Starting /dee2/code/volunteer_pipeline.sh SRR12671345 current disk space = 3048732930048 free memory = 1404012352 SRR12671345 SRAfilesize fb85694b232d101c7858e2633ad65905 SRR12671345.sra SRR12671345.sra file validated SRR12671345 is paired end SRR12671345 is conventional basespace SRR12671345 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671345_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 36.6745 37.0 37.0 37.0 37.0 37.0 2 36.39775 37.0 37.0 37.0 37.0 37.0 3 36.668 37.0 37.0 37.0 37.0 37.0 4 36.562 37.0 37.0 37.0 37.0 37.0 5 36.651 37.0 37.0 37.0 37.0 37.0 6 36.6805 37.0 37.0 37.0 37.0 37.0 7 36.5155 37.0 37.0 37.0 37.0 37.0 8 36.634 37.0 37.0 37.0 37.0 37.0 9 36.6605 37.0 37.0 37.0 37.0 37.0 10-14 36.635000000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.623799999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.588699999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.555899999999994 37.0 37.0 37.0 37.0 37.0 30-34 36.513999999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.504000000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.4922 37.0 37.0 37.0 37.0 37.0 45-49 36.4628 37.0 37.0 37.0 37.0 37.0 50-54 36.4327 37.0 37.0 37.0 37.0 37.0 55-59 36.399899999999995 37.0 37.0 37.0 37.0 37.0 60-64 36.412 37.0 37.0 37.0 37.0 37.0 65-69 36.3711 37.0 37.0 37.0 37.0 37.0 70-74 36.3692 37.0 37.0 37.0 37.0 37.0 75-79 36.345400000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.3236 37.0 37.0 37.0 37.0 37.0 85-89 36.2575 37.0 37.0 37.0 37.0 37.0 90-94 36.302 37.0 37.0 37.0 37.0 37.0 95-99 36.262899999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.23979999999999 37.0 37.0 37.0 37.0 37.0 105-109 36.244 37.0 37.0 37.0 37.0 37.0 110-114 36.18579999999999 37.0 37.0 37.0 37.0 37.0 115-119 36.1988 37.0 37.0 37.0 37.0 37.0 120-124 36.1426 37.0 37.0 37.0 37.0 37.0 125-129 36.14029999999999 37.0 37.0 37.0 37.0 37.0 130-134 36.071600000000004 37.0 37.0 37.0 37.0 37.0 135-139 36.080200000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.9014 37.0 37.0 37.0 37.0 37.0 145-149 35.9557 37.0 37.0 37.0 37.0 37.0 150-151 35.929 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 1.0 22 2.0 23 3.0 24 3.0 25 3.0 26 3.0 27 7.0 28 5.0 29 18.0 30 15.0 31 28.0 32 52.0 33 63.0 34 114.0 35 229.0 36 2957.0 37 495.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.625 11.75 5.800000000000001 34.825 2 19.63882618510158 12.214697767745172 37.873087534487084 30.273388512666166 3 19.85 16.425 27.975 35.75 4 23.5 23.425 23.599999999999998 29.475 5 23.974999999999998 29.549999999999997 25.174999999999997 21.3 6 19.625 33.7 23.075000000000003 23.599999999999998 7 14.875 27.325 41.15 16.650000000000002 8 16.975 25.974999999999998 33.475 23.575 9 15.925 24.099999999999998 35.949999999999996 24.025 10-14 19.580000000000002 30.195 27.875 22.35 15-19 20.22 28.51 27.66 23.61 20-24 19.925 27.965 28.384999999999998 23.724999999999998 25-29 20.115 28.53 28.54 22.814999999999998 30-34 20.5 28.720000000000002 27.55 23.23 35-39 20.03 28.335 28.175 23.46 40-44 19.865 29.42 27.465 23.25 45-49 19.64 28.82 27.41 24.13 50-54 20.21 28.389999999999997 27.400000000000002 24.0 55-59 19.79 28.505000000000003 28.335 23.369999999999997 60-64 20.064999999999998 28.99 27.38 23.565 65-69 19.634999999999998 28.83 27.76 23.775 70-74 19.945 28.875 27.474999999999998 23.705000000000002 75-79 20.674999999999997 28.185 28.02 23.119999999999997 80-84 20.630000000000003 28.26 27.29 23.82 85-89 20.855 28.315 27.05 23.78 90-94 20.87 27.689999999999998 27.55 23.89 95-99 20.45 27.6 28.060000000000002 23.89 100-104 20.775 28.084999999999997 27.36 23.78 105-109 20.865000000000002 28.68 26.584999999999997 23.87 110-114 20.794999999999998 28.63 27.224999999999998 23.35 115-119 21.654999999999998 28.215 26.650000000000002 23.48 120-124 21.615000000000002 27.67 27.12 23.595 125-129 21.279999999999998 28.74 26.779999999999998 23.200000000000003 130-134 20.965 27.73 27.400000000000002 23.905 135-139 21.01 28.249999999999996 27.3 23.44 140-144 21.785 27.435 27.015 23.765 145-149 20.94 28.585 27.025 23.45 150-151 21.95 27.6375 27.0 23.4125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 1.0 2 0.5 3 0.0 4 0.0 5 0.0 6 1.5 7 2.0 8 1.5 9 1.0 10 0.0 11 0.0 12 0.5 13 1.0 14 0.5 15 0.0 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 3.0 22 4.5 23 3.0 24 3.5 25 7.0 26 8.0 27 10.0 28 13.0 29 13.5 30 15.0 31 22.0 32 29.5 33 37.5 34 48.5 35 65.5 36 91.5 37 109.5 38 122.0 39 142.0 40 174.5 41 196.5 42 229.5 43 265.5 44 262.5 45 253.5 46 265.0 47 264.5 48 246.0 49 205.0 50 176.0 51 159.5 52 128.0 53 102.5 54 81.5 55 64.0 56 59.5 57 46.0 58 20.0 59 14.5 60 9.0 61 3.5 62 2.0 63 1.0 64 1.0 65 1.5 66 2.0 67 1.5 68 0.0 69 0.0 70 0.0 71 0.0 72 1.5 73 1.5 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 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.325 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.125 #Duplication Level Percentage of deduplicated Percentage of total 1 84.15037593984962 69.95 2 12.511278195488723 20.8 3 2.556390977443609 6.375 4 0.5112781954887218 1.7000000000000002 5 0.21052631578947367 0.8750000000000001 6 0.06015037593984962 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 GTTGCCAATTAAGCACCAGCTATCTAGATCTTTAAAAGGGAACTGGTTTT 6 0.15 No Hit GTCCATCATAGTACCCTGGGGACTGGTGGTGCTCGCGGTAGACCCAACCT 6 0.15 No Hit ATTCTGAGTATTACTTGCCATTTGAAAACAAAGAACTTGAAGTCATTTGC 5 0.125 No Hit GCCCGTATTGCTTTGAAAAATTGATCTCCCTGAATTCCGCGAGCGGCACT 5 0.125 No Hit GGCCTGGTCTTTCCTCAGAAAATCTTGGAAGTTGAACGAGTGAATTCACT 5 0.125 No Hit CCCAGGGCAAATTAAGGCACATTTTTTAAGAGGACAAGTTGTCAATAATG 5 0.125 No Hit AGAGGATTGAGTTTGTTCTTGACGTTCAGGGCTACGGATTTTTTTGGAAG 5 0.125 No Hit GTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACC 5 0.125 No Hit GTTGAATCGAACCACCACCGGGTAGCGGCTCCTGGGGTCCTGATCAACAG 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.16249999999999998 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.4 0.0 0.0 0.0 0.0 88-89 0.5375 0.0 0.0 0.0 0.0 90-91 0.625 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.7 0.0 0.0 0.0 0.0 96-97 0.8500000000000001 0.0 0.0 0.0 0.0 98-99 0.95 0.0 0.0 0.0 0.0 100-101 1.1125 0.0 0.0 0.0 0.0 102-103 1.25 0.0 0.0 0.0 0.0 104-105 1.4375 0.0 0.0 0.0 0.0 106-107 1.5 0.0 0.0 0.0 0.0 108-109 1.575 0.0 0.0 0.0 0.0 110-111 1.7374999999999998 0.0 0.0 0.0 0.0 112-113 1.9874999999999998 0.0 0.0 0.0 0.0 114-115 2.1125 0.0 0.0 0.0 0.0 116-117 2.2 0.0 0.0 0.0 0.0 118-119 2.4000000000000004 0.0 0.0 0.0 0.0 120-121 2.65 0.0 0.0 0.0 0.0 122-123 2.875 0.0 0.0 0.0 0.0 124-125 3.2125000000000004 0.0 0.0 0.0 0.0 126-127 3.475 0.0 0.0 0.0 0.0 128-129 3.575 0.0 0.0 0.0 0.0 130-131 3.7875 0.0 0.0 0.0 0.0 132-133 4.225 0.0 0.0 0.0 0.0 134-135 4.6125 0.0 0.0 0.0 0.0 136-137 4.95 0.0 0.0 0.0 0.0 138-139 5.3125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACTCTA 10 0.006830828 145.0 4 >>END_MODULE SRR12671345 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671345_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 36.35 37.0 37.0 37.0 37.0 37.0 2 36.1955 37.0 37.0 37.0 37.0 37.0 3 36.2855 37.0 37.0 37.0 37.0 37.0 4 36.3615 37.0 37.0 37.0 37.0 37.0 5 36.345 37.0 37.0 37.0 37.0 37.0 6 36.3765 37.0 37.0 37.0 37.0 37.0 7 36.2975 37.0 37.0 37.0 37.0 37.0 8 36.4045 37.0 37.0 37.0 37.0 37.0 9 36.4425 37.0 37.0 37.0 37.0 37.0 10-14 36.3908 37.0 37.0 37.0 37.0 37.0 15-19 36.4079 37.0 37.0 37.0 37.0 37.0 20-24 36.3147 37.0 37.0 37.0 37.0 37.0 25-29 36.283 37.0 37.0 37.0 37.0 37.0 30-34 36.2269 37.0 37.0 37.0 37.0 37.0 35-39 36.2352 37.0 37.0 37.0 37.0 37.0 40-44 36.2334 37.0 37.0 37.0 37.0 37.0 45-49 36.2068 37.0 37.0 37.0 37.0 37.0 50-54 36.1834 37.0 37.0 37.0 37.0 37.0 55-59 36.1553 37.0 37.0 37.0 37.0 37.0 60-64 36.142399999999995 37.0 37.0 37.0 37.0 37.0 65-69 36.131099999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.1132 37.0 37.0 37.0 37.0 37.0 75-79 36.069599999999994 37.0 37.0 37.0 37.0 37.0 80-84 36.0129 37.0 37.0 37.0 37.0 37.0 85-89 36.0656 37.0 37.0 37.0 37.0 37.0 90-94 36.0585 37.0 37.0 37.0 37.0 37.0 95-99 36.014599999999994 37.0 37.0 37.0 37.0 37.0 100-104 35.9987 37.0 37.0 37.0 37.0 37.0 105-109 35.885299999999994 37.0 37.0 37.0 37.0 37.0 110-114 35.8825 37.0 37.0 37.0 37.0 37.0 115-119 35.9568 37.0 37.0 37.0 37.0 37.0 120-124 35.8925 37.0 37.0 37.0 37.0 37.0 125-129 35.8666 37.0 37.0 37.0 37.0 37.0 130-134 35.7245 37.0 37.0 37.0 37.0 37.0 135-139 35.6823 37.0 37.0 37.0 37.0 37.0 140-144 35.7388 37.0 37.0 37.0 37.0 37.0 145-149 35.6342 37.0 37.0 37.0 37.0 37.0 150-151 35.34425 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 1.0 14 2.0 15 3.0 16 1.0 17 2.0 18 1.0 19 1.0 20 0.0 21 5.0 22 2.0 23 4.0 24 6.0 25 6.0 26 4.0 27 10.0 28 12.0 29 18.0 30 19.0 31 39.0 32 32.0 33 84.0 34 131.0 35 441.0 36 2818.0 37 356.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.974999999999994 22.95 8.924999999999999 24.15 2 27.224999999999998 25.825 31.2 15.75 3 21.425 27.925 33.275 17.375 4 24.95 34.725 22.7 17.625 5 24.45 39.074999999999996 21.05 15.425 6 20.575 39.4 22.05 17.974999999999998 7 19.45 22.025 38.925 19.6 8 20.474999999999998 25.15 29.95 24.425 9 22.75 24.25 29.2 23.799999999999997 10-14 23.69 29.005 26.279999999999998 21.025 15-19 23.715 27.200000000000003 27.544999999999998 21.54 20-24 23.365 28.515 27.439999999999998 20.68 25-29 23.455000000000002 27.544999999999998 28.189999999999998 20.810000000000002 30-34 22.925 27.994999999999997 27.884999999999998 21.195 35-39 22.895 27.77 27.339999999999996 21.995 40-44 23.244999999999997 27.435 28.084999999999997 21.235 45-49 23.0 27.465 28.15 21.385 50-54 23.57 27.605 27.07 21.755 55-59 23.56 27.24 27.785 21.415 60-64 22.86 27.865000000000002 27.93 21.345 65-69 22.89 27.85 28.01 21.25 70-74 23.535 27.62 27.534999999999997 21.310000000000002 75-79 23.25 27.455000000000002 27.275 22.02 80-84 23.630000000000003 27.495000000000005 27.175 21.7 85-89 23.575 28.08 27.205000000000002 21.14 90-94 23.724999999999998 26.905 27.965 21.404999999999998 95-99 24.015 27.66 27.275 21.05 100-104 24.015 27.060000000000002 27.43 21.495 105-109 23.68 27.625 27.04 21.654999999999998 110-114 24.395 27.775 26.974999999999998 20.855 115-119 24.044999999999998 27.925 27.060000000000002 20.97 120-124 24.33 27.560000000000002 27.405 20.705000000000002 125-129 24.845 27.650000000000002 27.155 20.349999999999998 130-134 24.29 28.165000000000003 27.229999999999997 20.315 135-139 24.65 27.24 27.98 20.13 140-144 24.705 27.439999999999998 27.589999999999996 20.265 145-149 26.65766576657666 27.567756775677566 25.81258125812581 19.96199619961996 150-151 25.324999999999996 28.075 27.0875 19.5125 >>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 0.5 6 0.5 7 0.5 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 1.0 17 1.5 18 0.5 19 0.5 20 1.5 21 1.0 22 1.5 23 2.5 24 1.5 25 2.0 26 2.5 27 1.5 28 4.0 29 7.0 30 9.0 31 12.5 32 19.5 33 34.0 34 54.0 35 62.5 36 67.5 37 95.5 38 132.0 39 166.0 40 176.5 41 186.5 42 233.5 43 278.5 44 281.0 45 259.0 46 257.5 47 269.5 48 253.0 49 223.0 50 190.0 51 153.5 52 121.0 53 95.0 54 89.5 55 71.5 56 47.0 57 33.0 58 24.0 59 19.5 60 12.5 61 6.0 62 7.5 63 7.0 64 1.5 65 2.0 66 3.0 67 1.5 68 0.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.5 81 0.5 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.5 88 1.0 89 0.5 90 0.0 91 0.0 92 0.0 93 0.0 94 1.5 95 1.5 96 1.0 97 1.0 98 0.5 99 0.5 100 1.0 >>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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 84.37876960193003 69.95 2 12.092882991556092 20.05 3 2.6537997587454765 6.6000000000000005 4 0.5126658624849216 1.7000000000000002 5 0.27141133896260555 1.125 6 0.060313630880579006 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.030156815440289503 0.27499999999999997 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 11 0.27499999999999997 No Hit ACGCCAGGCAGATCGCCTTATTAAGATTGGGTTGGAGGGCTTTGCGGCCA 6 0.15 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 6 0.15 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit GGAAGTTGGGGCACTTCAATTGTTGGCGAAGACTATGCCATGTTGGTTAA 5 0.125 No Hit CTTCGATTAACAGCTGGTGTCTCACCTCTGTCTCTGCCTCTAAGAGATCA 5 0.125 No Hit TGGAAGCTTAAATACCCAACTTCAAAGATGGATGACTGTGCTGTTGTTTG 5 0.125 No Hit ATTTGTTATTAAGTATATTGCAGAAATTGAGCCCACACACGAGCCGCTTT 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit GGAAAATCCAAGAAGGGTGTTGTTGATGAAACTCAAAGGCTGGCAATGGA 5 0.125 No Hit CCACAGTTAACCGCACCCCTGCACAGGCCAACATGGTTGCACCATTCAAC 5 0.125 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.16249999999999998 0.0 0.0 0.0 0.0 84-85 0.2625 0.0 0.0 0.0 0.0 86-87 0.4125 0.0 0.0 0.0 0.0 88-89 0.5625 0.0 0.0 0.0 0.0 90-91 0.65 0.0 0.0 0.0 0.0 92-93 0.7 0.0 0.0 0.0 0.0 94-95 0.725 0.0 0.0 0.0 0.0 96-97 0.875 0.0 0.0 0.0 0.0 98-99 0.975 0.0 0.0 0.0 0.0 100-101 1.1375 0.0 0.0 0.0 0.0 102-103 1.25 0.0 0.0 0.0 0.0 104-105 1.4375 0.0 0.0 0.0 0.0 106-107 1.5 0.0 0.0 0.0 0.0 108-109 1.575 0.0 0.0 0.0 0.0 110-111 1.7374999999999998 0.0 0.0 0.0 0.0 112-113 1.9874999999999998 0.0 0.0 0.0 0.0 114-115 2.1125 0.0 0.0 0.0 0.0 116-117 2.2 0.0 0.0 0.0 0.0 118-119 2.4125 0.0 0.0 0.0 0.0 120-121 2.675 0.0 0.0 0.0 0.0 122-123 2.9000000000000004 0.0 0.0 0.0 0.0 124-125 3.2375 0.0 0.0 0.0 0.0 126-127 3.5 0.0 0.0 0.0 0.0 128-129 3.5999999999999996 0.0 0.0 0.0 0.0 130-131 3.8125 0.0 0.0 0.0 0.0 132-133 4.25 0.0 0.0 0.0 0.0 134-135 4.6375 0.0 0.0 0.0 0.0 136-137 4.975 0.0 0.0 0.0 0.0 138-139 5.3375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGCTTC 10 0.006830828 145.0 8 >>END_MODULE Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035461 spots for SRR12671345.sra Written 1035461 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra Read 1035450 spots for SRR12671345.sra Written 1035450 spots for SRR12671345.sra SRR ids: ['SRR12671345.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dijo91pz SRR12671345.sra spots: 20709011 blocks: [[1, 1035450], [1035451, 2070900], [2070901, 3106350], [3106351, 4141800], [4141801, 5177250], [5177251, 6212700], [6212701, 7248150], [7248151, 8283600], [8283601, 9319050], [9319051, 10354500], [10354501, 11389950], [11389951, 12425400], [12425401, 13460850], [13460851, 14496300], [14496301, 15531750], [15531751, 16567200], [16567201, 17602650], [17602651, 18638100], [18638101, 19673550], [19673551, 20709011]] SRR12671345 file size 7016127 SRR12671345 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 SRR12671345 SRR12671345_1.fastq SRR12671345_2.fastq Input file: SRR12671345_1.fastq Paired file: SRR12671345_2.fastq trimmed: SRR12671345-trimmed-pair1.fastq, SRR12671345-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 16:41:50 2025 >> started Tue Feb 11 16:42:13 2025 >> done (23.816s) 20709011 read pairs processed; of these: 203 ( 0.00%) short read pairs filtered out after trimming by size control 11463 ( 0.06%) empty read pairs filtered out after trimming by size control 20697345 (99.94%) read pairs available; of these: 1595870 ( 7.71%) trimmed read pairs available after processing 19101475 (92.29%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 14 0.00% 19 24 0.00% 20 15 0.00% 21 12 0.00% 22 20 0.00% 23 23 0.00% 24 29 0.00% 25 24 0.00% 26 32 0.00% 27 32 0.00% 28 38 0.00% 29 34 0.00% 30 33 0.00% 31 43 0.00% 32 30 0.00% 33 29 0.00% 34 32 0.00% 35 38 0.00% 36 30 0.00% 37 50 0.00% 38 33 0.00% 39 46 0.00% 40 55 0.00% 41 41 0.00% 42 41 0.00% 43 62 0.00% 44 51 0.00% 45 58 0.00% 46 63 0.00% 47 79 0.00% 48 88 0.00% 49 83 0.00% 50 100 0.00% 51 128 0.00% 52 143 0.00% 53 126 0.00% 54 158 0.00% 55 151 0.00% 56 187 0.00% 57 208 0.00% 58 222 0.00% 59 292 0.00% 60 334 0.00% 61 337 0.00% 62 442 0.00% 63 521 0.00% 64 548 0.00% 65 583 0.00% 66 660 0.00% 67 743 0.00% 68 895 0.00% 69 989 0.00% 70 1099 0.01% 71 1222 0.01% 72 1436 0.01% 73 1569 0.01% 74 1704 0.01% 75 1975 0.01% 76 2210 0.01% 77 2382 0.01% 78 2572 0.01% 79 2923 0.01% 80 3209 0.02% 81 3528 0.02% 82 3873 0.02% 83 4300 0.02% 84 4750 0.02% 85 5161 0.02% 86 5576 0.03% 87 5911 0.03% 88 6365 0.03% 89 6239 0.03% 90 6825 0.03% 91 7302 0.04% 92 7709 0.04% 93 8310 0.04% 94 9078 0.04% 95 9740 0.05% 96 10241 0.05% 97 10903 0.05% 98 10845 0.05% 99 11253 0.05% 100 11983 0.06% 101 12152 0.06% 102 13055 0.06% 103 13517 0.07% 104 13871 0.07% 105 14780 0.07% 106 15542 0.08% 107 15918 0.08% 108 16473 0.08% 109 16995 0.08% 110 17184 0.08% 111 18007 0.09% 112 18746 0.09% 113 18656 0.09% 114 19699 0.10% 115 20248 0.10% 116 21225 0.10% 117 22179 0.11% 118 22615 0.11% 119 22914 0.11% 120 23825 0.12% 121 24801 0.12% 122 24964 0.12% 123 25409 0.12% 124 26572 0.13% 125 26520 0.13% 126 27946 0.14% 127 28839 0.14% 128 29166 0.14% 129 30731 0.15% 130 31112 0.15% 131 31196 0.15% 132 31813 0.15% 133 32794 0.16% 134 33211 0.16% 135 34340 0.17% 136 35419 0.17% 137 35821 0.17% 138 36430 0.18% 139 38769 0.19% 140 38984 0.19% 141 39443 0.19% 142 40020 0.19% 143 40773 0.20% 144 41561 0.20% 145 41806 0.20% 146 43343 0.21% 147 44390 0.21% 148 46367 0.22% 149 46474 0.22% 150 48013 0.23% 151 19101475 92.29% 20697345 reads passed initial QC criterion=sequence-density sequence-density=0.71 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=19 prefix-density=0.72 prefix-fanout=2.0 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=24 fanout-score=323.90 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=13.6 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCGGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=sequence-density sequence-density=0.72 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=19 prefix-density=0.73 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=12.46 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=2.3 sequence=CCACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTC SRR12671345 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 16:42:58 Started mapping on | Feb 11 16:42:58 Finished on | Feb 11 16:45:09 Mapping speed, Million of reads per hour | 568.78 Number of input reads | 20697345 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 19400137 Uniquely mapped reads % | 93.73% Average mapped length | 296.73 Number of splices: Total | 19248071 Number of splices: Annotated (sjdb) | 18882994 Number of splices: GT/AG | 18863304 Number of splices: GC/AG | 321106 Number of splices: AT/AC | 11893 Number of splices: Non-canonical | 51768 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.03% Deletion average length | 2.91 Insertion rate per base | 0.02% Insertion average length | 2.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 469568 % of reads mapped to multiple loci | 2.27% Number of reads mapped to too many loci | 35816 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.72% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 827640 827640 827640 N_multimapping 469568 469568 469568 N_noFeature 583140 19040709 689813 N_ambiguous 380197 1319 126801 UnstrandedReadsAssigned:18436800 PositiveStrandReadsAssigned:358109 NegativeStrandReadsAssigned:18583523 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671345 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: SRR12671345-trimmed-pair1.fastq SRR12671345-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,697,345 reads, 18,541,887 reads pseudoaligned [quant] estimated average fragment length: 266.784 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,104 rounds 52401 SRR12671345.ke.tsv 34699 SRR12671345.se.tsv 87100 total ==> SRR12671345.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1752.22 497 11.9181 Potri.005G024800.1.v4.1 1035 769.216 209 11.4166 Potri.004G059700.1.v4.1 961 695.335 3 0.181286 Potri.007G009000.2.v4.1 1416 1150.22 0 0 Potri.003G141000.2.v4.1 2943 2677.22 935 14.6746 Potri.016G087400.1.v4.1 270 77.4946 936 507.506 Potri.015G069301.1.v4.1 564 309.201 0 0 Potri.010G195200.1.v4.1 1773 1507.22 68 1.8957 Potri.012G127500.1.v4.1 977 711.296 161 9.5107 ==> SRR12671345.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 198 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 397 Potri.001G212900.v4.1 11 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR12671345 completed mapping pipeline successfully