Starting /dee2/code/volunteer_pipeline.sh SRR12670107 current disk space = 3057670774784 free memory = 1505227328 SRR12670107 SRAfilesize fd51a2b9682ead9c6942e2afbf942a0e SRR12670107.sra SRR12670107.sra file validated SRR12670107 is paired end SRR12670107 is conventional basespace SRR12670107 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670107_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 36.6775 37.0 37.0 37.0 37.0 37.0 2 36.4865 37.0 37.0 37.0 37.0 37.0 3 36.658 37.0 37.0 37.0 37.0 37.0 4 36.633 37.0 37.0 37.0 37.0 37.0 5 36.6965 37.0 37.0 37.0 37.0 37.0 6 36.6805 37.0 37.0 37.0 37.0 37.0 7 36.624 37.0 37.0 37.0 37.0 37.0 8 36.6915 37.0 37.0 37.0 37.0 37.0 9 36.635 37.0 37.0 37.0 37.0 37.0 10-14 36.622299999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.5904 37.0 37.0 37.0 37.0 37.0 20-24 36.521699999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.5185 37.0 37.0 37.0 37.0 37.0 30-34 36.471000000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.510600000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.4754 37.0 37.0 37.0 37.0 37.0 45-49 36.4071 37.0 37.0 37.0 37.0 37.0 50-54 36.3996 37.0 37.0 37.0 37.0 37.0 55-59 36.36450000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.39880000000001 37.0 37.0 37.0 37.0 37.0 65-69 36.3281 37.0 37.0 37.0 37.0 37.0 70-74 36.332800000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.296 37.0 37.0 37.0 37.0 37.0 80-84 36.3012 37.0 37.0 37.0 37.0 37.0 85-89 36.2716 37.0 37.0 37.0 37.0 37.0 90-94 36.225699999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.1779 37.0 37.0 37.0 37.0 37.0 100-104 36.225899999999996 37.0 37.0 37.0 37.0 37.0 105-109 36.2072 37.0 37.0 37.0 37.0 37.0 110-114 36.1141 37.0 37.0 37.0 37.0 37.0 115-119 36.18920000000001 37.0 37.0 37.0 37.0 37.0 120-124 36.0643 37.0 37.0 37.0 37.0 37.0 125-129 35.9828 37.0 37.0 37.0 37.0 37.0 130-134 35.930099999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.8282 37.0 37.0 37.0 37.0 37.0 140-144 35.604699999999994 37.0 37.0 37.0 37.0 37.0 145-149 35.629599999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.30625 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 1.0 24 1.0 25 2.0 26 5.0 27 8.0 28 10.0 29 13.0 30 19.0 31 35.0 32 58.0 33 60.0 34 124.0 35 349.0 36 2953.0 37 361.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.725 11.0 7.675 41.6 2 18.612224448897795 12.775551102204407 36.47294589178357 32.139278557114224 3 18.4 16.400000000000002 27.800000000000004 37.4 4 21.025 25.5 23.325000000000003 30.15 5 22.7 29.5 25.324999999999996 22.475 6 20.1 34.1 23.75 22.05 7 15.225 25.324999999999996 41.175 18.275 8 16.725 26.424999999999997 32.2 24.65 9 17.25 22.7 35.75 24.3 10-14 19.905 28.935 27.529999999999998 23.630000000000003 15-19 19.38 27.810000000000002 28.615000000000002 24.195 20-24 19.925 28.720000000000002 27.63 23.724999999999998 25-29 19.235 28.845 27.855 24.065 30-34 19.935 27.765 28.365000000000002 23.935000000000002 35-39 19.585 28.249999999999996 28.005000000000003 24.16 40-44 19.615 27.839999999999996 28.26 24.285 45-49 20.24 27.834999999999997 27.98 23.945 50-54 20.055 28.189999999999998 27.52 24.235 55-59 20.04 28.025 27.76 24.175 60-64 20.435 28.67 27.750000000000004 23.145 65-69 20.465 27.845 27.66 24.03 70-74 20.75 28.275 27.775 23.200000000000003 75-79 19.935 28.365000000000002 28.015 23.685000000000002 80-84 20.580000000000002 28.33 27.605 23.485 85-89 20.62 28.925 27.189999999999998 23.265 90-94 20.69 28.305000000000003 26.985 24.02 95-99 21.055 28.27 26.63 24.044999999999998 100-104 21.025 28.599999999999998 26.900000000000002 23.474999999999998 105-109 20.974999999999998 28.48 26.685 23.86 110-114 21.545 28.93 26.290000000000003 23.235 115-119 21.325 29.115000000000002 25.580000000000002 23.98 120-124 20.505000000000003 29.53 25.490000000000002 24.474999999999998 125-129 20.19 28.185 26.38 25.245 130-134 20.43 28.16 26.07 25.34 135-139 21.22 27.935 24.959999999999997 25.885 140-144 21.145 27.875 25.19 25.790000000000003 145-149 21.64 27.229999999999997 26.195 24.935 150-151 22.375 27.3 25.174999999999997 25.15 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 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 0.0 19 0.0 20 0.0 21 0.5 22 0.5 23 0.5 24 2.5 25 6.0 26 5.0 27 6.5 28 11.5 29 13.0 30 11.0 31 16.0 32 32.5 33 46.0 34 52.5 35 67.5 36 88.5 37 103.0 38 117.5 39 142.0 40 174.5 41 206.0 42 242.0 43 269.5 44 267.0 45 250.0 46 257.0 47 264.5 48 251.5 49 213.5 50 172.0 51 145.0 52 113.5 53 96.5 54 91.0 55 67.0 56 44.5 57 38.0 58 34.5 59 26.5 60 15.0 61 10.5 62 6.5 63 5.5 64 5.0 65 2.0 66 1.0 67 3.5 68 3.0 69 0.5 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 0.2 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 80.25 #Duplication Level Percentage of deduplicated Percentage of total 1 82.05607476635514 65.85 2 13.208722741433021 21.2 3 3.3956386292834893 8.175 4 0.8411214953271028 2.7 5 0.4049844236760125 1.625 6 0.09345794392523366 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CTGGGATTCTCTCCTTGAGGTTGTAAAGCAAGACATGCTCAAACAGTATG 6 0.15 No Hit CTCCACCAAATCATTCATATCATTAACCCCGTTAGATTTAGCCCTTTGAT 6 0.15 No Hit TTTGTGATCAGGTTGCTCATGGCATCATCAATAACTTCTGTTTCCAGCTG 6 0.15 No Hit GTGGTGCAGCTACTGGCTTTTCTGCCCCAGGTCCCATGGCTAATCGTTCT 5 0.125 No Hit CCAACAATCTCCCTATCTCATATTTTTGCATCAACACATTCCCTTTGTTC 5 0.125 No Hit CTTCCTTTCAAGGGTAGATATCTCATTCATAATTCGTTCTCCCTTGGTTT 5 0.125 No Hit GCCTTGTTCAATTTTTCCCAGCGTTTCCTCATTGTCTCGTGTCCAAATTC 5 0.125 No Hit CTGTGTGCCTGCAAAATATCGAAGATTTTTTCTGCCGTGTATTTTTGATG 5 0.125 No Hit GCATAGGCTTCAGGGGATGAGTATGCAAAGTAGCCTCCAGGTCTAAGCAA 5 0.125 No Hit CATCTCCATCTTAAAGTAACCGTTGTCGCCCCAGTCTTCTCCCCAAGAGT 5 0.125 No Hit TGTGGAACCACAACCGTAGGTTCAGCCTTAAACTCCCCTTTTTCATCACC 5 0.125 No Hit GCTGTATATTGTCTGGATTTTGATCTCCCTGGCTGCTTGTCAACTCAGCA 5 0.125 No Hit GGACAGGATCGGTTGAGGAACAGGTTCAATTTCACCGGCATCATTAGCCA 5 0.125 No Hit GTCCATTCTCACCATACATGATGTTGACCAAATCCTTGGCATATGTAAGA 5 0.125 No Hit CTTGAATGGAAGAATTCTTAAGTCAGTAAAGTCAAAGCTCCCATCTCATA 5 0.125 No Hit GCTACTGCGGCCCTCACTGAACAGTTTTGTATATGATCTGAGCTTCACTC 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 0.0 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 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.07500000000000001 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1375 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.21250000000000002 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.325 0.0 0.0 0.0 0.0 68-69 0.425 0.0 0.0 0.0 0.0 70-71 0.7124999999999999 0.0 0.0 0.0 0.0 72-73 0.85 0.0 0.0 0.0 0.0 74-75 1.175 0.0 0.0 0.0 0.0 76-77 1.4125 0.0 0.0 0.0 0.0 78-79 1.6125 0.0 0.0 0.0 0.0 80-81 1.8250000000000002 0.0 0.0 0.0 0.0 82-83 2.25 0.0 0.0 0.0 0.0 84-85 2.775 0.0 0.0 0.0 0.0 86-87 3.45 0.0 0.0 0.0 0.0 88-89 4.1 0.0 0.0 0.0 0.0 90-91 4.65 0.0 0.0 0.0 0.0 92-93 5.1625 0.0 0.0 0.0 0.0 94-95 5.9875 0.0 0.0 0.0 0.0 96-97 6.637499999999999 0.0 0.0 0.0 0.0 98-99 7.35 0.0 0.0 0.0 0.0 100-101 8.399999999999999 0.0 0.0 0.0 0.0 102-103 9.4625 0.0 0.0 0.0 0.0 104-105 10.412500000000001 0.0 0.0 0.0 0.0 106-107 11.6 0.0 0.0 0.0 0.0 108-109 12.7125 0.0 0.0 0.0 0.0 110-111 13.837499999999999 0.0 0.0 0.0 0.0 112-113 14.8625 0.0 0.0 0.0 0.0 114-115 15.425 0.0 0.0 0.0 0.0 116-117 16.4375 0.0 0.0 0.0 0.0 118-119 17.675 0.0 0.0 0.0 0.0 120-121 18.775 0.0 0.0 0.0 0.0 122-123 19.95 0.0 0.0 0.0 0.0 124-125 20.925 0.0 0.0 0.0 0.0 126-127 21.8375 0.0 0.0 0.0 0.0 128-129 22.6 0.0 0.0 0.0 0.0 130-131 23.475 0.0 0.0 0.0 0.0 132-133 24.525 0.0 0.0 0.0 0.0 134-135 25.637500000000003 0.0 0.0 0.0 0.0 136-137 26.4625 0.0 0.0 0.0 0.0 138-139 27.4625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGG 10 0.006830828 145.0 9 CTGAGGA 10 0.006830828 145.0 1 TGAGGAA 10 0.006830828 145.0 2 GTTCGCT 10 0.006830828 145.0 1 >>END_MODULE SRR12670107 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670107_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 36.2855 37.0 37.0 37.0 37.0 37.0 2 36.2095 37.0 37.0 37.0 37.0 37.0 3 36.317 37.0 37.0 37.0 37.0 37.0 4 36.3015 37.0 37.0 37.0 37.0 37.0 5 36.3445 37.0 37.0 37.0 37.0 37.0 6 36.3775 37.0 37.0 37.0 37.0 37.0 7 36.316 37.0 37.0 37.0 37.0 37.0 8 36.356 37.0 37.0 37.0 37.0 37.0 9 36.3065 37.0 37.0 37.0 37.0 37.0 10-14 36.37579999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.3141 37.0 37.0 37.0 37.0 37.0 20-24 36.2817 37.0 37.0 37.0 37.0 37.0 25-29 36.28680000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.207100000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.2113 37.0 37.0 37.0 37.0 37.0 40-44 36.2434 37.0 37.0 37.0 37.0 37.0 45-49 36.195499999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.187799999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.0963 37.0 37.0 37.0 37.0 37.0 60-64 36.1066 37.0 37.0 37.0 37.0 37.0 65-69 36.071 37.0 37.0 37.0 37.0 37.0 70-74 36.0637 37.0 37.0 37.0 37.0 37.0 75-79 36.068400000000004 37.0 37.0 37.0 37.0 37.0 80-84 36.0422 37.0 37.0 37.0 37.0 37.0 85-89 36.0116 37.0 37.0 37.0 37.0 37.0 90-94 35.964 37.0 37.0 37.0 37.0 37.0 95-99 35.968199999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.840700000000005 37.0 37.0 37.0 37.0 37.0 105-109 35.781499999999994 37.0 37.0 37.0 37.0 37.0 110-114 35.6839 37.0 37.0 37.0 37.0 37.0 115-119 35.6818 37.0 37.0 37.0 37.0 37.0 120-124 35.3938 37.0 37.0 37.0 37.0 37.0 125-129 35.178399999999996 37.0 37.0 37.0 32.2 37.0 130-134 34.9861 37.0 37.0 37.0 25.0 37.0 135-139 34.6084 37.0 37.0 37.0 25.0 37.0 140-144 34.39450000000001 37.0 37.0 37.0 25.0 37.0 145-149 33.9365 37.0 37.0 37.0 25.0 37.0 150-151 33.573499999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 5.0 14 4.0 15 0.0 16 3.0 17 1.0 18 1.0 19 4.0 20 5.0 21 3.0 22 2.0 23 1.0 24 3.0 25 5.0 26 11.0 27 14.0 28 12.0 29 18.0 30 38.0 31 53.0 32 58.0 33 142.0 34 256.0 35 539.0 36 2494.0 37 327.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.550000000000004 20.175 11.65 27.625 2 26.875 25.924999999999997 31.075000000000003 16.125 3 21.75 28.549999999999997 31.574999999999996 18.125 4 23.599999999999998 34.0 23.425 18.975 5 24.9 36.075 21.475 17.549999999999997 6 21.55 38.800000000000004 22.3 17.349999999999998 7 21.4 21.9 38.275 18.425 8 21.3 24.975 28.375 25.35 9 22.6 24.125 30.325000000000003 22.95 10-14 23.205000000000002 28.33 27.27 21.195 15-19 23.974999999999998 27.515 28.189999999999998 20.32 20-24 23.21 28.939999999999998 27.555000000000003 20.294999999999998 25-29 22.945 27.93 28.785 20.34 30-34 23.369999999999997 27.994999999999997 27.82 20.815 35-39 23.105 28.375 27.375 21.145 40-44 22.919999999999998 28.26 28.18 20.64 45-49 22.975 28.665000000000003 27.915 20.445 50-54 23.45 28.305000000000003 27.634999999999998 20.61 55-59 23.335 28.249999999999996 27.750000000000004 20.665 60-64 22.71 28.075 28.08 21.135 65-69 24.3 27.16 27.900000000000002 20.64 70-74 23.115 28.035 27.57 21.279999999999998 75-79 23.745 28.095 27.860000000000003 20.3 80-84 24.154999999999998 28.43 27.395000000000003 20.02 85-89 23.415 28.360000000000003 26.900000000000002 21.325 90-94 24.485 28.13 27.165 20.22 95-99 24.495 28.265 26.979999999999997 20.26 100-104 24.995 28.43 26.58 19.994999999999997 105-109 25.235000000000003 28.785 26.07 19.91 110-114 25.82 28.804999999999996 26.445 18.93 115-119 27.29 28.09 26.125 18.495 120-124 27.150000000000002 28.435 25.795 18.62 125-129 28.26 28.315 25.165 18.26 130-134 29.020000000000003 27.99 25.05 17.94 135-139 30.285 26.169999999999998 25.5 18.045 140-144 31.11 26.669999999999998 25.09 17.130000000000003 145-149 32.595 25.88 24.605 16.919999999999998 150-151 32.925 25.35 25.3125 16.412499999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 1.0 3 1.0 4 0.0 5 0.0 6 1.0 7 1.0 8 0.0 9 0.5 10 0.5 11 0.0 12 0.0 13 1.0 14 1.5 15 1.0 16 0.5 17 1.0 18 1.5 19 0.5 20 1.0 21 1.5 22 2.0 23 1.5 24 1.5 25 2.0 26 5.0 27 10.5 28 9.0 29 8.5 30 13.0 31 18.0 32 32.5 33 46.5 34 56.0 35 59.0 36 77.0 37 116.0 38 136.5 39 170.0 40 195.5 41 193.0 42 239.5 43 291.0 44 267.0 45 250.5 46 271.0 47 267.5 48 241.5 49 192.0 50 151.5 51 134.0 52 117.0 53 85.5 54 68.0 55 59.5 56 47.0 57 37.0 58 18.0 59 14.0 60 16.5 61 15.5 62 10.0 63 7.0 64 4.0 65 1.0 66 2.5 67 2.0 68 2.5 69 3.5 70 3.0 71 2.5 72 1.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.5 78 0.5 79 0.5 80 0.5 81 0.0 82 0.5 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 0.5 98 0.5 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 80.4 #Duplication Level Percentage of deduplicated Percentage of total 1 82.18283582089553 66.07499999999999 2 13.277363184079602 21.349999999999998 3 3.1405472636815923 7.575 4 0.8395522388059702 2.7 5 0.4975124378109453 2.0 6 0.06218905472636816 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source AAACAATTGTGGCATGCTTCACTATACATCAGGTGGCCAGTTTACTATAC 6 0.15 No Hit GAAGGATGTGCTTGCAAGGTATAATCTGCACTCCAATAACCTCGACAAAA 6 0.15 No Hit ATGAAGGTGAAGGGTAATGTGTTCAAGAACAAGAGAGTTCTAATGGAAAG 5 0.125 No Hit ATGATGTTCATCAAAACAAGATCCAGTTTGCCCTGGAAAGAGGAATCCCT 5 0.125 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit TCAAAATCTGTGTTCTAAATGTTATGGTGATCTTCGTCAATCACAGCCCC 5 0.125 No Hit CTGTACGACTTATAGTGGTAGTGGGAGGTGTAGATGAACACTTACCATCA 5 0.125 No Hit CGTTACACAGGTCATTTGAATAGCTCTCTTCAGGAACCAATTGAAGTTTC 5 0.125 No Hit GGTGAATCACCCATACATTTGGCGGTGGATTGAGGACTTCAACTGAATTT 5 0.125 No Hit CATGCATGCTGTTACTGGTGCTTACGCAAAACCCATCTTTGTGGACAAGC 5 0.125 No Hit GTTTTATTTATGTTTGGAGTTCTTAGACATAGACATCAATGGTAATTATG 5 0.125 No Hit CAACCACTGCTGTTTGATCATGGCAGCAACCATCTCAACCGTTGGAGCTG 5 0.125 No Hit GTTTACACCACCAGCACTTGTGGCAGTACTCCCATGGATGTGAACCATGC 5 0.125 No Hit CAGCAGGTGTGATCGCACTTATTCTCTATAAGTTCAGCACTACTATCGAG 5 0.125 No Hit GTAGTGTCATCAGAGACGAAAGATCTTGAGAGATCATCATCAAAACCCAG 5 0.125 No Hit GTTGTTGCTAGTGAGCCTCTACTAGATCATTCTGATGCAGCCATTCCTTT 5 0.125 No Hit AGAATGTTAACCTACCTAACCTTAAATACCCTGGGAGTTTCTAAGGATAG 5 0.125 No Hit ATTGAAGGAAATGCGGTGAAAAGAACATATCAAAAGGCCTTACTCTGTCT 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 0.0 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 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.07500000000000001 0.0 0.0 0.0 0.0 54-55 0.1 0.0 0.0 0.0 0.0 56-57 0.1375 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.2 0.0 0.0 0.0 0.0 62-63 0.21250000000000002 0.0 0.0 0.0 0.0 64-65 0.275 0.0 0.0 0.0 0.0 66-67 0.325 0.0 0.0 0.0 0.0 68-69 0.425 0.0 0.0 0.0 0.0 70-71 0.6875 0.0 0.0 0.0 0.0 72-73 0.8374999999999999 0.0 0.0 0.0 0.0 74-75 1.175 0.0 0.0 0.0 0.0 76-77 1.4125 0.0 0.0 0.0 0.0 78-79 1.6125 0.0 0.0 0.0 0.0 80-81 1.8250000000000002 0.0 0.0 0.0 0.0 82-83 2.25 0.0 0.0 0.0 0.0 84-85 2.775 0.0 0.0 0.0 0.0 86-87 3.45 0.0 0.0 0.0 0.0 88-89 4.1 0.0 0.0 0.0 0.0 90-91 4.675000000000001 0.0 0.0 0.0 0.0 92-93 5.2125 0.0 0.0 0.0 0.0 94-95 6.0375 0.0 0.0 0.0 0.0 96-97 6.6625 0.0 0.0 0.0 0.0 98-99 7.3875 0.0 0.0 0.0 0.0 100-101 8.45 0.0 0.0 0.0 0.0 102-103 9.5125 0.0 0.0 0.0 0.0 104-105 10.4375 0.0 0.0 0.0 0.0 106-107 11.6125 0.0 0.0 0.0 0.0 108-109 12.7125 0.0 0.0 0.0 0.0 110-111 13.837499999999999 0.0 0.0 0.0 0.0 112-113 14.850000000000001 0.0 0.0 0.0 0.0 114-115 15.4 0.0 0.0 0.0 0.0 116-117 16.4375 0.0 0.0 0.0 0.0 118-119 17.675 0.0 0.0 0.0 0.0 120-121 18.75 0.0 0.0 0.0 0.0 122-123 19.925 0.0 0.0 0.0 0.0 124-125 20.9 0.0 0.0 0.0 0.0 126-127 21.8375 0.0 0.0 0.0 0.0 128-129 22.6 0.0 0.0 0.0 0.0 130-131 23.487499999999997 0.0 0.0 0.0 0.0 132-133 24.55 0.0 0.0 0.0 0.0 134-135 25.675 0.0 0.0 0.0 0.0 136-137 26.512500000000003 0.0 0.0 0.0 0.0 138-139 27.6625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCTACCC 10 0.006830828 145.0 6 ACCACCT 10 0.006830828 145.0 2 CCACCTA 10 0.006830828 145.0 3 CACCTAC 10 0.006830828 145.0 4 CACCACC 10 0.006830828 145.0 1 TACCCAT 10 0.006830828 145.0 8 ACCTACC 10 0.006830828 145.0 5 GGGGGGG 45 6.5511256E-4 19.333332 140-144 >>END_MODULE Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703019 spots for SRR12670107.sra Written 703019 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra Read 703000 spots for SRR12670107.sra Written 703000 spots for SRR12670107.sra SRR ids: ['SRR12670107.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ol4gmk16 SRR12670107.sra spots: 14060019 blocks: [[1, 703000], [703001, 1406000], [1406001, 2109000], [2109001, 2812000], [2812001, 3515000], [3515001, 4218000], [4218001, 4921000], [4921001, 5624000], [5624001, 6327000], [6327001, 7030000], [7030001, 7733000], [7733001, 8436000], [8436001, 9139000], [9139001, 9842000], [9842001, 10545000], [10545001, 11248000], [11248001, 11951000], [11951001, 12654000], [12654001, 13357000], [13357001, 14060019]] SRR12670107 file size 4756509 SRR12670107 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 SRR12670107 SRR12670107_1.fastq SRR12670107_2.fastq Input file: SRR12670107_1.fastq Paired file: SRR12670107_2.fastq trimmed: SRR12670107-trimmed-pair1.fastq, SRR12670107-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 Mon Feb 10 23:30:52 2025 >> started Mon Feb 10 23:31:15 2025 >> done (22.368s) 14060019 read pairs processed; of these: 70 ( 0.00%) short read pairs filtered out after trimming by size control 12113 ( 0.09%) empty read pairs filtered out after trimming by size control 14047836 (99.91%) read pairs available; of these: 4427392 (31.52%) trimmed read pairs available after processing 9620444 (68.48%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 5 0.00% 20 14 0.00% 21 7 0.00% 22 5 0.00% 23 15 0.00% 24 21 0.00% 25 15 0.00% 26 35 0.00% 27 14 0.00% 28 37 0.00% 29 54 0.00% 30 50 0.00% 31 75 0.00% 32 60 0.00% 33 68 0.00% 34 75 0.00% 35 105 0.00% 36 128 0.00% 37 155 0.00% 38 162 0.00% 39 237 0.00% 40 295 0.00% 41 323 0.00% 42 341 0.00% 43 360 0.00% 44 375 0.00% 45 419 0.00% 46 444 0.00% 47 578 0.00% 48 706 0.01% 49 891 0.01% 50 1069 0.01% 51 1155 0.01% 52 1294 0.01% 53 1295 0.01% 54 1366 0.01% 55 1545 0.01% 56 1738 0.01% 57 2051 0.01% 58 2436 0.02% 59 2847 0.02% 60 3339 0.02% 61 3843 0.03% 62 4246 0.03% 63 4712 0.03% 64 5103 0.04% 65 5349 0.04% 66 5845 0.04% 67 6457 0.05% 68 7105 0.05% 69 8239 0.06% 70 9480 0.07% 71 11053 0.08% 72 12504 0.09% 73 13858 0.10% 74 14833 0.11% 75 15636 0.11% 76 16954 0.12% 77 17748 0.13% 78 19357 0.14% 79 21014 0.15% 80 22751 0.16% 81 25975 0.18% 82 28524 0.20% 83 30647 0.22% 84 33145 0.24% 85 35260 0.25% 86 36001 0.26% 87 37425 0.27% 88 39075 0.28% 89 40134 0.29% 90 42866 0.31% 91 45639 0.32% 92 47491 0.34% 93 51305 0.37% 94 52795 0.38% 95 55780 0.40% 96 55505 0.40% 97 56553 0.40% 98 56517 0.40% 99 57043 0.41% 100 58925 0.42% 101 59756 0.43% 102 62155 0.44% 103 64190 0.46% 104 64957 0.46% 105 66209 0.47% 106 66918 0.48% 107 65954 0.47% 108 66050 0.47% 109 64604 0.46% 110 64232 0.46% 111 65743 0.47% 112 67639 0.48% 113 67381 0.48% 114 68702 0.49% 115 69872 0.50% 116 69334 0.49% 117 68776 0.49% 118 69366 0.49% 119 67373 0.48% 120 67282 0.48% 121 67844 0.48% 122 67770 0.48% 123 68243 0.49% 124 69811 0.50% 125 69089 0.49% 126 69264 0.49% 127 69155 0.49% 128 67138 0.48% 129 66537 0.47% 130 66659 0.47% 131 64947 0.46% 132 65483 0.47% 133 65326 0.47% 134 65405 0.47% 135 66414 0.47% 136 65950 0.47% 137 65479 0.47% 138 64872 0.46% 139 64935 0.46% 140 63725 0.45% 141 62924 0.45% 142 62578 0.45% 143 62211 0.44% 144 63802 0.45% 145 63267 0.45% 146 63241 0.45% 147 63575 0.45% 148 63191 0.45% 149 61956 0.44% 150 61208 0.44% 151 9620444 68.48% 14047836 reads passed initial QC criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=23 prefix-density=0.50 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGG criterion=fanout-score sequence-density=0.09 sequence-density-rank=26 fanout-score=35.01 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=10.7 sequence=CCATTCTTGAGTTCCTTCACCTTCAACTCAGCGAATGCTTCGGGATCGTCAGCCAAGCCCAGTGGGTCGAAGCTTCCACCTGGGTAGATTGGGTCAGTTACCTCACCGAGTGGCCCGCCAGCAATTCTGTAACCCTCAACGGCACCCATCAAGACCACCTGTGTAGCCCAGATGGCCAAGATGCTTTGTGCGTGGATCAAGCTTGGGTTGCCCAAGTAGTCAAGTCCACCCTCGCTGAAGATCTGGGCTCCAGCCTTGAACCATACAGCCTCGCCGAACTTGACACCGTTGCGGGACAAGAGCTCGGGGAAGACGCATCCAAGAGC criterion=sequence-density sequence-density=0.92 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=28 prefix-density=0.93 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.11 sequence-density-rank=30 fanout-score=35.44 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=12.7 sequence=AAAGAAAAGAAAA SRR12670107 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:31:57 Started mapping on | Feb 10 23:31:57 Finished on | Feb 10 23:33:45 Mapping speed, Million of reads per hour | 468.26 Number of input reads | 14047836 Average input read length | 279 UNIQUE READS: Uniquely mapped reads number | 12982965 Uniquely mapped reads % | 92.42% Average mapped length | 278.23 Number of splices: Total | 12030273 Number of splices: Annotated (sjdb) | 11716993 Number of splices: GT/AG | 11783218 Number of splices: GC/AG | 187237 Number of splices: AT/AC | 8723 Number of splices: Non-canonical | 51095 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.86 Insertion rate per base | 0.02% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 365697 % of reads mapped to multiple loci | 2.60% Number of reads mapped to too many loci | 196116 % of reads mapped to too many loci | 1.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.32% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 699174 699174 699174 N_multimapping 365697 365697 365697 N_noFeature 624833 12789214 708767 N_ambiguous 194177 818 83959 UnstrandedReadsAssigned:12163955 PositiveStrandReadsAssigned:192933 NegativeStrandReadsAssigned:12190239 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=126 echo kmer=121 SRR12670107 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: SRR12670107-trimmed-pair1.fastq SRR12670107-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,047,836 reads, 12,277,704 reads pseudoaligned [quant] estimated average fragment length: 198.858 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,108 rounds 52401 SRR12670107.ke.tsv 34699 SRR12670107.se.tsv 87100 total ==> SRR12670107.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1820.14 753 34.3947 Potri.005G024800.1.v4.1 1035 837.142 318 31.5813 Potri.004G059700.1.v4.1 961 763.209 1 0.108933 Potri.007G009000.2.v4.1 1416 1218.14 0 0 Potri.003G141000.2.v4.1 2943 2745.14 1121.22 33.9569 Potri.016G087400.1.v4.1 270 116.422 1049 749.103 Potri.015G069301.1.v4.1 564 373.399 0 0 Potri.010G195200.1.v4.1 1773 1575.14 157 8.28671 Potri.012G127500.1.v4.1 977 779.168 48 5.12168 ==> SRR12670107.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 106 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 184 Potri.001G212900.v4.1 8 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 34 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 45 SRR12670107 completed mapping pipeline successfully