Starting /dee2/code/volunteer_pipeline.sh SRR12666468 current disk space = 1542980255744 free memory = 1596900844 SRR12666468 SRAfilesize 37810911f38b14e64bc87b79de209efb SRR12666468.sra SRR12666468.sra file validated SRR12666468 is paired end SRR12666468 is conventional basespace SRR12666468 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666468_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4615 37.0 37.0 37.0 37.0 37.0 2 36.336 37.0 37.0 37.0 37.0 37.0 3 36.507 37.0 37.0 37.0 37.0 37.0 4 36.5085 37.0 37.0 37.0 37.0 37.0 5 36.573 37.0 37.0 37.0 37.0 37.0 6 36.5825 37.0 37.0 37.0 37.0 37.0 7 36.533 37.0 37.0 37.0 37.0 37.0 8 36.576 37.0 37.0 37.0 37.0 37.0 9 36.555 37.0 37.0 37.0 37.0 37.0 10-14 36.539100000000005 37.0 37.0 37.0 37.0 37.0 15-19 36.5604 37.0 37.0 37.0 37.0 37.0 20-24 36.5088 37.0 37.0 37.0 37.0 37.0 25-29 36.470800000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.4738 37.0 37.0 37.0 37.0 37.0 35-39 36.422900000000006 37.0 37.0 37.0 37.0 37.0 40-44 36.4099 37.0 37.0 37.0 37.0 37.0 45-49 36.3735 37.0 37.0 37.0 37.0 37.0 50-54 36.39 37.0 37.0 37.0 37.0 37.0 55-59 36.3327 37.0 37.0 37.0 37.0 37.0 60-64 36.3626 37.0 37.0 37.0 37.0 37.0 65-69 36.28349999999999 37.0 37.0 37.0 37.0 37.0 70-74 36.3397 37.0 37.0 37.0 37.0 37.0 75-79 36.2937 37.0 37.0 37.0 37.0 37.0 80-84 36.2744 37.0 37.0 37.0 37.0 37.0 85-89 36.239999999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.206999999999994 37.0 37.0 37.0 37.0 37.0 95-99 36.1634 37.0 37.0 37.0 37.0 37.0 100-104 36.1558 37.0 37.0 37.0 37.0 37.0 105-109 36.22189999999999 37.0 37.0 37.0 37.0 37.0 110-114 36.118399999999994 37.0 37.0 37.0 37.0 37.0 115-119 36.071999999999996 37.0 37.0 37.0 37.0 37.0 120-124 36.0538 37.0 37.0 37.0 37.0 37.0 125-129 35.9879 37.0 37.0 37.0 37.0 37.0 130-134 36.0241 37.0 37.0 37.0 37.0 37.0 135-139 35.9611 37.0 37.0 37.0 37.0 37.0 140-144 35.8264 37.0 37.0 37.0 37.0 37.0 145-149 35.7359 37.0 37.0 37.0 37.0 37.0 150-151 35.47125 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 25 2.0 26 3.0 27 11.0 28 13.0 29 17.0 30 27.0 31 35.0 32 55.0 33 95.0 34 137.0 35 301.0 36 2855.0 37 449.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.9 11.375 8.975 38.75 2 21.47147147147147 16.441441441441444 36.711711711711715 25.375375375375377 3 20.0 21.525 26.25 32.225 4 26.125 29.275000000000002 20.1 24.5 5 25.05 33.324999999999996 22.45 19.175 6 20.325 34.5 24.05 21.125 7 16.075 21.625 42.65 19.650000000000002 8 19.05 22.075 29.625 29.25 9 20.549999999999997 20.3 31.825 27.325 10-14 22.445 27.3 24.97 25.285000000000004 15-19 22.28 26.165 25.85 25.705 20-24 23.03 25.41 26.205000000000002 25.355 25-29 22.634999999999998 26.295 26.135 24.935 30-34 23.09 25.924999999999997 25.385 25.6 35-39 22.86 25.965 25.755 25.419999999999998 40-44 22.55 26.400000000000002 25.264999999999997 25.785000000000004 45-49 22.875 25.69 25.424999999999997 26.009999999999998 50-54 23.0 25.729999999999997 26.05 25.22 55-59 23.494999999999997 26.11 25.36 25.035 60-64 23.135 25.779999999999998 25.669999999999998 25.415 65-69 23.215 25.885 25.490000000000002 25.41 70-74 23.14 26.275 24.9 25.685000000000002 75-79 23.06 25.740000000000002 25.415 25.785000000000004 80-84 23.355 25.679999999999996 25.005 25.96 85-89 22.875 26.07 26.1 24.955 90-94 23.325000000000003 26.02 25.215 25.44 95-99 23.119999999999997 25.974999999999998 25.61 25.295 100-104 22.925 25.874999999999996 25.324999999999996 25.874999999999996 105-109 23.845 25.474999999999998 24.725 25.955000000000002 110-114 23.145 25.224999999999998 25.835 25.795 115-119 23.75 25.840000000000003 25.39 25.019999999999996 120-124 23.91 25.729999999999997 25.055 25.305 125-129 23.855 25.174999999999997 25.319999999999997 25.650000000000002 130-134 23.745 26.090000000000003 24.37 25.795 135-139 24.15 26.150000000000002 24.135 25.564999999999998 140-144 24.165 26.275 24.59 24.97 145-149 23.845 25.369999999999997 24.97 25.814999999999998 150-151 24.637500000000003 26.5 23.65 25.2125 >>END_MODULE >>Per sequence GC content fail #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 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.5 24 0.5 25 0.0 26 0.0 27 1.5 28 2.0 29 4.0 30 8.5 31 9.5 32 18.5 33 25.0 34 28.5 35 40.0 36 44.0 37 55.5 38 82.5 39 111.5 40 131.5 41 140.0 42 157.5 43 194.5 44 219.5 45 216.5 46 214.0 47 216.5 48 194.5 49 189.0 50 186.5 51 163.5 52 143.0 53 124.5 54 118.0 55 108.5 56 98.0 57 89.5 58 75.5 59 71.0 60 64.5 61 57.5 62 57.0 63 51.0 64 49.5 65 45.5 66 42.0 67 38.5 68 32.5 69 23.0 70 16.5 71 15.0 72 9.5 73 4.5 74 3.0 75 2.5 76 2.0 77 1.0 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 0.1 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 90.85 #Duplication Level Percentage of deduplicated Percentage of total 1 90.97413318657127 82.65 2 8.145294441386902 14.799999999999999 3 0.7429829389102918 2.025 4 0.1100715465052284 0.4 5 0.0275178866263071 0.125 6 0.0 0.0 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 GTAGAGGATATGCTTCGGCAGGTAAGGCTCCTCCTCGACATCGAAGGCCT 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 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.25 0.0 0.0 0.0 0.0 88-89 0.3375 0.0 0.0 0.0 0.0 90-91 0.3625 0.0 0.0 0.0 0.0 92-93 0.4125 0.0 0.0 0.0 0.0 94-95 0.5249999999999999 0.0 0.0 0.0 0.0 96-97 0.6375 0.0 0.0 0.0 0.0 98-99 0.675 0.0 0.0 0.0 0.0 100-101 0.75 0.0 0.0 0.0 0.0 102-103 0.85 0.0 0.0 0.0 0.0125 104-105 0.925 0.0 0.0 0.0 0.025 106-107 1.075 0.0 0.0 0.0 0.025 108-109 1.3 0.0 0.0 0.0 0.025 110-111 1.4875 0.0 0.0 0.0 0.025 112-113 1.6749999999999998 0.0 0.0 0.0 0.025 114-115 1.8125 0.0 0.0 0.0 0.025 116-117 2.0375 0.0 0.0 0.0 0.025 118-119 2.3875 0.0 0.0 0.0 0.025 120-121 2.7750000000000004 0.0 0.0 0.0 0.025 122-123 3.225 0.0 0.0 0.0 0.025 124-125 3.5625 0.0 0.0 0.0 0.025 126-127 3.8375 0.0 0.0 0.0 0.025 128-129 4.4375 0.0 0.0 0.0 0.025 130-131 4.9625 0.0 0.0 0.0 0.025 132-133 5.512499999999999 0.0 0.0 0.0 0.025 134-135 6.25 0.0 0.0 0.0 0.025 136-137 6.9375 0.0 0.0 0.0 0.025 138-139 7.475 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACACGT 30 0.0014437955 24.166668 140-144 >>END_MODULE SRR12666468 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666468_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.002 37.0 37.0 37.0 37.0 37.0 2 35.7655 37.0 37.0 37.0 37.0 37.0 3 35.995 37.0 37.0 37.0 37.0 37.0 4 36.1455 37.0 37.0 37.0 37.0 37.0 5 36.1825 37.0 37.0 37.0 37.0 37.0 6 36.175 37.0 37.0 37.0 37.0 37.0 7 36.0935 37.0 37.0 37.0 37.0 37.0 8 36.167 37.0 37.0 37.0 37.0 37.0 9 36.2035 37.0 37.0 37.0 37.0 37.0 10-14 36.2495 37.0 37.0 37.0 37.0 37.0 15-19 36.1636 37.0 37.0 37.0 37.0 37.0 20-24 36.1605 37.0 37.0 37.0 37.0 37.0 25-29 36.1421 37.0 37.0 37.0 37.0 37.0 30-34 36.1194 37.0 37.0 37.0 37.0 37.0 35-39 36.1242 37.0 37.0 37.0 37.0 37.0 40-44 36.1139 37.0 37.0 37.0 37.0 37.0 45-49 36.0647 37.0 37.0 37.0 37.0 37.0 50-54 35.9871 37.0 37.0 37.0 37.0 37.0 55-59 36.0043 37.0 37.0 37.0 37.0 37.0 60-64 35.9567 37.0 37.0 37.0 37.0 37.0 65-69 35.941700000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.949200000000005 37.0 37.0 37.0 37.0 37.0 75-79 35.906800000000004 37.0 37.0 37.0 37.0 37.0 80-84 35.8299 37.0 37.0 37.0 37.0 37.0 85-89 35.8589 37.0 37.0 37.0 37.0 37.0 90-94 35.88440000000001 37.0 37.0 37.0 37.0 37.0 95-99 35.8237 37.0 37.0 37.0 37.0 37.0 100-104 35.8707 37.0 37.0 37.0 37.0 37.0 105-109 35.7688 37.0 37.0 37.0 37.0 37.0 110-114 35.7395 37.0 37.0 37.0 37.0 37.0 115-119 35.627599999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.7791 37.0 37.0 37.0 37.0 37.0 125-129 35.7748 37.0 37.0 37.0 37.0 37.0 130-134 35.661500000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.5215 37.0 37.0 37.0 37.0 37.0 140-144 35.4406 37.0 37.0 37.0 37.0 37.0 145-149 35.362100000000005 37.0 37.0 37.0 37.0 37.0 150-151 35.07775 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 2.0 15 1.0 16 1.0 17 2.0 18 1.0 19 1.0 20 4.0 21 1.0 22 7.0 23 10.0 24 8.0 25 11.0 26 11.0 27 14.0 28 21.0 29 16.0 30 27.0 31 45.0 32 54.0 33 78.0 34 202.0 35 494.0 36 2638.0 37 350.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.575 15.225 10.549999999999999 32.65 2 27.375 21.15 31.8 19.675 3 24.474999999999998 24.349999999999998 29.375 21.8 4 27.075 31.924999999999997 19.025 21.975 5 27.825 31.900000000000002 20.625 19.650000000000002 6 21.55 34.725 20.45 23.275000000000002 7 22.15 15.625 38.05 24.175 8 22.325 21.7 23.799999999999997 32.175 9 23.225 22.15 26.025 28.599999999999998 10-14 25.745 26.1 22.830000000000002 25.324999999999996 15-19 26.064999999999998 25.330000000000002 23.925 24.68 20-24 25.06 25.44 24.58 24.92 25-29 26.145000000000003 24.825 24.97 24.060000000000002 30-34 25.28 24.94 24.985 24.795 35-39 25.535000000000004 25.455 24.185000000000002 24.825 40-44 25.35 25.035 24.84 24.775 45-49 25.6 25.130000000000003 24.825 24.445 50-54 25.6 25.83 24.759999999999998 23.810000000000002 55-59 26.095000000000002 25.88 24.165 23.86 60-64 25.480000000000004 25.05 25.335 24.135 65-69 25.924999999999997 25.180000000000003 25.419999999999998 23.474999999999998 70-74 25.82 24.990000000000002 24.865000000000002 24.325 75-79 26.395000000000003 25.16 24.545 23.9 80-84 26.179999999999996 25.455 25.085 23.28 85-89 26.125 25.485000000000003 24.935 23.455000000000002 90-94 26.029999999999998 25.605 24.47 23.895 95-99 25.740000000000002 25.619999999999997 25.045 23.595 100-104 26.035000000000004 25.945 24.59 23.43 105-109 26.035000000000004 25.535000000000004 24.795 23.635 110-114 26.27 25.619999999999997 24.54 23.57 115-119 26.479999999999997 25.805 24.525 23.189999999999998 120-124 26.555 25.61 24.86 22.975 125-129 26.985 25.745 24.6 22.67 130-134 26.63 26.400000000000002 24.275 22.695 135-139 27.439999999999998 25.645 24.705 22.21 140-144 27.224999999999998 26.275 24.11 22.39 145-149 27.565 25.509999999999998 24.14 22.785 150-151 27.625 25.112499999999997 24.6625 22.6 >>END_MODULE >>Per sequence GC content fail #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 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.0 23 1.0 24 1.0 25 1.0 26 1.0 27 1.0 28 2.0 29 4.0 30 4.5 31 7.5 32 13.5 33 13.0 34 20.0 35 37.0 36 47.0 37 51.0 38 66.0 39 96.0 40 122.5 41 141.0 42 154.0 43 180.5 44 193.5 45 182.5 46 180.0 47 184.5 48 176.5 49 167.5 50 160.0 51 148.5 52 149.0 53 132.0 54 125.5 55 116.0 56 95.5 57 94.0 58 85.5 59 84.5 60 82.5 61 76.0 62 77.0 63 77.5 64 63.0 65 52.5 66 57.0 67 54.0 68 46.0 69 45.0 70 35.5 71 20.0 72 20.5 73 16.0 74 7.5 75 5.0 76 4.5 77 3.5 78 1.0 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.5 89 1.5 90 1.5 91 0.5 92 0.0 93 0.0 94 0.0 95 0.5 96 1.0 97 0.5 98 0.5 99 0.5 100 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 90.925 #Duplication Level Percentage of deduplicated Percentage of total 1 91.28402529557327 83.0 2 7.72614792411328 14.05 3 0.8248556502612043 2.25 4 0.10998075336816059 0.4 5 0.027495188342040146 0.125 6 0.0 0.0 7 0.027495188342040146 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 7 0.17500000000000002 No Hit AGGAGTTCCACAAGGAAACCTGCCGCAAGGTGAAAGCGCTCCATCAGTAT 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 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1125 0.0 0.0 0.0 0.0 80-81 0.1375 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.25 0.0 0.0 0.0 0.0 88-89 0.3375 0.0 0.0 0.0 0.0 90-91 0.3625 0.0 0.0 0.0 0.0 92-93 0.4125 0.0 0.0 0.0 0.0 94-95 0.5249999999999999 0.0 0.0 0.0 0.0 96-97 0.6375 0.0 0.0 0.0 0.0 98-99 0.675 0.0 0.0 0.0 0.0 100-101 0.7625 0.0 0.0 0.0 0.0 102-103 0.875 0.0 0.0 0.0 0.0 104-105 0.95 0.0 0.0 0.0 0.0 106-107 1.1 0.0 0.0 0.0 0.0 108-109 1.325 0.0 0.0 0.0 0.0 110-111 1.5375 0.0 0.0 0.0 0.0 112-113 1.725 0.0 0.0 0.0 0.0 114-115 1.8624999999999998 0.0 0.0 0.0 0.0 116-117 2.0999999999999996 0.0 0.0 0.0 0.0 118-119 2.45 0.0 0.0 0.0 0.0 120-121 2.825 0.0 0.0 0.0 0.0 122-123 3.275 0.0 0.0 0.0 0.0 124-125 3.65 0.0 0.0 0.0 0.0 126-127 3.9375 0.0 0.0 0.0 0.0 128-129 4.512499999999999 0.0 0.0 0.0 0.0 130-131 5.0125 0.0 0.0 0.0 0.0 132-133 5.5625 0.0 0.0 0.0 0.0 134-135 6.300000000000001 0.0 0.0 0.0 0.0 136-137 6.9625 0.0 0.0 0.0 0.0 138-139 7.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTTGG 10 0.006830828 145.0 5 CGTCGTG 35 0.0035366106 20.714287 140-144 >>END_MODULE Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724159 spots for SRR12666468.sra Written 1724159 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra Read 1724144 spots for SRR12666468.sra Written 1724144 spots for SRR12666468.sra SRR ids: ['SRR12666468.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5f19m3nh SRR12666468.sra spots: 34482895 blocks: [[1, 1724144], [1724145, 3448288], [3448289, 5172432], [5172433, 6896576], [6896577, 8620720], [8620721, 10344864], [10344865, 12069008], [12069009, 13793152], [13793153, 15517296], [15517297, 17241440], [17241441, 18965584], [18965585, 20689728], [20689729, 22413872], [22413873, 24138016], [24138017, 25862160], [25862161, 27586304], [27586305, 29310448], [29310449, 31034592], [31034593, 32758736], [32758737, 34482895]] SRR12666468 file size 11697095 SRR12666468 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 SRR12666468 SRR12666468_1.fastq SRR12666468_2.fastq Input file: SRR12666468_1.fastq Paired file: SRR12666468_2.fastq trimmed: SRR12666468-trimmed-pair1.fastq, SRR12666468-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 Sat Dec 7 13:52:32 2024 >> started Sat Dec 7 13:53:33 2024 >> done (60.808s) 34482895 read pairs processed; of these: 60 ( 0.00%) short read pairs filtered out after trimming by size control 14482 ( 0.04%) empty read pairs filtered out after trimming by size control 34468353 (99.96%) read pairs available; of these: 3580552 (10.39%) trimmed read pairs available after processing 30887801 (89.61%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 12 0.00% 20 6 0.00% 21 15 0.00% 22 18 0.00% 23 16 0.00% 24 21 0.00% 25 26 0.00% 26 19 0.00% 27 33 0.00% 28 35 0.00% 29 29 0.00% 30 37 0.00% 31 35 0.00% 32 36 0.00% 33 57 0.00% 34 39 0.00% 35 46 0.00% 36 56 0.00% 37 53 0.00% 38 86 0.00% 39 86 0.00% 40 85 0.00% 41 64 0.00% 42 94 0.00% 43 70 0.00% 44 91 0.00% 45 107 0.00% 46 112 0.00% 47 94 0.00% 48 145 0.00% 49 159 0.00% 50 162 0.00% 51 175 0.00% 52 193 0.00% 53 202 0.00% 54 212 0.00% 55 255 0.00% 56 246 0.00% 57 296 0.00% 58 342 0.00% 59 345 0.00% 60 429 0.00% 61 460 0.00% 62 534 0.00% 63 592 0.00% 64 635 0.00% 65 618 0.00% 66 708 0.00% 67 847 0.00% 68 910 0.00% 69 987 0.00% 70 1163 0.00% 71 1314 0.00% 72 1614 0.00% 73 1854 0.01% 74 1903 0.01% 75 2203 0.01% 76 2558 0.01% 77 2724 0.01% 78 3073 0.01% 79 3511 0.01% 80 3926 0.01% 81 4311 0.01% 82 5266 0.02% 83 5630 0.02% 84 6204 0.02% 85 6950 0.02% 86 7461 0.02% 87 8168 0.02% 88 8980 0.03% 89 9656 0.03% 90 10853 0.03% 91 11890 0.03% 92 13110 0.04% 93 14631 0.04% 94 15952 0.05% 95 17493 0.05% 96 18302 0.05% 97 19770 0.06% 98 20025 0.06% 99 21592 0.06% 100 22876 0.07% 101 24584 0.07% 102 26394 0.08% 103 28333 0.08% 104 30377 0.09% 105 32001 0.09% 106 33047 0.10% 107 34125 0.10% 108 35679 0.10% 109 36879 0.11% 110 38297 0.11% 111 40569 0.12% 112 43020 0.12% 113 44772 0.13% 114 46849 0.14% 115 48762 0.14% 116 50641 0.15% 117 51929 0.15% 118 52558 0.15% 119 54036 0.16% 120 55522 0.16% 121 56787 0.16% 122 59013 0.17% 123 61863 0.18% 124 64725 0.19% 125 66275 0.19% 126 67801 0.20% 127 69904 0.20% 128 70601 0.20% 129 71353 0.21% 130 73090 0.21% 131 73546 0.21% 132 75814 0.22% 133 78384 0.23% 134 80910 0.23% 135 84055 0.24% 136 86191 0.25% 137 86902 0.25% 138 88391 0.26% 139 89101 0.26% 140 89506 0.26% 141 90712 0.26% 142 92339 0.27% 143 93775 0.27% 144 97038 0.28% 145 99759 0.29% 146 101491 0.29% 147 103663 0.30% 148 104447 0.30% 149 104088 0.30% 150 104756 0.30% 151 30887801 89.61% 34468353 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=4.36 fanout-score-rank=25 prefix-density=0.26 prefix-fanout=3.5 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=163.95 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=14.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.32 sequence-density-rank=1 fanout-score=2.27 fanout-score-rank=33 prefix-density=0.33 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.06 sequence-density-rank=28 fanout-score=257.33 fanout-score-rank=1 prefix-density=0.81 prefix-fanout=20.5 sequence=CCGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12666468 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:54:16 Started mapping on | Dec 07 13:54:16 Finished on | Dec 07 13:58:51 Mapping speed, Million of reads per hour | 451.22 Number of input reads | 34468353 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 32719069 Uniquely mapped reads % | 94.92% Average mapped length | 295.89 Number of splices: Total | 35350465 Number of splices: Annotated (sjdb) | 33134762 Number of splices: GT/AG | 34849411 Number of splices: GC/AG | 401111 Number of splices: AT/AC | 23556 Number of splices: Non-canonical | 76387 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 3.04 Insertion rate per base | 0.02% Insertion average length | 2.46 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 525222 % of reads mapped to multiple loci | 1.52% Number of reads mapped to too many loci | 44326 % of reads mapped to too many loci | 0.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.64% % of reads unmapped: other | 0.78% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1224062 1224062 1224062 N_multimapping 525222 525222 525222 N_noFeature 1200439 31898896 1471055 N_ambiguous 650041 4297 102211 UnstrandedReadsAssigned:30868589 PositiveStrandReadsAssigned:815876 NegativeStrandReadsAssigned:31145803 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666468 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12666468-trimmed-pair1.fastq SRR12666468-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 34,468,353 reads, 31,391,123 reads pseudoaligned [quant] estimated average fragment length: 275.519 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,224 rounds 52973 SRR12666468.ke.tsv 35125 SRR12666468.se.tsv 88098 total ==> SRR12666468.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 662.27 0 0 PNS24247 1044 769.481 178.802 11.6222 PNS24249 1928 1653.48 135.639 4.10298 PNS24246 1044 769.481 178.802 11.6222 PNS24248 1044 769.481 178.802 11.6222 PNS24244 1471 1196.48 397.954 16.6357 PNS24243 293 95.0495 7 3.68351 KQK14069 1603 1328.48 9261.32 348.684 KQK14071 474 230.722 167.199 36.2458 ==> SRR12666468.se.tsv <== BRADI_1g14170v3 10513 BRADI_1g53295v3 1559 BRADI_1g59795v3 265 BRADI_1g07683v3 0 BRADI_1g00485v3 105 BRADI_1g20270v3 2806 BRADI_1g74790v3 152 BRADI_1g09890v3 0 BRADI_1g77505v3 269 BRADI_1g48960v3 0 SRR12666468 completed mapping pipeline successfully