Starting /dee2/code/volunteer_pipeline.sh SRR12690138 current disk space = 3057448484864 free memory = 1578396404 SRR12690138 SRAfilesize fb4ce507948a3e7299011d91abf86c77 SRR12690138.sra SRR12690138.sra file validated SRR12690138 is paired end SRR12690138 is conventional basespace SRR12690138 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12690138_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.7175 37.0 37.0 37.0 37.0 37.0 2 36.35125 37.0 37.0 37.0 37.0 37.0 3 36.613 37.0 37.0 37.0 37.0 37.0 4 36.5875 37.0 37.0 37.0 37.0 37.0 5 36.634 37.0 37.0 37.0 37.0 37.0 6 36.585 37.0 37.0 37.0 37.0 37.0 7 36.6225 37.0 37.0 37.0 37.0 37.0 8 36.6175 37.0 37.0 37.0 37.0 37.0 9 36.5705 37.0 37.0 37.0 37.0 37.0 10-14 36.626099999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.6077 37.0 37.0 37.0 37.0 37.0 20-24 36.587300000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.527300000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.518100000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.4886 37.0 37.0 37.0 37.0 37.0 40-44 36.4674 37.0 37.0 37.0 37.0 37.0 45-49 36.3075 37.0 37.0 37.0 37.0 37.0 50-54 36.3146 37.0 37.0 37.0 37.0 37.0 55-59 36.1558 37.0 37.0 37.0 37.0 37.0 60-64 36.125099999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.0636 37.0 37.0 37.0 37.0 37.0 70-74 36.1828 37.0 37.0 37.0 37.0 37.0 75-79 36.315999999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.239999999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.2182 37.0 37.0 37.0 37.0 37.0 90-94 36.2342 37.0 37.0 37.0 37.0 37.0 95-99 36.2014 37.0 37.0 37.0 37.0 37.0 100-104 36.172000000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.132400000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.1533 37.0 37.0 37.0 37.0 37.0 115-119 36.075 37.0 37.0 37.0 37.0 37.0 120-124 36.0177 37.0 37.0 37.0 37.0 37.0 125-129 35.98539999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.9798 37.0 37.0 37.0 37.0 37.0 135-139 35.995000000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.7213 37.0 37.0 37.0 37.0 37.0 145-149 35.64319999999999 37.0 37.0 37.0 37.0 37.0 150-151 35.4975 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 2.0 24 1.0 25 2.0 26 1.0 27 8.0 28 15.0 29 26.0 30 34.0 31 31.0 32 53.0 33 86.0 34 146.0 35 274.0 36 2914.0 37 407.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.0 12.5 6.675000000000001 35.825 2 19.85940246045694 13.256339442631182 33.84383630429325 33.04042179261863 3 15.6 15.299999999999999 30.099999999999998 39.0 4 19.7 22.35 26.575 31.374999999999996 5 25.1 26.875 25.650000000000002 22.375 6 23.875 31.05 23.35 21.725 7 16.925 29.175 36.875 17.025000000000002 8 17.825 27.700000000000003 30.8 23.674999999999997 9 18.45 24.474999999999998 32.775 24.3 10-14 20.785 28.715000000000003 27.500000000000004 23.0 15-19 20.25 27.029999999999998 27.625 25.095 20-24 21.39 27.295 27.639999999999997 23.674999999999997 25-29 20.735 27.275 28.13 23.86 30-34 20.285 27.455000000000002 28.035 24.224999999999998 35-39 21.01 27.084999999999997 27.675 24.23 40-44 20.59 27.529999999999998 28.12 23.76 45-49 21.725 26.955000000000002 27.37 23.95 50-54 21.654999999999998 26.35 27.92 24.075 55-59 20.805 26.22 28.37 24.605 60-64 21.285 26.985 27.91 23.82 65-69 21.7 26.96 27.189999999999998 24.15 70-74 22.55 27.145000000000003 26.815 23.49 75-79 22.384999999999998 26.834999999999997 26.724999999999998 24.055 80-84 23.064999999999998 26.69 26.395000000000003 23.849999999999998 85-89 22.814999999999998 26.615 26.83 23.74 90-94 22.770000000000003 26.25 26.924999999999997 24.055 95-99 22.564999999999998 26.66 27.395000000000003 23.380000000000003 100-104 23.455000000000002 26.96 26.88 22.705000000000002 105-109 23.525 25.47 27.605 23.400000000000002 110-114 23.255 26.924999999999997 26.939999999999998 22.88 115-119 23.185 26.75 26.815 23.25 120-124 23.31 26.265 26.91 23.515 125-129 23.28 26.590000000000003 26.064999999999998 24.065 130-134 23.02 26.985 26.755000000000003 23.24 135-139 23.7 26.555 26.505000000000003 23.24 140-144 23.395 26.795 25.89 23.919999999999998 145-149 23.875 26.145000000000003 25.674999999999997 24.305 150-151 24.212500000000002 25.825 25.75 24.212500000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 3.0 1 1.5 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 1.0 12 2.0 13 1.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.0 22 1.0 23 2.0 24 2.0 25 2.0 26 3.5 27 3.5 28 6.0 29 10.0 30 13.0 31 13.0 32 18.0 33 29.0 34 35.5 35 44.0 36 60.5 37 79.0 38 101.5 39 113.5 40 117.5 41 150.5 42 187.5 43 221.0 44 257.5 45 281.5 46 273.0 47 278.0 48 276.5 49 244.0 50 212.0 51 169.0 52 144.5 53 125.5 54 100.5 55 81.0 56 75.0 57 62.0 58 40.0 59 35.5 60 26.0 61 11.0 62 6.5 63 3.5 64 5.0 65 12.5 66 13.5 67 14.0 68 15.5 69 8.5 70 2.5 71 0.0 72 0.0 73 1.0 74 1.0 75 0.0 76 0.0 77 0.5 78 0.5 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 0.42500000000000004 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 89.275 #Duplication Level Percentage of deduplicated Percentage of total 1 90.67488098571829 80.95 2 8.288994679361524 14.799999999999999 3 0.8401008120974517 2.25 4 0.05600672080649678 0.2 5 0.05600672080649678 0.25 6 0.02800336040324839 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.05600672080649678 1.4000000000000001 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGCTGTTATCTCGTAT 35 0.8750000000000001 TruSeq Adapter, Index 10 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGCTGTTATCGCGTAT 21 0.525 TruSeq Adapter, Index 10 (97% over 38bp) GTCATTGTTAGCCTTTCTGGTGACCGGGAAAGCTGAGGTAGACTTGAGGC 6 0.15 No Hit CCTGCATGCATTGAACTCTTCCGCCATTGCTTGCAATGGAAGTAATGTCA 5 0.125 No Hit GTGAAATCAATTTTGCAATTGTTTGTCTCAGCAACAGGGTTTCTCAAACT 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 0.0 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.07500000000000001 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.4875 0.0 0.0 0.0 0.0 86-87 0.55 0.0 0.0 0.0 0.0 88-89 0.75 0.0 0.0 0.0 0.0 90-91 0.9375 0.0 0.0 0.0 0.0 92-93 1.025 0.0 0.0 0.0 0.0 94-95 1.1875 0.0 0.0 0.0 0.0 96-97 1.4249999999999998 0.0 0.0 0.0 0.0 98-99 1.675 0.0 0.0 0.0 0.0 100-101 1.975 0.0 0.0 0.0 0.0 102-103 2.275 0.0 0.0 0.0 0.0 104-105 2.775 0.0 0.0 0.0 0.0 106-107 3.1125 0.0 0.0 0.0 0.0 108-109 3.5375 0.0 0.0 0.0 0.0 110-111 4.050000000000001 0.0 0.0 0.0 0.0 112-113 4.637499999999999 0.0 0.0 0.0 0.0 114-115 5.175000000000001 0.0 0.0 0.0 0.0 116-117 5.7625 0.0 0.0 0.0 0.0 118-119 6.475 0.0 0.0 0.0 0.0 120-121 7.0875 0.0 0.0 0.0 0.0 122-123 7.675000000000001 0.0 0.0 0.0 0.0 124-125 8.7125 0.0 0.0 0.0 0.0 126-127 9.8 0.0 0.0 0.0 0.0 128-129 10.5125 0.0 0.0 0.0 0.0 130-131 11.4375 0.0 0.0 0.0 0.0 132-133 12.2875 0.0 0.0 0.0 0.0 134-135 13.55 0.0 0.0 0.0 0.0 136-137 14.774999999999999 0.0 0.0 0.0 0.0 138-139 16.012500000000003 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTTTGCC 10 0.006830828 145.0 4 GCCAAGG 10 0.006830828 145.0 8 GCATTTT 10 0.006830828 145.0 1 CCAAGGT 10 0.006830828 145.0 9 ATTTTGC 10 0.006830828 145.0 3 GTTACAA 10 0.006830828 145.0 1 >>END_MODULE SRR12690138 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12690138_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 36.475 37.0 37.0 37.0 37.0 37.0 2 36.2265 37.0 37.0 37.0 37.0 37.0 3 36.228 37.0 37.0 37.0 37.0 37.0 4 36.241 37.0 37.0 37.0 37.0 37.0 5 36.3315 37.0 37.0 37.0 37.0 37.0 6 36.234 37.0 37.0 37.0 37.0 37.0 7 36.287 37.0 37.0 37.0 37.0 37.0 8 36.193 37.0 37.0 37.0 37.0 37.0 9 36.1985 37.0 37.0 37.0 37.0 37.0 10-14 36.1026 37.0 37.0 37.0 37.0 37.0 15-19 36.1178 37.0 37.0 37.0 37.0 37.0 20-24 36.071 37.0 37.0 37.0 37.0 37.0 25-29 35.979699999999994 37.0 37.0 37.0 37.0 37.0 30-34 35.883799999999994 37.0 37.0 37.0 37.0 37.0 35-39 35.8851 37.0 37.0 37.0 37.0 37.0 40-44 35.8455 37.0 37.0 37.0 37.0 37.0 45-49 35.8916 37.0 37.0 37.0 37.0 37.0 50-54 35.815599999999996 37.0 37.0 37.0 37.0 37.0 55-59 35.9005 37.0 37.0 37.0 37.0 37.0 60-64 35.8627 37.0 37.0 37.0 37.0 37.0 65-69 35.7976 37.0 37.0 37.0 37.0 37.0 70-74 35.659000000000006 37.0 37.0 37.0 37.0 37.0 75-79 35.6944 37.0 37.0 37.0 37.0 37.0 80-84 35.67099999999999 37.0 37.0 37.0 37.0 37.0 85-89 35.811400000000006 37.0 37.0 37.0 37.0 37.0 90-94 35.7724 37.0 37.0 37.0 37.0 37.0 95-99 35.8501 37.0 37.0 37.0 37.0 37.0 100-104 35.9116 37.0 37.0 37.0 37.0 37.0 105-109 35.880700000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.799099999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.7461 37.0 37.0 37.0 37.0 37.0 120-124 35.66799999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.5397 37.0 37.0 37.0 37.0 37.0 130-134 35.5326 37.0 37.0 37.0 37.0 37.0 135-139 35.391999999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.1999 37.0 37.0 37.0 32.2 37.0 145-149 34.8844 37.0 37.0 37.0 25.0 37.0 150-151 34.43425 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 5.0 14 3.0 15 3.0 16 3.0 17 6.0 18 1.0 19 2.0 20 8.0 21 6.0 22 9.0 23 14.0 24 9.0 25 19.0 26 16.0 27 18.0 28 15.0 29 30.0 30 27.0 31 32.0 32 44.0 33 75.0 34 139.0 35 464.0 36 2738.0 37 314.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.825 25.624999999999996 9.975000000000001 23.575 2 29.799999999999997 29.175 24.349999999999998 16.675 3 22.8 29.025000000000002 29.075 19.1 4 25.05 36.25 21.3 17.4 5 26.924999999999997 36.1 19.575 17.4 6 22.55 38.824999999999996 20.674999999999997 17.95 7 22.075 23.325000000000003 35.175 19.425 8 24.7 26.75 24.675 23.875 9 22.400000000000002 26.8 27.3 23.5 10-14 25.324999999999996 29.015 24.57 21.09 15-19 24.725 28.63 25.624999999999996 21.02 20-24 24.955 28.194999999999997 25.88 20.97 25-29 24.705 28.95 25.71 20.635 30-34 23.724999999999998 28.115000000000002 25.965 22.195 35-39 24.13 28.244999999999997 26.275 21.349999999999998 40-44 24.365000000000002 28.235 26.13 21.27 45-49 25.045 27.26 26.400000000000002 21.295 50-54 24.060000000000002 28.4 25.775 21.765 55-59 24.825 27.689999999999998 26.395000000000003 21.09 60-64 23.71 28.084999999999997 26.575 21.63 65-69 24.875 26.384999999999998 26.33 22.41 70-74 24.345 27.43 26.375 21.85 75-79 24.37 27.700000000000003 26.275 21.654999999999998 80-84 24.315 28.27 25.874999999999996 21.54 85-89 24.654999999999998 27.415 26.155 21.775 90-94 25.619999999999997 27.24 25.740000000000002 21.4 95-99 25.69 27.88 25.069999999999997 21.36 100-104 25.5 27.54 25.605 21.355 105-109 25.64 27.235 26.064999999999998 21.060000000000002 110-114 25.290000000000003 27.63 25.740000000000002 21.34 115-119 26.19 28.000000000000004 25.155 20.655 120-124 26.474999999999998 26.97 26.22 20.335 125-129 26.745 28.285 25.56 19.41 130-134 27.98 27.965 24.775 19.28 135-139 27.975 27.275 24.98 19.77 140-144 29.14 26.939999999999998 24.51 19.41 145-149 29.885 26.86 24.685000000000002 18.57 150-151 30.175 26.8375 24.675 18.3125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 1.0 8 1.0 9 0.5 10 1.0 11 0.5 12 0.0 13 1.0 14 2.5 15 1.5 16 0.5 17 0.5 18 0.5 19 3.0 20 5.0 21 3.0 22 1.0 23 2.5 24 2.0 25 1.0 26 1.0 27 0.5 28 2.0 29 3.5 30 3.5 31 4.0 32 8.0 33 14.5 34 20.5 35 28.5 36 40.5 37 61.5 38 100.5 39 116.0 40 143.5 41 204.5 42 237.0 43 254.5 44 276.0 45 289.5 46 281.5 47 285.5 48 275.0 49 248.0 50 217.0 51 166.5 52 138.5 53 124.5 54 105.0 55 75.0 56 48.5 57 37.0 58 30.0 59 25.5 60 17.0 61 7.0 62 5.0 63 5.5 64 3.0 65 1.0 66 0.5 67 1.0 68 1.5 69 1.5 70 2.0 71 1.0 72 0.0 73 0.0 74 0.5 75 1.0 76 1.5 77 2.0 78 1.0 79 0.0 80 0.5 81 1.5 82 1.5 83 0.5 84 1.0 85 1.5 86 2.0 87 1.5 88 1.0 89 1.5 90 1.5 91 1.5 92 2.0 93 1.5 94 1.5 95 3.0 96 2.5 97 3.0 98 5.0 99 7.0 100 7.0 >>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 89.60000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 90.234375 80.85 2 8.621651785714286 15.45 3 0.9207589285714286 2.475 4 0.08370535714285714 0.3 5 0.027901785714285712 0.125 6 0.055803571428571425 0.3 7 0.027901785714285712 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.027901785714285712 0.325 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 13 0.325 No Hit ACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCC 7 0.17500000000000002 No Hit CTCGCCTCAGATCTCTAGAATGTCGAGCGTTAACTTGGTAGTGATGGTGG 6 0.15 No Hit CACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTC 6 0.15 No Hit AGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATT 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 0.0 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 0.0125 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 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.07500000000000001 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.3125 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.4875 0.0 0.0 0.0 0.0 86-87 0.5375 0.0 0.0 0.0 0.0 88-89 0.7250000000000001 0.0 0.0 0.0 0.0 90-91 0.9125 0.0 0.0 0.0 0.0 92-93 1.0 0.0 0.0 0.0 0.0 94-95 1.1625 0.0 0.0 0.0 0.0 96-97 1.4 0.0 0.0 0.0 0.0 98-99 1.65 0.0 0.0 0.0 0.0 100-101 1.95 0.0 0.0 0.0 0.0 102-103 2.25 0.0 0.0 0.0 0.0 104-105 2.775 0.0 0.0 0.0 0.0 106-107 3.125 0.0 0.0 0.0 0.0 108-109 3.5625 0.0 0.0 0.0 0.0 110-111 4.1 0.0 0.0 0.0 0.0 112-113 4.6875 0.0 0.0 0.0 0.0 114-115 5.199999999999999 0.0 0.0 0.0 0.0 116-117 5.7875 0.0 0.0 0.0 0.0 118-119 6.5 0.0 0.0 0.0 0.0 120-121 7.1125 0.0 0.0 0.0 0.0 122-123 7.699999999999999 0.0 0.0 0.0 0.0 124-125 8.7625 0.0 0.0 0.0 0.0 126-127 9.825 0.0 0.0 0.0 0.0 128-129 10.575 0.0 0.0 0.0 0.0 130-131 11.5125 0.0 0.0 0.0 0.0 132-133 12.4125 0.0 0.0 0.0 0.0 134-135 13.65 0.0 0.0 0.0 0.0 136-137 14.8875 0.0 0.0 0.0 0.0 138-139 16.1625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTGCATC 10 0.006830828 145.0 2 ATCAGCT 10 0.006830828 145.0 6 GAAGAGC 90 0.0048656333 11.277777 135-139 >>END_MODULE Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra Read 984168 spots for SRR12690138.sra Written 984168 spots for SRR12690138.sra Read 984164 spots for SRR12690138.sra Written 984164 spots for SRR12690138.sra SRR ids: ['SRR12690138.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2dprvsh0 SRR12690138.sra spots: 19683284 blocks: [[1, 984164], [984165, 1968328], [1968329, 2952492], [2952493, 3936656], [3936657, 4920820], [4920821, 5904984], [5904985, 6889148], [6889149, 7873312], [7873313, 8857476], [8857477, 9841640], [9841641, 10825804], [10825805, 11809968], [11809969, 12794132], [12794133, 13778296], [13778297, 14762460], [14762461, 15746624], [15746625, 16730788], [16730789, 17714952], [17714953, 18699116], [18699117, 19683284]] SRR12690138 file size 6667540 SRR12690138 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 SRR12690138 SRR12690138_1.fastq SRR12690138_2.fastq Input file: SRR12690138_1.fastq Paired file: SRR12690138_2.fastq trimmed: SRR12690138-trimmed-pair1.fastq, SRR12690138-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 18:36:43 2025 >> started Mon Feb 10 18:37:14 2025 >> done (31.410s) 19683284 read pairs processed; of these: 156 ( 0.00%) short read pairs filtered out after trimming by size control 190078 ( 0.97%) empty read pairs filtered out after trimming by size control 19493050 (99.03%) read pairs available; of these: 4785949 (24.55%) trimmed read pairs available after processing 14707101 (75.45%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 8 0.00% 20 48 0.00% 21 39 0.00% 22 48 0.00% 23 60 0.00% 24 76 0.00% 25 108 0.00% 26 167 0.00% 27 138 0.00% 28 167 0.00% 29 166 0.00% 30 159 0.00% 31 216 0.00% 32 184 0.00% 33 203 0.00% 34 178 0.00% 35 175 0.00% 36 194 0.00% 37 184 0.00% 38 214 0.00% 39 275 0.00% 40 229 0.00% 41 262 0.00% 42 318 0.00% 43 305 0.00% 44 355 0.00% 45 350 0.00% 46 398 0.00% 47 336 0.00% 48 431 0.00% 49 492 0.00% 50 521 0.00% 51 548 0.00% 52 593 0.00% 53 657 0.00% 54 730 0.00% 55 688 0.00% 56 822 0.00% 57 810 0.00% 58 942 0.00% 59 973 0.00% 60 1081 0.01% 61 1166 0.01% 62 1308 0.01% 63 1380 0.01% 64 1433 0.01% 65 1607 0.01% 66 1768 0.01% 67 1923 0.01% 68 1958 0.01% 69 2223 0.01% 70 2470 0.01% 71 2784 0.01% 72 3128 0.02% 73 3505 0.02% 74 3822 0.02% 75 4294 0.02% 76 4675 0.02% 77 5301 0.03% 78 5687 0.03% 79 6045 0.03% 80 6952 0.04% 81 7754 0.04% 82 8491 0.04% 83 9248 0.05% 84 10181 0.05% 85 11347 0.06% 86 12174 0.06% 87 13241 0.07% 88 14165 0.07% 89 15345 0.08% 90 16505 0.08% 91 17959 0.09% 92 19383 0.10% 93 21466 0.11% 94 22704 0.12% 95 24851 0.13% 96 25931 0.13% 97 27308 0.14% 98 29269 0.15% 99 30749 0.16% 100 32264 0.17% 101 34016 0.17% 102 35604 0.18% 103 37547 0.19% 104 40102 0.21% 105 41792 0.21% 106 43397 0.22% 107 45562 0.23% 108 47482 0.24% 109 49482 0.25% 110 50725 0.26% 111 52141 0.27% 112 55013 0.28% 113 57148 0.29% 114 59094 0.30% 115 61952 0.32% 116 64798 0.33% 117 67112 0.34% 118 68754 0.35% 119 70263 0.36% 120 73420 0.38% 121 75910 0.39% 122 77393 0.40% 123 80604 0.41% 124 82756 0.42% 125 84930 0.44% 126 87728 0.45% 127 90221 0.46% 128 92727 0.48% 129 95442 0.49% 130 97635 0.50% 131 98447 0.51% 132 102072 0.52% 133 105356 0.54% 134 107479 0.55% 135 109771 0.56% 136 111430 0.57% 137 113461 0.58% 138 115053 0.59% 139 118545 0.61% 140 119193 0.61% 141 121349 0.62% 142 124416 0.64% 143 126905 0.65% 144 130488 0.67% 145 133597 0.69% 146 132564 0.68% 147 134860 0.69% 148 136257 0.70% 149 136299 0.70% 150 139030 0.71% 151 14707101 75.45% 19493050 reads passed initial QC criterion=sequence-density sequence-density=1.06 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=23 prefix-density=1.06 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=58.64 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=8.5 sequence=AACAAGAAATCAAGACACGAACATTCAGTGGTTCAAAACCAGCATTTATTGCACATTACATTACTTTATTCCCATGAAATAGCCCGGCCGAAGTCGTTACTCCTGAGCATTTAGTAGAGAAAGTAGTCTATCACAAGACGCTGTGACAAAGTAGGCAAAAATCCTTCTGCAAATGCAGCAAGAGCAGCAGAATCGAGGTACTCTTGCAAACCTGACTTGCTCTCAAATGTAGATTCAAAGGCATGAGTGTATCCTCGGTTTAGCTCCGCAGACTCCATGCCCAAATCCGTGCCCCAATTGAAACTCTTCATGGTTGGAATGAGATCGAGCAGATTGGTATAGTCATTAATGTAGTTGTCGATTTGTTCTCGTGTGATCTCATCCTTGAACCGAGTCAACAATGTGTGCTTCACAAGCTTTGGAGTTCTGGTTGCCATGTCTTCTCTTTCTCTCTATGGATGTATGCTGCTCTCT criterion=sequence-density sequence-density=0.91 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=25 prefix-density=0.89 prefix-fanout=2.0 sequence=TACCTTCTTCGC criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=94.86 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=6.7 sequence=ACAACTTCAAGGGCAGTAGTCTTAAACCATACTCTAAAATCTTCTTATAATTCCAGTTGTAATATTCTGCTAGCATATAATGGCTTCTTCAATGAGCTTGAAGCTGGCCTGTGCCATGCTTGTAGCGATGGTTGTTAGTGCACCACTAGCAGAAGCTGCCATCTCATGTGGCCAGGTGTCAAGCAGCTTGGCACAATGTATAACCTACCTCCAGAAGGGTGGGGCTGTGCCTGCAGCTTGCTGCAGTGGGTTGAAAGGACTTAATTCTGCAGCCACGACCACCGCCGACCGCCAAGGGGTCTGCAACTGTTTGAAATCCTTGGCTGGTAAGATCTCTGGCATCAACTATGGCGTGGCTGCTGGCCTCCCTTCAAAGTGTGGTGTATCCATCTCCTACAAAATCAGTCCTTCCACAGATTGCAAAAGCGTGAAGTGAAGAATTGAAGCAGATTATGAAGTATGATAATAAGCTAGTGCTAGAATAAAAGGGGTGCTCGAGCATGTTTGAGCT SRR12690138 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 18:37:55 Started mapping on | Feb 10 18:37:55 Finished on | Feb 10 18:40:15 Mapping speed, Million of reads per hour | 501.25 Number of input reads | 19493050 Average input read length | 290 UNIQUE READS: Uniquely mapped reads number | 18324807 Uniquely mapped reads % | 94.01% Average mapped length | 289.35 Number of splices: Total | 17923013 Number of splices: Annotated (sjdb) | 17608312 Number of splices: GT/AG | 17557284 Number of splices: GC/AG | 306279 Number of splices: AT/AC | 15810 Number of splices: Non-canonical | 43640 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.02% Deletion average length | 2.71 Insertion rate per base | 0.02% Insertion average length | 2.50 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 525349 % of reads mapped to multiple loci | 2.70% Number of reads mapped to too many loci | 262055 % of reads mapped to too many loci | 1.34% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.68% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 642894 642894 642894 N_multimapping 525349 525349 525349 N_noFeature 388785 18128253 438425 N_ambiguous 289927 785 142634 UnstrandedReadsAssigned:17646095 PositiveStrandReadsAssigned:195769 NegativeStrandReadsAssigned:17743748 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=144 echo kmer=139 SRR12690138 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: SRR12690138-trimmed-pair1.fastq SRR12690138-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,493,050 reads, 18,060,592 reads pseudoaligned [quant] estimated average fragment length: 184.241 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,173 rounds 52401 SRR12690138.ke.tsv 34699 SRR12690138.se.tsv 87100 total ==> SRR12690138.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1834.76 383 9.04594 Potri.005G024800.1.v4.1 1035 851.759 205 10.4297 Potri.004G059700.1.v4.1 961 777.759 98 5.46028 Potri.007G009000.2.v4.1 1416 1232.76 0 0 Potri.003G141000.2.v4.1 2943 2759.76 233 3.65863 Potri.016G087400.1.v4.1 270 97.6756 1774.5 787.27 Potri.015G069301.1.v4.1 564 381.014 0 0 Potri.010G195200.1.v4.1 1773 1589.76 12 0.327102 Potri.012G127500.1.v4.1 977 793.759 2024 110.498 ==> SRR12690138.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 54 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 408 Potri.001G212900.v4.1 34 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 32 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 5 SRR12690138 completed mapping pipeline successfully