 60-64 23.515 27.0 27.79 21.695 65-69 23.605 26.965 27.985 21.445 70-74 24.23 27.98 26.805 20.985 75-79 24.485 27.855 26.43 21.23 80-84 23.755000000000003 28.595 26.39 21.26 85-89 25.130000000000003 27.755000000000003 26.155 20.96 90-94 25.759999999999998 27.975 26.325 19.939999999999998 95-99 25.240000000000002 27.800000000000004 26.3 20.66 100-104 27.55 27.675 25.685000000000002 19.09 105-109 27.0 27.139999999999997 26.105 19.755 110-114 27.72 27.075 26.400000000000002 18.805 115-119 28.525 27.26 26.115 18.099999999999998 120-124 28.705000000000002 27.400000000000002 25.805 18.09 125-129 29.84 26.950000000000003 25.55 17.66 130-134 30.835 26.605 25.430000000000003 17.130000000000003 135-139 31.900000000000002 25.474999999999998 25.805 16.82 140-144 32.815 25.145 24.955 17.085 145-149 33.945 24.610000000000003 24.755 16.689999999999998 150-151 34.9375 24.3875 24.349999999999998 16.325 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 1.0 4 1.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 1.0 11 1.0 12 0.0 13 0.5 14 0.5 15 0.5 16 0.5 17 0.0 18 0.5 19 1.5 20 1.0 21 0.5 22 1.5 23 3.0 24 5.5 25 5.0 26 3.5 27 7.5 28 9.0 29 8.5 30 12.5 31 19.0 32 23.5 33 28.0 34 40.0 35 58.5 36 73.5 37 82.0 38 104.5 39 139.5 40 164.5 41 212.5 42 263.5 43 257.0 44 258.0 45 277.0 46 270.5 47 242.0 48 214.0 49 218.5 50 198.5 51 156.5 52 131.5 53 95.5 54 78.0 55 72.5 56 50.5 57 42.5 58 40.5 59 30.5 60 21.0 61 14.5 62 10.5 63 6.5 64 4.0 65 3.0 66 2.0 67 1.5 68 2.0 69 1.0 70 0.0 71 0.5 72 1.0 73 1.0 74 3.0 75 2.5 76 0.0 77 1.0 78 1.0 79 0.0 80 0.0 81 0.0 82 0.0 83 1.0 84 1.0 85 0.0 86 0.0 87 0.0 88 1.0 89 1.5 90 0.5 91 0.5 92 0.5 93 0.5 94 1.0 95 1.0 96 0.5 97 1.0 98 1.0 99 1.0 100 2.5 >>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 82.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 84.3155031731641 69.75 2 12.027802961619825 19.900000000000002 3 2.5687518887881535 6.375 4 0.8159564823209429 2.7 5 0.1511030522816561 0.625 6 0.060441220912662436 0.3 7 0.060441220912662436 0.35000000000000003 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 GGACTGGGCAAAACCAGGTTCCATGGGCAAGCAGTATTTCCTGGGATTCG 7 0.17500000000000002 No Hit CATATCAGACCTTGGACAGATTGCACGTGCTGTGTATGATGTTGAGGAGG 7 0.17500000000000002 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 6 0.15 No Hit GGTTCTTGCCTTTTCCATATGTGGACAGTTCTCCTCATCCATCGAGATCT 6 0.15 No Hit TCCTGGTGTTAAAGGAAGCCACAAGAAGTGAAGTTTATTACAAGAAATAA 5 0.125 No Hit CTGTCTTCGAGATTTTCTGTTCCCTAAAACACCCACAAGTGTTACTGGTT 5 0.125 No Hit TGTAGCGATGGGCCCAAGTGGCCGGACCATTACCAAGGAAGCTCGGATGC 5 0.125 No Hit GAGAACTGAGTGGAAGAATCGCTGGCAGTCTCAGCTATCAGAGTTGAAGA 5 0.125 No Hit CTTACTCTGACAACCAGCCAGGTGTGCTCATCCAAGTTTATGAGGGTGAG 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 0.0 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 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.2 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.3125 0.0 0.0 0.0 0.0 60-61 0.5 0.0 0.0 0.0 0.0 62-63 0.6875 0.0 0.0 0.0 0.0 64-65 0.8500000000000001 0.0 0.0 0.0 0.0 66-67 1.0375 0.0 0.0 0.0 0.0 68-69 1.15 0.0 0.0 0.0 0.0 70-71 1.4874999999999998 0.0 0.0 0.0 0.0 72-73 2.025 0.0 0.0 0.0 0.0 74-75 2.5 0.0 0.0 0.0 0.0 76-77 2.9875 0.0 0.0 0.0 0.0 78-79 3.675 0.0 0.0 0.0 0.0 80-81 4.375 0.0 0.0 0.0 0.0 82-83 5.275 0.0 0.0 0.0 0.0 84-85 6.225 0.0 0.0 0.0 0.0 86-87 6.9 0.0 0.0 0.0 0.0 88-89 7.65 0.0 0.0 0.0 0.0 90-91 8.6625 0.0 0.0 0.0 0.0 92-93 9.8 0.0 0.0 0.0 0.0 94-95 11.0625 0.0 0.0 0.0 0.0 96-97 12.1875 0.0 0.0 0.0 0.0 98-99 13.1125 0.0 0.0 0.0 0.0 100-101 14.212499999999999 0.0 0.0 0.0 0.0 102-103 15.5125 0.0 0.0 0.0 0.0 104-105 16.575000000000003 0.0 0.0 0.0 0.0 106-107 17.700000000000003 0.0 0.0 0.0 0.0 108-109 18.924999999999997 0.0 0.0 0.0 0.0 110-111 19.725 0.0 0.0 0.0 0.0 112-113 20.612499999999997 0.0 0.0 0.0 0.0 114-115 21.65 0.0 0.0 0.0 0.0 116-117 22.9 0.0 0.0 0.0 0.0 118-119 23.875 0.0 0.0 0.0 0.0 120-121 25.0875 0.0 0.0 0.0 0.0 122-123 25.9375 0.0 0.0 0.0 0.0 124-125 27.0375 0.0 0.0 0.0 0.0 126-127 28.0375 0.0 0.0 0.0 0.0 128-129 29.15 0.0 0.0 0.0 0.0 130-131 30.125 0.0 0.0 0.0 0.0 132-133 31.0625 0.0 0.0 0.0 0.0 134-135 32.05 0.0 0.0 0.0 0.0 136-137 32.775000000000006 0.0 0.0 0.0 0.0 138-139 33.7 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGTCTG 10 0.006830828 145.0 9 >>END_MODULE Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598568 spots for SRR12670165.sra Written 598568 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra Read 598554 spots for SRR12670165.sra Written 598554 spots for SRR12670165.sra SRR ids: ['SRR12670165.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3wbcd5zv SRR12670165.sra spots: 11971094 blocks: [[1, 598554], [598555, 1197108], [1197109, 1795662], [1795663, 2394216], [2394217, 2992770], [2992771, 3591324], [3591325, 4189878], [4189879, 4788432], [4788433, 5386986], [5386987, 5985540], [5985541, 6584094], [6584095, 7182648], [7182649, 7781202], [7781203, 8379756], [8379757, 8978310], [8978311, 9576864], [9576865, 10175418], [10175419, 10773972], [10773973, 11372526], [11372527, 11971094]] SRR12670165 file size 4046601 SRR12670165 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 SRR12670165 SRR12670165_1.fastq SRR12670165_2.fastq Input file: SRR12670165_1.fastq Paired file: SRR12670165_2.fastq trimmed: SRR12670165-trimmed-pair1.fastq, SRR12670165-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 08:56:29 2025 >> started Tue Feb 11 08:56:42 2025 >> done (13.111s) 11971094 read pairs processed; of these: 129 ( 0.00%) short read pairs filtered out after trimming by size control 23843 ( 0.20%) empty read pairs filtered out after trimming by size control 11947122 (99.80%) read pairs available; of these: 4273812 (35.77%) trimmed read pairs available after processing 7673310 (64.23%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 7 0.00% 20 7 0.00% 21 10 0.00% 22 15 0.00% 23 25 0.00% 24 18 0.00% 25 37 0.00% 26 50 0.00% 27 53 0.00% 28 59 0.00% 29 81 0.00% 30 136 0.00% 31 144 0.00% 32 154 0.00% 33 194 0.00% 34 205 0.00% 35 293 0.00% 36 317 0.00% 37 391 0.00% 38 506 0.00% 39 617 0.01% 40 802 0.01% 41 871 0.01% 42 851 0.01% 43 935 0.01% 44 913 0.01% 45 1084 0.01% 46 1213 0.01% 47 1487 0.01% 48 1868 0.02% 49 2319 0.02% 50 2655 0.02% 51 2941 0.02% 52 3177 0.03% 53 3435 0.03% 54 3442 0.03% 55 3697 0.03% 56 4069 0.03% 57 4837 0.04% 58 5593 0.05% 59 6411 0.05% 60 7589 0.06% 61 8860 0.07% 62 9648 0.08% 63 10318 0.09% 64 10558 0.09% 65 11139 0.09% 66 11792 0.10% 67 13079 0.11% 68 14424 0.12% 69 16197 0.14% 70 18452 0.15% 71 20443 0.17% 72 23446 0.20% 73 25069 0.21% 74 26527 0.22% 75 28145 0.24% 76 28474 0.24% 77 29397 0.25% 78 31666 0.27% 79 34298 0.29% 80 36873 0.31% 81 40614 0.34% 82 44147 0.37% 83 46509 0.39% 84 48765 0.41% 85 50097 0.42% 86 49842 0.42% 87 50363 0.42% 88 51995 0.44% 89 53579 0.45% 90 55616 0.47% 91 58531 0.49% 92 59661 0.50% 93 63146 0.53% 94 64384 0.54% 95 64400 0.54% 96 63577 0.53% 97 62606 0.52% 98 62254 0.52% 99 61879 0.52% 100 63192 0.53% 101 63372 0.53% 102 64937 0.54% 103 66128 0.55% 104 66232 0.55% 105 65942 0.55% 106 64964 0.54% 107 62828 0.53% 108 62106 0.52% 109 60344 0.51% 110 60229 0.50% 111 60456 0.51% 112 60840 0.51% 113 61013 0.51% 114 60626 0.51% 115 61198 0.51% 116 59870 0.50% 117 59001 0.49% 118 57615 0.48% 119 55664 0.47% 120 54807 0.46% 121 56018 0.47% 122 54864 0.46% 123 55056 0.46% 124 56220 0.47% 125 54376 0.46% 126 54196 0.45% 127 52941 0.44% 128 51852 0.43% 129 50722 0.42% 130 50405 0.42% 131 49247 0.41% 132 49202 0.41% 133 49785 0.42% 134 48867 0.41% 135 48988 0.41% 136 48015 0.40% 137 48119 0.40% 138 47049 0.39% 139 46584 0.39% 140 45104 0.38% 141 45567 0.38% 142 44757 0.37% 143 44440 0.37% 144 44797 0.37% 145 44405 0.37% 146 44378 0.37% 147 43978 0.37% 148 43860 0.37% 149 42404 0.35% 150 41967 0.35% 151 7673310 64.23% 11947122 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=3.07 fanout-score-rank=24 prefix-density=0.42 prefix-fanout=2.5 sequence=GAGGAAGCCATCTCTTACA criterion=fanout-score sequence-density=0.03 sequence-density-rank=42 fanout-score=122.09 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=14.0 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=3.10 fanout-score-rank=17 prefix-density=0.55 prefix-fanout=2.6 sequence=ACAAGCCAACATGGTGGCACCATTCAATGGTCTCAAGTCTGCCGCAGCTTTCCCAGTCAGTACCAGAAAGGCTAATGACATTACTTCCATTGCAAGCAATGGTGGACGAGTTCAATGCATGCAGGTGTGGCCACCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCACAGAGGAGGAATTGGCCAAGGAAATTGATTACCTTCTTCGCTCGAAGTGGGTTCCTTGCTTGGAATTCGAGTTGGAGAAAGGTTGGGTCTACCGTGAGCACCACAGCTCACCAGGGTACTATGATGGACGCTACTGGACTATGTGGAAGCTACCCATGTTTGGATGCACTGAGGCATCTCAAGTGTTGCTTGAGCTTGAGGAGGCAAAGAAAGCTTACCCTAACGCCTTTATCCGTATAATCGGATTCGACAACACGCGTCAAGTGCAGTGCATCAGCTTTATTGCCGCCAAGCC criterion=fanout-score sequence-density=0.12 sequence-density-rank=20 fanout-score=33.78 fanout-score-rank=1 prefix-density=0.34 prefix-fanout=12.0 sequence=AAAGAAAAGAAAA SRR12670165 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 08:57:23 Started mapping on | Feb 11 08:57:23 Finished on | Feb 11 08:58:36 Mapping speed, Million of reads per hour | 589.17 Number of input reads | 11947122 Average input read length | 272 UNIQUE READS: Uniquely mapped reads number | 10948289 Uniquely mapped reads % | 91.64% Average mapped length | 269.74 Number of splices: Total | 9713945 Number of splices: Annotated (sjdb) | 9499450 Number of splices: GT/AG | 9508524 Number of splices: GC/AG | 166563 Number of splices: AT/AC | 6173 Number of splices: Non-canonical | 32685 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 2.77 Insertion rate per base | 0.02% Insertion average length | 2.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 282425 % of reads mapped to multiple loci | 2.36% Number of reads mapped to too many loci | 62587 % of reads mapped to too many loci | 0.52% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.26% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 716408 716408 716408 N_multimapping 282425 282425 282425 N_noFeature 424434 10783483 506097 N_ambiguous 147839 582 64329 UnstrandedReadsAssigned:10376016 PositiveStrandReadsAssigned:164224 NegativeStrandReadsAssigned:10377863 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=113 echo kmer=109 SRR12670165 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: SRR12670165-trimmed-pair1.fastq SRR12670165-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,947,122 reads, 10,496,668 reads pseudoaligned [quant] estimated average fragment length: 193.843 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,033 rounds 52401 SRR12670165.ke.tsv 34699 SRR12670165.se.tsv 87100 total ==> SRR12670165.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1825.16 485 28.8278 Potri.005G024800.1.v4.1 1035 842.157 142 18.2921 Potri.004G059700.1.v4.1 961 768.271 10 1.41207 Potri.007G009000.2.v4.1 1416 1223.16 0 0 Potri.003G141000.2.v4.1 2943 2750.16 525 20.7096 Potri.016G087400.1.v4.1 270 128.429 404 341.261 Potri.015G069301.1.v4.1 564 381.223 0 0 Potri.010G195200.1.v4.1 1773 1580.16 41 2.81484 Potri.012G127500.1.v4.1 977 784.219 84 11.6201 ==> SRR12670165.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 150 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 185 Potri.001G212900.v4.1 5 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 2 SRR12670165 completed mapping pipeline successfully