Starting /dee2/code/volunteer_pipeline.sh SRR18694432 current disk space = 1526034046976 free memory = 1602364960 SRR18694432 SRAfilesize 581cdc3a2644a01a4553b115a7159a91 SRR18694432.sra SRR18694432.sra file validated SRR18694432 is paired end SRR18694432 is conventional basespace SRR18694432 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694432_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1885 37.0 37.0 37.0 37.0 37.0 2 35.98575 37.0 37.0 37.0 37.0 37.0 3 36.4935 37.0 37.0 37.0 37.0 37.0 4 36.529 37.0 37.0 37.0 37.0 37.0 5 36.539 37.0 37.0 37.0 37.0 37.0 6 36.5915 37.0 37.0 37.0 37.0 37.0 7 36.532 37.0 37.0 37.0 37.0 37.0 8 36.6475 37.0 37.0 37.0 37.0 37.0 9 36.6125 37.0 37.0 37.0 37.0 37.0 10-14 36.6215 37.0 37.0 37.0 37.0 37.0 15-19 36.6279 37.0 37.0 37.0 37.0 37.0 20-24 36.6417 37.0 37.0 37.0 37.0 37.0 25-29 36.5741 37.0 37.0 37.0 37.0 37.0 30-34 36.525600000000004 37.0 37.0 37.0 37.0 37.0 35-39 36.67659999999999 37.0 37.0 37.0 37.0 37.0 40-44 36.6238 37.0 37.0 37.0 37.0 37.0 45-49 36.4363 37.0 37.0 37.0 37.0 37.0 50-54 36.5423 37.0 37.0 37.0 37.0 37.0 55-59 36.528000000000006 37.0 37.0 37.0 37.0 37.0 60-64 36.5797 37.0 37.0 37.0 37.0 37.0 65-69 36.3608 37.0 37.0 37.0 37.0 37.0 70-74 36.4262 37.0 37.0 37.0 37.0 37.0 75-79 36.5262 37.0 37.0 37.0 37.0 37.0 80-84 36.4465 37.0 37.0 37.0 37.0 37.0 85-89 36.2082 37.0 37.0 37.0 37.0 37.0 90-94 35.402 37.0 37.0 37.0 29.8 37.0 95-99 36.13680000000001 37.0 37.0 37.0 37.0 37.0 100-104 36.1214 37.0 37.0 37.0 37.0 37.0 105-109 36.167199999999994 37.0 37.0 37.0 37.0 37.0 110-114 36.2268 37.0 37.0 37.0 37.0 37.0 115-119 36.4814 37.0 37.0 37.0 37.0 37.0 120-124 36.6128 37.0 37.0 37.0 37.0 37.0 125-129 36.533699999999996 37.0 37.0 37.0 37.0 37.0 130-134 36.547700000000006 37.0 37.0 37.0 37.0 37.0 135-139 36.3838 37.0 37.0 37.0 37.0 37.0 140-144 36.2524 37.0 37.0 37.0 37.0 37.0 145-149 36.2243 37.0 37.0 37.0 37.0 37.0 150-151 33.74725 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 0.0 24 2.0 25 0.0 26 0.0 27 3.0 28 5.0 29 6.0 30 5.0 31 10.0 32 21.0 33 55.0 34 123.0 35 332.0 36 3242.0 37 195.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.475 9.950000000000001 5.075 35.5 2 21.62773172569706 10.097965335342879 36.096458176337606 32.177844762622456 3 20.75 13.475000000000001 25.900000000000002 39.875 4 26.6 21.0 22.650000000000002 29.75 5 27.625 26.75 22.75 22.875 6 23.799999999999997 31.825 22.55 21.825 7 18.75 26.650000000000002 37.95 16.650000000000002 8 20.5 23.075000000000003 30.0 26.424999999999997 9 20.349999999999998 20.8 34.175 24.675 10-14 22.755 26.900000000000002 25.900000000000002 24.445 15-19 23.1 24.745 26.090000000000003 26.064999999999998 20-24 22.99 25.629999999999995 25.669999999999998 25.71 25-29 23.05 25.685000000000002 25.264999999999997 26.0 30-34 23.189999999999998 25.835 25.1 25.874999999999996 35-39 23.49 25.490000000000002 25.624999999999996 25.395 40-44 23.56 25.97 25.585 24.884999999999998 45-49 23.369999999999997 25.055 25.380000000000003 26.195 50-54 23.23 25.435000000000002 25.385 25.95 55-59 23.195 25.21 25.595000000000002 26.0 60-64 23.46 25.455 25.185000000000002 25.900000000000002 65-69 23.62 25.330000000000002 25.77 25.28 70-74 23.26 25.41 25.52 25.81 75-79 23.785 25.224999999999998 25.47 25.52 80-84 23.580000000000002 25.595000000000002 25.215 25.61 85-89 24.169999999999998 24.755 25.380000000000003 25.695 90-94 23.39 25.874999999999996 25.0 25.735000000000003 95-99 23.035 25.3 25.385 26.279999999999998 100-104 24.145 25.115 24.990000000000002 25.75 105-109 23.885 25.05 25.119999999999997 25.945 110-114 23.455000000000002 25.115 25.355 26.075 115-119 24.169999999999998 26.165 24.485 25.180000000000003 120-124 23.919999999999998 25.945 24.42 25.715 125-129 23.7 25.490000000000002 24.9 25.91 130-134 23.765 25.924999999999997 24.755 25.555 135-139 24.085 25.215 24.67 26.029999999999998 140-144 24.104999999999997 25.215 24.42 26.26 145-149 24.560000000000002 26.02 24.08 25.34 150-151 23.1875 25.4875 24.349999999999998 26.974999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 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 0.5 23 1.5 24 1.0 25 0.0 26 0.5 27 2.0 28 4.0 29 5.5 30 8.0 31 12.0 32 17.0 33 25.0 34 33.0 35 41.0 36 49.5 37 57.5 38 71.5 39 86.5 40 120.0 41 141.5 42 148.0 43 171.0 44 185.0 45 206.5 46 213.0 47 194.5 48 186.5 49 179.0 50 154.0 51 147.0 52 150.0 53 127.5 54 114.0 55 103.0 56 90.0 57 87.0 58 82.5 59 84.0 60 85.5 61 77.5 62 66.5 63 63.0 64 70.5 65 59.5 66 53.5 67 61.5 68 55.0 69 38.5 70 21.5 71 14.5 72 9.5 73 6.5 74 5.5 75 4.0 76 2.5 77 1.5 78 0.5 79 0.5 80 0.5 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 0.475 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 84.2 #Duplication Level Percentage of deduplicated Percentage of total 1 84.85748218527316 71.45 2 12.5 21.05 3 2.048693586698337 5.175 4 0.3859857482185273 1.3 5 0.11876484560570072 0.5 6 0.02969121140142518 0.15 7 0.02969121140142518 0.17500000000000002 8 0.02969121140142518 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GGGTGTCTTCGTCCATGCCCGAGCCCTCCATGTCAGCACCGGCGCCCTGG 8 0.2 No Hit CCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTCTCCTC 7 0.17500000000000002 No Hit GGCTGATGTACTCTTGGGAGCTGAGGACGGCCACGTGGGTACCGTCGCCC 6 0.15 No Hit CATGAATGTAATCTACTCTAACATGGTCCCAACCCTATTTTTACAACCAA 5 0.125 No Hit GCCTGATTAAAATCACCAGTGTGGTACAAAACAACAGCTAGAAGGCTATA 5 0.125 No Hit GTCGATGATCTCGCCGAAGGAGGAGAAGGCATCCTGGAGACCACGGTCGT 5 0.125 No Hit CCTAACAATCACTAGAAACACTGCATGTACAAGTTTACGGCCTACAAGTA 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 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 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 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.037500000000000006 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 0.07500000000000001 0.0 0.0 0.0 0.0 72-73 0.1125 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.175 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.3125 0.0 0.0 0.0 0.0 84-85 0.425 0.0 0.0 0.0 0.0 86-87 0.5125 0.0 0.0 0.0 0.0 88-89 0.525 0.0 0.0 0.0 0.0 90-91 0.6125 0.0 0.0 0.0 0.0 92-93 0.7 0.0 0.0 0.0 0.0 94-95 0.8875 0.0 0.0 0.0 0.0 96-97 1.1 0.0 0.0 0.0 0.0 98-99 1.2625000000000002 0.0 0.0 0.0 0.0 100-101 1.475 0.0 0.0 0.0 0.0 102-103 1.9 0.0 0.0 0.0 0.0 104-105 2.1625 0.0 0.0 0.0 0.0 106-107 2.4749999999999996 0.0 0.0 0.0 0.0 108-109 2.825 0.0 0.0 0.0 0.0 110-111 3.2750000000000004 0.0 0.0 0.0 0.0 112-113 3.825 0.0 0.0 0.0 0.0 114-115 4.175000000000001 0.0 0.0 0.0 0.0 116-117 4.675 0.0 0.0 0.0 0.0 118-119 5.2625 0.0 0.0 0.0 0.0 120-121 5.949999999999999 0.0 0.0 0.0 0.0 122-123 6.4625 0.0 0.0 0.0 0.0 124-125 6.85 0.0 0.0 0.0 0.0 126-127 7.4625 0.0 0.0 0.0 0.0 128-129 7.824999999999999 0.0 0.0 0.0 0.0 130-131 8.5125 0.0 0.0 0.0 0.0 132-133 9.2625 0.0 0.0 0.0 0.0 134-135 9.8125 0.0 0.0 0.0 0.0 136-137 10.5 0.0 0.0 0.0 0.0 138-139 11.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGTG 10 0.006830828 145.0 5 >>END_MODULE SRR18694432 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694432_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 34.2405 37.0 37.0 37.0 25.0 37.0 2 35.0605 37.0 37.0 37.0 25.0 37.0 3 35.307 37.0 37.0 37.0 25.0 37.0 4 35.391 37.0 37.0 37.0 37.0 37.0 5 35.1375 37.0 37.0 37.0 25.0 37.0 6 35.1695 37.0 37.0 37.0 25.0 37.0 7 35.165 37.0 37.0 37.0 25.0 37.0 8 35.4195 37.0 37.0 37.0 37.0 37.0 9 35.579 37.0 37.0 37.0 37.0 37.0 10-14 35.5368 37.0 37.0 37.0 37.0 37.0 15-19 35.6476 37.0 37.0 37.0 37.0 37.0 20-24 35.4382 37.0 37.0 37.0 34.6 37.0 25-29 35.5361 37.0 37.0 37.0 32.2 37.0 30-34 35.7886 37.0 37.0 37.0 37.0 37.0 35-39 35.625299999999996 37.0 37.0 37.0 37.0 37.0 40-44 35.3264 37.0 37.0 37.0 29.8 37.0 45-49 35.5216 37.0 37.0 37.0 37.0 37.0 50-54 35.0106 37.0 37.0 37.0 32.2 37.0 55-59 34.41019999999999 37.0 37.0 37.0 25.0 37.0 60-64 35.0518 37.0 37.0 37.0 27.4 37.0 65-69 34.2687 37.0 34.6 37.0 27.4 37.0 70-74 33.055699999999995 37.0 29.8 37.0 22.2 37.0 75-79 33.668099999999995 37.0 34.6 37.0 22.2 37.0 80-84 34.4748 37.0 37.0 37.0 25.0 37.0 85-89 32.593399999999995 37.0 32.2 37.0 19.4 37.0 90-94 34.2029 37.0 37.0 37.0 25.0 37.0 95-99 33.8899 37.0 37.0 37.0 25.0 37.0 100-104 33.488299999999995 37.0 37.0 37.0 25.0 37.0 105-109 34.2624 37.0 37.0 37.0 25.0 37.0 110-114 34.552 37.0 37.0 37.0 25.0 37.0 115-119 34.4465 37.0 37.0 37.0 25.0 37.0 120-124 34.13369999999999 37.0 37.0 37.0 25.0 37.0 125-129 33.977700000000006 37.0 37.0 37.0 25.0 37.0 130-134 33.7128 37.0 34.6 37.0 25.0 37.0 135-139 32.141200000000005 37.0 25.0 37.0 13.8 37.0 140-144 31.5043 37.0 25.0 37.0 11.0 37.0 145-149 31.1051 37.0 25.0 37.0 11.0 37.0 150-151 30.782249999999998 37.0 25.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 2.0 17 4.0 18 1.0 19 5.0 20 4.0 21 7.0 22 5.0 23 9.0 24 3.0 25 8.0 26 9.0 27 9.0 28 23.0 29 50.0 30 70.0 31 154.0 32 275.0 33 531.0 34 1145.0 35 1462.0 36 224.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.550000000000004 19.475 7.775 27.200000000000003 2 28.825 24.25 27.125 19.8 3 22.725 24.025 31.025000000000002 22.225 4 26.900000000000002 30.75 21.025 21.325 5 28.65 30.349999999999998 21.55 19.45 6 23.474999999999998 35.875 20.45 20.200000000000003 7 24.975 18.85 32.975 23.200000000000003 8 22.5 23.549999999999997 24.325 29.625 9 23.825 22.900000000000002 26.85 26.424999999999997 10-14 26.075 26.009999999999998 23.45 24.465 15-19 26.195 25.085 24.73 23.990000000000002 20-24 25.485000000000003 25.319999999999997 24.355 24.84 25-29 25.94 25.169999999999998 24.305 24.585 30-34 25.314999999999998 25.580000000000002 24.959999999999997 24.145 35-39 25.8 25.16 24.72 24.32 40-44 26.545 24.14 25.180000000000003 24.135 45-49 25.61 25.235000000000003 24.995 24.16 50-54 24.560000000000002 25.35 26.005 24.085 55-59 25.8 25.580000000000002 24.75 23.87 60-64 26.21 25.345000000000002 24.43 24.015 65-69 26.19 25.66 24.235 23.915 70-74 26.605 24.725 24.52 24.15 75-79 27.235 23.54 25.069999999999997 24.154999999999998 80-84 26.39 25.485000000000003 24.665 23.46 85-89 24.575 27.66 24.104999999999997 23.66 90-94 26.105 25.205 24.585 24.104999999999997 95-99 25.86 26.275 24.355 23.51 100-104 26.565 25.34 24.87 23.225 105-109 25.77 25.445 24.855 23.93 110-114 26.625 25.825 24.59 22.96 115-119 27.384999999999998 25.28 23.985 23.35 120-124 27.339999999999996 25.05 24.235 23.375 125-129 26.97 25.715 25.03 22.285 130-134 26.895000000000003 25.14 25.014999999999997 22.95 135-139 26.640000000000004 25.665 25.155 22.54 140-144 27.500000000000004 25.31 24.385 22.805 145-149 27.894999999999996 25.56 24.4 22.145 150-151 25.7375 24.75 27.450000000000003 22.0625 >>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 0.5 12 1.5 13 1.0 14 1.0 15 1.0 16 0.0 17 0.0 18 0.5 19 1.0 20 1.5 21 1.5 22 1.5 23 1.0 24 1.0 25 1.5 26 0.5 27 1.0 28 3.5 29 7.5 30 10.0 31 10.5 32 17.0 33 24.0 34 27.0 35 35.0 36 46.5 37 54.5 38 71.0 39 89.5 40 106.0 41 118.5 42 143.5 43 160.0 44 171.0 45 187.0 46 186.5 47 189.0 48 181.0 49 164.5 50 150.5 51 140.0 52 135.5 53 123.0 54 121.5 55 119.5 56 115.5 57 116.5 58 106.5 59 94.5 60 90.0 61 84.0 62 75.0 63 69.5 64 63.0 65 64.5 66 62.5 67 56.5 68 47.5 69 40.0 70 34.5 71 22.5 72 15.0 73 12.0 74 6.5 75 3.5 76 1.5 77 2.0 78 1.0 79 1.0 80 1.0 81 0.0 82 0.0 83 0.5 84 0.5 85 0.0 86 0.0 87 0.5 88 0.5 89 0.5 90 1.0 91 0.5 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 0.0 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 85.425 #Duplication Level Percentage of deduplicated Percentage of total 1 86.30377524143987 73.725 2 11.179397131987123 19.1 3 1.9607843137254901 5.025 4 0.4389815627743635 1.5 5 0.029265437518290898 0.125 6 0.029265437518290898 0.15 7 0.029265437518290898 0.17500000000000002 8 0.029265437518290898 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GTTTGAGGACAAGATGAAGGAGCTGGAGAGCCTGTGCAACCCGATCATCG 8 0.2 No Hit GGTCAGGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAG 7 0.17500000000000002 No Hit GGTGGGTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGT 6 0.15 No Hit GCAGGACATTATTAGCCTGGTGCCAGTACATAAGCAAGTCGCCTGCTCAT 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 0.025 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.0875 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.225 0.0 0.0 0.0 0.0 82-83 0.2875 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.4875 0.0 0.0 0.0 0.0 88-89 0.5 0.0 0.0 0.0 0.0 90-91 0.5874999999999999 0.0 0.0 0.0 0.0 92-93 0.675 0.0 0.0 0.0 0.0 94-95 0.85 0.0 0.0 0.0 0.0 96-97 1.05 0.0 0.0 0.0 0.0 98-99 1.2125 0.0 0.0 0.0 0.0 100-101 1.4375 0.0 0.0 0.0 0.0 102-103 1.85 0.0 0.0 0.0 0.0 104-105 2.1125 0.0 0.0 0.0 0.0 106-107 2.425 0.0 0.0 0.0 0.0 108-109 2.775 0.0 0.0 0.0 0.0 110-111 3.2249999999999996 0.0 0.0 0.0 0.0 112-113 3.7750000000000004 0.0 0.0 0.0 0.0 114-115 4.125 0.0 0.0 0.0 0.0 116-117 4.625 0.0 0.0 0.0 0.0 118-119 5.2125 0.0 0.0 0.0 0.0 120-121 5.9 0.0 0.0 0.0 0.0 122-123 6.4125 0.0 0.0 0.0 0.0 124-125 6.775 0.0 0.0 0.0 0.0 126-127 7.375 0.0 0.0 0.0 0.0 128-129 7.725 0.0 0.0 0.0 0.0 130-131 8.399999999999999 0.0 0.0 0.0 0.0 132-133 9.1375 0.0 0.0 0.0 0.0 134-135 9.7 0.0 0.0 0.0 0.0 136-137 10.375 0.0 0.0 0.0 0.0 138-139 11.149999999999999 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542649 spots for SRR18694432.sra Written 542649 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra Read 542637 spots for SRR18694432.sra Written 542637 spots for SRR18694432.sra SRR ids: ['SRR18694432.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xaiugyao SRR18694432.sra spots: 10852752 blocks: [[1, 542637], [542638, 1085274], [1085275, 1627911], [1627912, 2170548], [2170549, 2713185], [2713186, 3255822], [3255823, 3798459], [3798460, 4341096], [4341097, 4883733], [4883734, 5426370], [5426371, 5969007], [5969008, 6511644], [6511645, 7054281], [7054282, 7596918], [7596919, 8139555], [8139556, 8682192], [8682193, 9224829], [9224830, 9767466], [9767467, 10310103], [10310104, 10852752]] SRR18694432 file size 3666539 SRR18694432 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 SRR18694432 SRR18694432_1.fastq SRR18694432_2.fastq Input file: SRR18694432_1.fastq Paired file: SRR18694432_2.fastq trimmed: SRR18694432-trimmed-pair1.fastq, SRR18694432-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 Dec 10 06:43:39 2024 >> started Tue Dec 10 06:43:52 2024 >> done (12.616s) 10852752 read pairs processed; of these: 91 ( 0.00%) short read pairs filtered out after trimming by size control 3479 ( 0.03%) empty read pairs filtered out after trimming by size control 10849182 (99.97%) read pairs available; of these: 1604521 (14.79%) trimmed read pairs available after processing 9244661 (85.21%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 7 0.00% 20 11 0.00% 21 14 0.00% 22 14 0.00% 23 18 0.00% 24 15 0.00% 25 16 0.00% 26 23 0.00% 27 13 0.00% 28 18 0.00% 29 28 0.00% 30 23 0.00% 31 30 0.00% 32 27 0.00% 33 19 0.00% 34 31 0.00% 35 30 0.00% 36 32 0.00% 37 40 0.00% 38 39 0.00% 39 37 0.00% 40 50 0.00% 41 57 0.00% 42 44 0.00% 43 55 0.00% 44 38 0.00% 45 51 0.00% 46 45 0.00% 47 54 0.00% 48 72 0.00% 49 80 0.00% 50 72 0.00% 51 121 0.00% 52 96 0.00% 53 133 0.00% 54 125 0.00% 55 131 0.00% 56 141 0.00% 57 155 0.00% 58 216 0.00% 59 239 0.00% 60 268 0.00% 61 373 0.00% 62 342 0.00% 63 391 0.00% 64 440 0.00% 65 431 0.00% 66 624 0.01% 67 602 0.01% 68 661 0.01% 69 867 0.01% 70 933 0.01% 71 1020 0.01% 72 1215 0.01% 73 1357 0.01% 74 1459 0.01% 75 1811 0.02% 76 1764 0.02% 77 2009 0.02% 78 2219 0.02% 79 2580 0.02% 80 2947 0.03% 81 3210 0.03% 82 3503 0.03% 83 3938 0.04% 84 4144 0.04% 85 4648 0.04% 86 4947 0.05% 87 5310 0.05% 88 5888 0.05% 89 6185 0.06% 90 6872 0.06% 91 7077 0.07% 92 7937 0.07% 93 8294 0.08% 94 8773 0.08% 95 9297 0.09% 96 9931 0.09% 97 10079 0.09% 98 10705 0.10% 99 11556 0.11% 100 11753 0.11% 101 12683 0.12% 102 13172 0.12% 103 13751 0.13% 104 14302 0.13% 105 15168 0.14% 106 15605 0.14% 107 16004 0.15% 108 16331 0.15% 109 17647 0.16% 110 17876 0.16% 111 18537 0.17% 112 19556 0.18% 113 20053 0.18% 114 21796 0.20% 115 22253 0.21% 116 22246 0.21% 117 23112 0.21% 118 23232 0.21% 119 24420 0.23% 120 25233 0.23% 121 25540 0.24% 122 26259 0.24% 123 26949 0.25% 124 28705 0.26% 125 29121 0.27% 126 29887 0.28% 127 29776 0.27% 128 30668 0.28% 129 31529 0.29% 130 31651 0.29% 131 32378 0.30% 132 33573 0.31% 133 34238 0.32% 134 34536 0.32% 135 35660 0.33% 136 36033 0.33% 137 36251 0.33% 138 36516 0.34% 139 37270 0.34% 140 37597 0.35% 141 38551 0.36% 142 39666 0.37% 143 40285 0.37% 144 41361 0.38% 145 41673 0.38% 146 41620 0.38% 147 42816 0.39% 148 43224 0.40% 149 43324 0.40% 150 44054 0.41% 151 9244661 85.21% 10849182 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=3.07 fanout-score-rank=14 prefix-density=0.63 prefix-fanout=2.9 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=27 fanout-score=129.59 fanout-score-rank=1 prefix-density=0.40 prefix-fanout=11.1 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.89 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=27 prefix-density=0.91 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=14.42 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.7 sequence=AGGGTTCCTCCCTAGTATACCCCCCCAACAATGGCCTAATACTGCCGGCAGCATGTAGCCCATGCTGCTAATTTTCTTCCAAGCTTCATTGGCGGCGCGCGAGGATCGGCAGCGGTGGTGCGCCGAGGATGTATCTACTATCCAGGCAGGTGTGTTAGGCCATGTAGGGCAACTATACATCTTT SRR18694432 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:44:39 Started mapping on | Dec 10 06:44:39 Finished on | Dec 10 06:45:51 Mapping speed, Million of reads per hour | 542.46 Number of input reads | 10849182 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 10199215 Uniquely mapped reads % | 94.01% Average mapped length | 293.09 Number of splices: Total | 10536498 Number of splices: Annotated (sjdb) | 9849844 Number of splices: GT/AG | 10385483 Number of splices: GC/AG | 128584 Number of splices: AT/AC | 4332 Number of splices: Non-canonical | 18099 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.01% Deletion average length | 2.45 Insertion rate per base | 0.01% Insertion average length | 2.45 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 143696 % of reads mapped to multiple loci | 1.32% Number of reads mapped to too many loci | 20717 % of reads mapped to too many loci | 0.19% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.05% % of reads unmapped: other | 1.42% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 506271 506271 506271 N_multimapping 143696 143696 143696 N_noFeature 529829 9908877 618088 N_ambiguous 241354 1365 39490 UnstrandedReadsAssigned:9428032 PositiveStrandReadsAssigned:288973 NegativeStrandReadsAssigned:9541637 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694432 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: SRR18694432-trimmed-pair1.fastq SRR18694432-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,849,182 reads, 9,691,245 reads pseudoaligned [quant] estimated average fragment length: 245.6 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,096 rounds 52973 SRR18694432.ke.tsv 35125 SRR18694432.se.tsv 88098 total ==> SRR18694432.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 691.962 0 0 PNS24247 1044 799.4 33.2739 6.19695 PNS24249 1928 1683.4 7.25073 0.641259 PNS24246 1044 799.4 33.2739 6.19695 PNS24248 1044 799.4 33.2739 6.19695 PNS24244 1471 1226.4 81.9277 9.94576 PNS24243 293 102.858 0 0 KQK14069 1603 1358.4 1161.09 127.255 KQK14071 474 249.581 17.9246 10.6924 ==> SRR18694432.se.tsv <== BRADI_1g14170v3 1323 BRADI_1g53295v3 34 BRADI_1g59795v3 610 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 299 BRADI_1g74790v3 97 BRADI_1g09890v3 1 BRADI_1g77505v3 107 BRADI_1g48960v3 0 SRR18694432 completed mapping pipeline successfully