Starting /dee2/code/volunteer_pipeline.sh SRR12671363 current disk space = 3053379923968 free memory = 1473914532 SRR12671363 SRAfilesize ac9d956398f3135486574ecf631e3b87 SRR12671363.sra SRR12671363.sra file validated SRR12671363 is paired end SRR12671363 is conventional basespace SRR12671363 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671363_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 36.555 37.0 37.0 37.0 37.0 37.0 2 36.4415 37.0 37.0 37.0 37.0 37.0 3 36.579 37.0 37.0 37.0 37.0 37.0 4 36.5825 37.0 37.0 37.0 37.0 37.0 5 36.58 37.0 37.0 37.0 37.0 37.0 6 36.5025 37.0 37.0 37.0 37.0 37.0 7 36.553 37.0 37.0 37.0 37.0 37.0 8 36.5625 37.0 37.0 37.0 37.0 37.0 9 36.5685 37.0 37.0 37.0 37.0 37.0 10-14 36.589999999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.59159999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.5492 37.0 37.0 37.0 37.0 37.0 25-29 36.5212 37.0 37.0 37.0 37.0 37.0 30-34 36.5418 37.0 37.0 37.0 37.0 37.0 35-39 36.4722 37.0 37.0 37.0 37.0 37.0 40-44 36.4851 37.0 37.0 37.0 37.0 37.0 45-49 36.4353 37.0 37.0 37.0 37.0 37.0 50-54 36.4271 37.0 37.0 37.0 37.0 37.0 55-59 36.40089999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.4185 37.0 37.0 37.0 37.0 37.0 65-69 36.3585 37.0 37.0 37.0 37.0 37.0 70-74 36.3467 37.0 37.0 37.0 37.0 37.0 75-79 36.3663 37.0 37.0 37.0 37.0 37.0 80-84 36.365 37.0 37.0 37.0 37.0 37.0 85-89 36.2616 37.0 37.0 37.0 37.0 37.0 90-94 36.2856 37.0 37.0 37.0 37.0 37.0 95-99 36.2487 37.0 37.0 37.0 37.0 37.0 100-104 36.2716 37.0 37.0 37.0 37.0 37.0 105-109 36.2164 37.0 37.0 37.0 37.0 37.0 110-114 36.1212 37.0 37.0 37.0 37.0 37.0 115-119 36.2048 37.0 37.0 37.0 37.0 37.0 120-124 36.1326 37.0 37.0 37.0 37.0 37.0 125-129 36.101 37.0 37.0 37.0 37.0 37.0 130-134 36.0392 37.0 37.0 37.0 37.0 37.0 135-139 35.9996 37.0 37.0 37.0 37.0 37.0 140-144 35.9446 37.0 37.0 37.0 37.0 37.0 145-149 35.990899999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.82925 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 0.0 21 1.0 22 0.0 23 2.0 24 3.0 25 1.0 26 6.0 27 1.0 28 11.0 29 14.0 30 24.0 31 25.0 32 47.0 33 64.0 34 131.0 35 244.0 36 2959.0 37 466.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.925000000000004 10.85 5.55 41.675000000000004 2 17.351026539809713 11.141712568853281 42.038057085628445 29.46920380570856 3 17.275 16.8 29.549999999999997 36.375 4 23.1 23.825 24.625 28.449999999999996 5 23.799999999999997 31.225 25.5 19.475 6 18.15 33.300000000000004 25.174999999999997 23.375 7 13.925 25.25 43.325 17.5 8 14.825 24.4 35.75 25.025 9 15.675 21.525 36.675000000000004 26.125 10-14 19.509999999999998 30.294999999999998 27.884999999999998 22.31 15-19 19.945 27.045 28.804999999999996 24.205 20-24 19.48 28.115000000000002 28.07 24.335 25-29 19.805 28.125 27.689999999999998 24.38 30-34 19.705000000000002 29.115000000000002 27.515 23.665 35-39 19.775000000000002 27.944999999999997 28.285 23.995 40-44 20.200000000000003 28.255000000000003 28.125 23.419999999999998 45-49 19.725 28.189999999999998 28.175 23.91 50-54 19.765 29.049999999999997 28.34 22.845 55-59 19.82 28.720000000000002 27.98 23.48 60-64 20.155 28.470000000000002 28.299999999999997 23.075000000000003 65-69 20.75 28.16 27.779999999999998 23.31 70-74 20.61 28.884999999999998 27.195000000000004 23.31 75-79 20.515 28.865000000000002 27.195000000000004 23.425 80-84 19.7 29.285 27.375 23.64 85-89 20.485 28.705000000000002 27.395000000000003 23.415 90-94 20.22 28.93 27.465 23.385 95-99 20.32 28.23 27.625 23.825 100-104 20.895 29.060000000000002 26.924999999999997 23.119999999999997 105-109 20.244999999999997 28.970000000000002 27.66 23.125 110-114 20.080000000000002 28.494999999999997 27.67 23.755000000000003 115-119 20.805 28.515 27.46 23.22 120-124 20.424999999999997 28.945 27.084999999999997 23.544999999999998 125-129 20.84 28.449999999999996 26.705000000000002 24.005000000000003 130-134 20.595 29.395 26.75 23.26 135-139 20.31 28.74 27.025 23.925 140-144 20.895 28.535 26.779999999999998 23.79 145-149 20.44 28.18 26.979999999999997 24.4 150-151 20.1125 28.1125 27.800000000000004 23.974999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 2.0 1 2.0 2 1.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 1.5 20 2.0 21 1.5 22 2.5 23 2.5 24 2.5 25 4.5 26 5.0 27 6.5 28 9.5 29 12.5 30 24.5 31 38.5 32 37.5 33 41.5 34 55.0 35 73.5 36 86.5 37 95.5 38 118.0 39 150.0 40 201.0 41 230.5 42 235.5 43 243.5 44 261.0 45 273.0 46 264.5 47 264.0 48 236.0 49 197.5 50 166.5 51 139.5 52 122.0 53 95.0 54 73.0 55 56.5 56 43.5 57 34.0 58 25.5 59 15.5 60 13.5 61 9.5 62 4.5 63 6.5 64 3.5 65 0.5 66 1.0 67 1.0 68 1.0 69 1.5 70 1.0 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 0.0 2 0.15 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 82.175 #Duplication Level Percentage of deduplicated Percentage of total 1 83.32826285366596 68.475 2 12.92972315181016 21.25 3 2.829327654396106 6.9750000000000005 4 0.6693033160937024 2.1999999999999997 5 0.18253726802555523 0.75 6 0.0304228780042592 0.15 7 0.0 0.0 8 0.0304228780042592 0.2 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 AGGCTAACCAATAACTGCAACGAATCCTCTCAAGGAAACATACAACCATA 8 0.2 No Hit TTCTGCTTTCAGGCACCCAAGAGGCACGGTAATCAGCACAGCATCTCCCA 6 0.15 No Hit CGCTGGTAAAATGCCGGTTTCCTGCAGAGTGAGTTGCAGGAGTGGCTTGA 5 0.125 No Hit CCGAAATCTATATCATCAATCCCAAGCCCTCCAGCAAGATACATGGAAGG 5 0.125 No Hit CTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCG 5 0.125 No Hit ACGCATGCCGGCGGTGGTGTTGATGTAGTTATTGTTGCCAGGGTCAGCAG 5 0.125 No Hit CTCTCCTTCAGTGAAGGATGCAGCTCCATACATGGTCAAGCAAATGCTTA 5 0.125 No Hit CCTTGCATTCATTGTTTCTCTGGATAACTAGGATTTCATCCCGAATACGT 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 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.037500000000000006 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 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 0.1 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.1875 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.325 0.0 0.0 0.0 0.0 84-85 0.375 0.0 0.0 0.0 0.0 86-87 0.4375 0.0 0.0 0.0 0.0 88-89 0.55 0.0 0.0 0.0 0.0 90-91 0.675 0.0 0.0 0.0 0.0 92-93 0.7625 0.0 0.0 0.0 0.0 94-95 1.0375 0.0 0.0 0.0 0.0 96-97 1.15 0.0 0.0 0.0 0.0 98-99 1.25 0.0 0.0 0.0 0.0 100-101 1.5375 0.0 0.0 0.0 0.0 102-103 1.725 0.0 0.0 0.0 0.0 104-105 1.8875 0.0 0.0 0.0 0.0 106-107 2.075 0.0 0.0 0.0 0.0 108-109 2.2125 0.0 0.0 0.0 0.0 110-111 2.525 0.0 0.0 0.0 0.0 112-113 2.7 0.0 0.0 0.0 0.0 114-115 3.2875 0.0 0.0 0.0 0.0 116-117 3.6875 0.0 0.0 0.0 0.0 118-119 4.025 0.0 0.0 0.0 0.0 120-121 4.3 0.0 0.0 0.0 0.0 122-123 4.65 0.0 0.0 0.0 0.0 124-125 5.0375 0.0 0.0 0.0 0.0 126-127 5.525 0.0 0.0 0.0 0.0 128-129 5.925 0.0 0.0 0.0 0.0 130-131 6.4625 0.0 0.0 0.0 0.0 132-133 7.175 0.0 0.0 0.0 0.0 134-135 7.5 0.0 0.0 0.0 0.0 136-137 8.0125 0.0 0.0 0.0 0.0 138-139 8.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671363 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671363_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 36.2775 37.0 37.0 37.0 37.0 37.0 2 35.866 37.0 37.0 37.0 37.0 37.0 3 36.1925 37.0 37.0 37.0 37.0 37.0 4 36.19 37.0 37.0 37.0 37.0 37.0 5 36.244 37.0 37.0 37.0 37.0 37.0 6 36.1615 37.0 37.0 37.0 37.0 37.0 7 36.0055 37.0 37.0 37.0 37.0 37.0 8 36.266 37.0 37.0 37.0 37.0 37.0 9 36.288 37.0 37.0 37.0 37.0 37.0 10-14 36.236900000000006 37.0 37.0 37.0 37.0 37.0 15-19 36.2607 37.0 37.0 37.0 37.0 37.0 20-24 36.2085 37.0 37.0 37.0 37.0 37.0 25-29 36.2078 37.0 37.0 37.0 37.0 37.0 30-34 36.087599999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.0689 37.0 37.0 37.0 37.0 37.0 40-44 36.0872 37.0 37.0 37.0 37.0 37.0 45-49 36.047999999999995 37.0 37.0 37.0 37.0 37.0 50-54 35.997 37.0 37.0 37.0 37.0 37.0 55-59 36.0281 37.0 37.0 37.0 37.0 37.0 60-64 35.9572 37.0 37.0 37.0 37.0 37.0 65-69 36.000800000000005 37.0 37.0 37.0 37.0 37.0 70-74 35.9348 37.0 37.0 37.0 37.0 37.0 75-79 35.9012 37.0 37.0 37.0 37.0 37.0 80-84 35.8418 37.0 37.0 37.0 37.0 37.0 85-89 35.8858 37.0 37.0 37.0 37.0 37.0 90-94 35.7598 37.0 37.0 37.0 37.0 37.0 95-99 35.7817 37.0 37.0 37.0 37.0 37.0 100-104 35.739200000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.71900000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.6289 37.0 37.0 37.0 37.0 37.0 115-119 35.715 37.0 37.0 37.0 37.0 37.0 120-124 35.67569999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.5834 37.0 37.0 37.0 37.0 37.0 130-134 35.5578 37.0 37.0 37.0 37.0 37.0 135-139 35.3671 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 35.3167 37.0 37.0 37.0 32.2 37.0 150-151 35.1335 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 2.0 15 2.0 16 2.0 17 1.0 18 1.0 19 0.0 20 1.0 21 3.0 22 3.0 23 3.0 24 3.0 25 8.0 26 12.0 27 8.0 28 10.0 29 31.0 30 23.0 31 53.0 32 64.0 33 115.0 34 239.0 35 552.0 36 2599.0 37 263.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.875 24.125 7.9 27.1 2 23.849999999999998 26.200000000000003 35.225 14.725 3 19.875 26.1 34.025 20.0 4 23.375 34.475 24.2 17.95 5 24.375 38.1 21.05 16.475 6 18.475 40.125 23.1 18.3 7 19.3 22.35 39.275 19.075 8 17.299999999999997 26.075 31.175000000000004 25.45 9 20.125 23.7 31.474999999999998 24.7 10-14 22.68 29.354999999999997 27.22 20.745 15-19 23.369999999999997 27.96 27.715 20.955 20-24 22.634999999999998 29.07 27.700000000000003 20.595 25-29 22.68 28.04 28.16 21.12 30-34 21.825 28.83 28.265 21.08 35-39 21.97 28.610000000000003 28.355000000000004 21.065 40-44 22.075 28.59 27.915 21.42 45-49 22.884999999999998 27.255000000000003 28.22 21.64 50-54 22.755 28.549999999999997 27.860000000000003 20.835 55-59 23.285 27.71 28.410000000000004 20.595 60-64 22.74 27.589999999999996 28.475 21.195 65-69 23.044999999999998 27.83 28.244999999999997 20.880000000000003 70-74 22.61 28.605000000000004 27.62 21.165 75-79 23.185 27.224999999999998 28.360000000000003 21.23 80-84 23.585 28.095 27.405 20.915 85-89 23.65 28.355000000000004 26.87 21.125 90-94 23.66 27.894999999999996 27.345000000000002 21.099999999999998 95-99 23.285 28.144999999999996 27.665 20.905 100-104 23.385 27.925 27.529999999999998 21.16 105-109 23.105 27.755000000000003 28.09 21.05 110-114 23.810000000000002 27.944999999999997 27.82 20.424999999999997 115-119 23.985 28.134999999999998 27.034999999999997 20.845 120-124 23.715 28.565 27.54 20.18 125-129 24.37 27.700000000000003 27.32 20.61 130-134 24.685000000000002 27.715 27.755000000000003 19.845 135-139 25.669999999999998 27.705000000000002 26.834999999999997 19.79 140-144 24.415 28.155 27.445000000000004 19.985 145-149 25.595119023804763 27.090418083616726 27.060412082416484 20.254050810162035 150-151 25.0625 28.1875 26.8375 19.9125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 1.0 23 3.0 24 2.5 25 4.0 26 7.0 27 6.5 28 8.5 29 11.0 30 18.5 31 31.5 32 41.5 33 48.0 34 57.0 35 71.0 36 89.0 37 111.0 38 133.5 39 178.5 40 223.5 41 233.5 42 243.5 43 279.5 44 288.0 45 265.5 46 251.5 47 228.0 48 209.0 49 176.0 50 139.0 51 128.5 52 115.0 53 93.0 54 66.0 55 49.5 56 45.5 57 32.0 58 24.0 59 21.0 60 17.0 61 13.5 62 7.5 63 6.5 64 4.0 65 2.0 66 1.0 67 0.5 68 1.5 69 1.0 70 0.0 71 0.0 72 0.5 73 0.5 74 1.0 75 1.0 76 0.5 77 1.0 78 0.5 79 0.5 80 0.5 81 0.5 82 1.0 83 0.5 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 0.5 >>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 0.02 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.525 #Duplication Level Percentage of deduplicated Percentage of total 1 83.82308391396546 69.175 2 12.602241744925779 20.8 3 2.5446834292638596 6.3 4 0.7573462587094819 2.5 5 0.18176310209027569 0.75 6 0.060587700696758555 0.3 7 0.030293850348379277 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 AGGCTCAGAGGGACTTGTTTGGGGCTCATACTTATGAGAGGACCGATCGT 7 0.17500000000000002 No Hit CTCATTGTATGATTAAAGGGGGTTACAGTAATGTTGTCGAGTCTCTTGGG 6 0.15 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit CAGACTCGCAAGCTTGACCCGCATATCGAAGAACAATTTGGTAGTGGTCG 5 0.125 No Hit CAGAGAGGAGAGGAGAGGAGAGGAGAGGAGAAACGACAAAAAGAATCCAT 5 0.125 No Hit AGAACAGAAGAGGAATTGATGAGAACTATTACTATTGGAGAAAACATAGA 5 0.125 No Hit GGCTTGTCATCCCCAGAGGCATTTCTGGAGCTCCATTTAGAGTTTCGCCC 5 0.125 No Hit AGGAGATTCAAGAAGTGAGGAGCTTGTAACTGTATCTCTACTCCTTCCGG 5 0.125 No Hit GCTAAATTTTCTTACCAGGTGCAATCTTTTGAAATAGAGATTGAAGAAGA 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 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.037500000000000006 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 0.0 0.0 0.0 0.0 52-53 0.1 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 0.1 0.0 0.0 0.0 0.0 64-65 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.1375 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.1875 0.0 0.0 0.0 0.0 74-75 0.25 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.2875 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.325 0.0 0.0 0.0 0.0 84-85 0.375 0.0 0.0 0.0 0.0 86-87 0.4375 0.0 0.0 0.0 0.0 88-89 0.55 0.0 0.0 0.0 0.0 90-91 0.675 0.0 0.0 0.0 0.0 92-93 0.7625 0.0 0.0 0.0 0.0 94-95 1.0375 0.0 0.0 0.0 0.0 96-97 1.15 0.0 0.0 0.0 0.0 98-99 1.25 0.0 0.0 0.0 0.0 100-101 1.5375 0.0 0.0 0.0 0.0 102-103 1.725 0.0 0.0 0.0 0.0 104-105 1.8875 0.0 0.0 0.0 0.0 106-107 2.075 0.0 0.0 0.0 0.0 108-109 2.2125 0.0 0.0 0.0 0.0 110-111 2.5 0.0 0.0 0.0 0.0 112-113 2.675 0.0 0.0 0.0 0.0 114-115 3.2625 0.0 0.0 0.0 0.0 116-117 3.6625 0.0 0.0 0.0 0.0 118-119 4.0 0.0 0.0 0.0 0.0 120-121 4.275 0.0 0.0 0.0 0.0 122-123 4.65 0.0 0.0 0.0 0.0 124-125 5.0375 0.0 0.0 0.0 0.0 126-127 5.525 0.0 0.0 0.0 0.0 128-129 5.925 0.0 0.0 0.0 0.0 130-131 6.4625 0.0 0.0 0.0 0.0 132-133 7.175 0.0 0.0 0.0 0.0 134-135 7.5 0.0 0.0 0.0 0.0 136-137 8.0125 0.0 0.0 0.0 0.0 138-139 8.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTGCTA 10 0.006830828 145.0 9 >>END_MODULE Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125711 spots for SRR12671363.sra Written 1125711 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra Read 1125699 spots for SRR12671363.sra Written 1125699 spots for SRR12671363.sra SRR ids: ['SRR12671363.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mv6qnbw0 SRR12671363.sra spots: 22513992 blocks: [[1, 1125699], [1125700, 2251398], [2251399, 3377097], [3377098, 4502796], [4502797, 5628495], [5628496, 6754194], [6754195, 7879893], [7879894, 9005592], [9005593, 10131291], [10131292, 11256990], [11256991, 12382689], [12382690, 13508388], [13508389, 14634087], [14634088, 15759786], [15759787, 16885485], [16885486, 18011184], [18011185, 19136883], [19136884, 20262582], [20262583, 21388281], [21388282, 22513992]] SRR12671363 file size 7629539 SRR12671363 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 SRR12671363 SRR12671363_1.fastq SRR12671363_2.fastq Input file: SRR12671363_1.fastq Paired file: SRR12671363_2.fastq trimmed: SRR12671363-trimmed-pair1.fastq, SRR12671363-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 19:33:35 2025 >> started Tue Feb 11 19:34:00 2025 >> done (25.396s) 22513992 read pairs processed; of these: 86 ( 0.00%) short read pairs filtered out after trimming by size control 2238 ( 0.01%) empty read pairs filtered out after trimming by size control 22511668 (99.99%) read pairs available; of these: 2268734 (10.08%) trimmed read pairs available after processing 20242934 (89.92%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 6 0.00% 20 10 0.00% 21 11 0.00% 22 10 0.00% 23 10 0.00% 24 18 0.00% 25 18 0.00% 26 20 0.00% 27 16 0.00% 28 27 0.00% 29 28 0.00% 30 31 0.00% 31 24 0.00% 32 28 0.00% 33 48 0.00% 34 38 0.00% 35 31 0.00% 36 30 0.00% 37 58 0.00% 38 59 0.00% 39 49 0.00% 40 54 0.00% 41 58 0.00% 42 55 0.00% 43 75 0.00% 44 80 0.00% 45 86 0.00% 46 89 0.00% 47 99 0.00% 48 108 0.00% 49 114 0.00% 50 173 0.00% 51 172 0.00% 52 168 0.00% 53 224 0.00% 54 235 0.00% 55 276 0.00% 56 301 0.00% 57 322 0.00% 58 420 0.00% 59 427 0.00% 60 515 0.00% 61 570 0.00% 62 709 0.00% 63 728 0.00% 64 845 0.00% 65 941 0.00% 66 1013 0.00% 67 1174 0.01% 68 1363 0.01% 69 1527 0.01% 70 1723 0.01% 71 2074 0.01% 72 2441 0.01% 73 2546 0.01% 74 2865 0.01% 75 3181 0.01% 76 3433 0.02% 77 3825 0.02% 78 4268 0.02% 79 4665 0.02% 80 4963 0.02% 81 5800 0.03% 82 6279 0.03% 83 6803 0.03% 84 7612 0.03% 85 8292 0.04% 86 8994 0.04% 87 9460 0.04% 88 10102 0.04% 89 10800 0.05% 90 11390 0.05% 91 12018 0.05% 92 12769 0.06% 93 13737 0.06% 94 14458 0.06% 95 15524 0.07% 96 16496 0.07% 97 17182 0.08% 98 18111 0.08% 99 18724 0.08% 100 19334 0.09% 101 20201 0.09% 102 20778 0.09% 103 21688 0.10% 104 22398 0.10% 105 23486 0.10% 106 24178 0.11% 107 25594 0.11% 108 25715 0.11% 109 26429 0.12% 110 27186 0.12% 111 27778 0.12% 112 28859 0.13% 113 29201 0.13% 114 29909 0.13% 115 31130 0.14% 116 32622 0.14% 117 33729 0.15% 118 34328 0.15% 119 34958 0.16% 120 35638 0.16% 121 36775 0.16% 122 37129 0.16% 123 37410 0.17% 124 38188 0.17% 125 38782 0.17% 126 40829 0.18% 127 41687 0.19% 128 42790 0.19% 129 43516 0.19% 130 43983 0.20% 131 44110 0.20% 132 45154 0.20% 133 45170 0.20% 134 45741 0.20% 135 46734 0.21% 136 48252 0.21% 137 47915 0.21% 138 49380 0.22% 139 51080 0.23% 140 51235 0.23% 141 51525 0.23% 142 52266 0.23% 143 52112 0.23% 144 53779 0.24% 145 53321 0.24% 146 54647 0.24% 147 54808 0.24% 148 56511 0.25% 149 56789 0.25% 150 57946 0.26% 151 20242934 89.92% 22511668 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=21 prefix-density=0.35 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=25.08 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=1.9 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGG criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=2.19 fanout-score-rank=29 prefix-density=0.61 prefix-fanout=2.1 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.15 sequence-density-rank=22 fanout-score=30.30 fanout-score-rank=1 prefix-density=0.40 prefix-fanout=11.2 sequence=AAAGAAAAGAAAA SRR12671363 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 19:34:44 Started mapping on | Feb 11 19:34:44 Finished on | Feb 11 19:37:16 Mapping speed, Million of reads per hour | 533.17 Number of input reads | 22511668 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 20859419 Uniquely mapped reads % | 92.66% Average mapped length | 294.87 Number of splices: Total | 20492519 Number of splices: Annotated (sjdb) | 20031015 Number of splices: GT/AG | 20084174 Number of splices: GC/AG | 329593 Number of splices: AT/AC | 12967 Number of splices: Non-canonical | 65785 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.03% Deletion average length | 2.93 Insertion rate per base | 0.03% Insertion average length | 2.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 545709 % of reads mapped to multiple loci | 2.42% Number of reads mapped to too many loci | 237851 % of reads mapped to too many loci | 1.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.64% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1106540 1106540 1106540 N_multimapping 545709 545709 545709 N_noFeature 887323 20536604 1002745 N_ambiguous 351079 1441 142887 UnstrandedReadsAssigned:19621017 PositiveStrandReadsAssigned:321374 NegativeStrandReadsAssigned:19713787 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671363 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: SRR12671363-trimmed-pair1.fastq SRR12671363-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,511,668 reads, 19,814,914 reads pseudoaligned [quant] estimated average fragment length: 281.696 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,148 rounds 52401 SRR12671363.ke.tsv 34699 SRR12671363.se.tsv 87100 total ==> SRR12671363.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1737.3 848 23.6718 Potri.005G024800.1.v4.1 1035 754.304 284 18.2593 Potri.004G059700.1.v4.1 961 680.682 11 0.783718 Potri.007G009000.2.v4.1 1416 1135.3 0 0 Potri.003G141000.2.v4.1 2943 2662.3 1023 18.635 Potri.016G087400.1.v4.1 270 88.8513 777.676 424.47 Potri.015G069301.1.v4.1 564 308.926 0 0 Potri.010G195200.1.v4.1 1773 1492.3 126 4.09473 Potri.012G127500.1.v4.1 977 696.47 184 12.8123 ==> SRR12671363.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 365 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 285 Potri.001G212900.v4.1 6 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 14 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 1 SRR12671363 completed mapping pipeline successfully