Starting /dee2/code/volunteer_pipeline.sh SRR7171870 current disk space = 3089258147840 free memory = 1579094520 SRR7171870 SRAfilesize dd986bd72ce77cd34723fb5f85132b69 SRR7171870.sra SRR7171870.sra file validated SRR7171870 is paired end SRR7171870 is conventional basespace SRR7171870 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171870_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 28.5475 32.0 25.0 33.0 18.0 33.0 2 29.85225 31.0 29.0 33.0 25.0 34.0 3 31.51475 32.0 32.0 33.0 27.0 33.0 4 31.7525 33.0 32.0 33.0 30.0 33.0 5 31.96125 33.0 32.0 33.0 31.0 33.0 6 36.33875 38.0 36.0 38.0 34.0 38.0 7 37.22275 38.0 38.0 38.0 36.0 38.0 8 37.485 38.0 38.0 38.0 37.0 38.0 9 37.63825 38.0 38.0 38.0 38.0 38.0 10-14 37.6229 38.0 38.0 38.0 38.0 38.0 15-19 37.58495 38.0 38.0 38.0 38.0 38.0 20-24 37.5595 38.0 38.0 38.0 38.0 38.0 25-29 37.537400000000005 38.0 38.0 38.0 37.8 38.0 30-34 37.50465 38.0 38.0 38.0 37.8 38.0 35-39 37.49065 38.0 38.0 38.0 37.6 38.0 40-44 37.4525 38.0 38.0 38.0 37.2 38.0 45-49 37.41305 38.0 38.0 38.0 37.0 38.0 50-54 37.3994 38.0 38.0 38.0 37.0 38.0 55-59 37.3477 38.0 38.0 38.0 37.0 38.0 60-64 37.3137 38.0 38.0 38.0 37.0 38.0 65-69 37.24830000000001 38.0 38.0 38.0 36.0 38.0 70-74 37.186550000000004 38.0 38.0 38.0 36.2 38.0 75-79 37.17005 38.0 38.0 38.0 36.0 38.0 80-84 37.0726 38.0 38.0 38.0 36.0 38.0 85-89 37.00675 38.0 38.0 38.0 36.0 38.0 90-94 36.88125 38.0 38.0 38.0 35.2 38.0 95-99 36.81745 38.0 38.0 38.0 35.0 38.0 100-104 36.74605 38.0 38.0 38.0 34.8 38.0 105-109 36.6346 38.0 38.0 38.0 34.2 38.0 110-114 36.462849999999996 38.0 38.0 38.0 34.0 38.0 115-119 36.34405 38.0 37.6 38.0 34.0 38.0 120-124 36.262449999999994 38.0 37.6 38.0 33.8 38.0 125-129 35.99335 38.0 37.0 38.0 33.0 38.0 130-134 35.7273 38.0 36.0 38.0 31.4 38.0 135-139 35.554899999999996 38.0 36.0 38.0 31.0 38.0 140-144 35.30915 38.0 36.0 38.0 30.6 38.0 145-149 34.7024 38.0 35.0 38.0 28.2 38.0 150-151 31.988750000000003 36.5 31.5 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 1.0 7 0.0 8 0.0 9 0.0 10 0.0 11 1.0 12 0.0 13 0.0 14 0.0 15 3.0 16 1.0 17 0.0 18 0.0 19 1.0 20 2.0 21 5.0 22 4.0 23 7.0 24 6.0 25 3.0 26 8.0 27 9.0 28 13.0 29 24.0 30 34.0 31 35.0 32 52.0 33 76.0 34 131.0 35 280.0 36 722.0 37 2581.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.85 12.950000000000001 12.025 33.175 2 20.375 18.825 37.45 23.35 3 19.775000000000002 27.025 25.074999999999996 28.125 4 24.224999999999998 33.975 21.75 20.05 5 21.65 35.125 26.150000000000002 17.075000000000003 6 17.349999999999998 36.175000000000004 26.325 20.150000000000002 7 15.15 23.3 41.725 19.825 8 18.9 22.225 29.825000000000003 29.049999999999997 9 19.225 22.575 31.624999999999996 26.575 10-14 20.02 30.044999999999998 26.634999999999998 23.3 15-19 20.555 28.96 26.995 23.49 20-24 20.26 28.335 27.905 23.5 25-29 20.805 28.51 27.965 22.720000000000002 30-34 20.52 28.405 27.99 23.085 35-39 20.36 28.51 27.515 23.615 40-44 21.240000000000002 28.465 27.415 22.88 45-49 20.445 28.999999999999996 27.034999999999997 23.52 50-54 20.22 28.655 27.689999999999998 23.435 55-59 20.885 28.310000000000002 27.47 23.335 60-64 20.880000000000003 27.85 28.03 23.24 65-69 20.695 28.125 27.52 23.66 70-74 21.035 28.645 27.72 22.6 75-79 20.84 27.705000000000002 28.325 23.13 80-84 20.765 27.900000000000002 27.925 23.41 85-89 21.175 28.494999999999997 27.29 23.04 90-94 21.47 28.285 27.46 22.785 95-99 21.205 27.975 27.694999999999997 23.125 100-104 21.33 28.04 27.725 22.905 105-109 21.26 28.044999999999998 27.485 23.21 110-114 21.3 27.93 27.37 23.400000000000002 115-119 21.415 28.07 27.560000000000002 22.955000000000002 120-124 20.695 28.360000000000003 27.38 23.565 125-129 21.63 27.605 27.46 23.305 130-134 21.66 28.144999999999996 27.089999999999996 23.105 135-139 21.475 27.884999999999998 27.51 23.13 140-144 20.97 28.199999999999996 27.35 23.48 145-149 21.89 27.939999999999998 27.05 23.119999999999997 150-151 21.2625 28.125 26.724999999999998 23.8875 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.5 21 1.5 22 0.5 23 1.0 24 2.5 25 3.0 26 2.5 27 5.5 28 8.5 29 14.5 30 22.0 31 28.5 32 33.0 33 38.0 34 52.5 35 68.5 36 91.0 37 108.0 38 132.0 39 174.0 40 188.5 41 207.0 42 239.0 43 243.0 44 261.5 45 274.5 46 278.0 47 259.5 48 219.5 49 196.5 50 171.0 51 151.5 52 119.0 53 91.5 54 77.5 55 53.5 56 35.5 57 33.5 58 28.5 59 18.5 60 16.0 61 13.0 62 9.0 63 6.5 64 4.0 65 2.5 66 2.0 67 2.0 68 1.0 69 0.0 70 0.5 71 1.5 72 1.0 73 1.0 74 1.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 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 99.675 #Duplication Level Percentage of deduplicated Percentage of total 1 99.69902182091799 99.375 2 0.27589666415851516 0.5499999999999999 3 0.025081514923501375 0.075 4 0.0 0.0 5 0.0 0.0 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 pass >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0125 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.0625 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.1875 0.0 0.0 0.0 0.0 96-97 0.25 0.0 0.0 0.0 0.0 98-99 0.25 0.0 0.0 0.0 0.0 100-101 0.25 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.375 0.0 0.0 0.0 0.0 106-107 0.4625 0.0 0.0 0.0 0.0 108-109 0.5125 0.0 0.0 0.0 0.0 110-111 0.5874999999999999 0.0 0.0 0.0 0.0 112-113 0.675 0.0 0.0 0.0 0.0 114-115 0.7625 0.0 0.0 0.0 0.0 116-117 0.8375 0.0 0.0 0.0 0.0 118-119 1.0125 0.0 0.0 0.0 0.0 120-121 1.0625 0.0 0.0 0.0 0.0 122-123 1.1375 0.0 0.0 0.0 0.0 124-125 1.4125 0.0 0.0 0.0 0.0 126-127 1.5499999999999998 0.0 0.0 0.0 0.0 128-129 1.6875 0.0 0.0 0.0 0.0 130-131 1.85 0.0 0.0 0.0 0.0 132-133 2.0625 0.0 0.0 0.0 0.0 134-135 2.3 0.0 0.0 0.0 0.0 136-137 2.4875 0.0 0.0 0.0 0.0 138-139 2.7375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATAATT 10 0.006830828 145.0 7 >>END_MODULE SRR7171870 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171870_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 33.14775 33.0 33.0 34.0 33.0 34.0 2 33.2005 34.0 33.0 34.0 33.0 34.0 3 33.27275 34.0 33.0 34.0 33.0 34.0 4 33.265 34.0 33.0 34.0 33.0 34.0 5 33.23025 34.0 33.0 34.0 33.0 34.0 6 37.41325 38.0 38.0 38.0 37.0 38.0 7 37.34425 38.0 38.0 38.0 37.0 38.0 8 37.29825 38.0 38.0 38.0 37.0 38.0 9 37.4895 38.0 38.0 38.0 38.0 38.0 10-14 37.34615 38.0 38.0 38.0 37.0 38.0 15-19 37.286649999999995 38.0 38.0 38.0 37.0 38.0 20-24 37.3119 38.0 38.0 38.0 37.0 38.0 25-29 37.347500000000004 38.0 38.0 38.0 37.0 38.0 30-34 37.279399999999995 38.0 38.0 38.0 37.0 38.0 35-39 37.13175 38.0 38.0 38.0 37.0 38.0 40-44 37.0774 38.0 38.0 38.0 36.8 38.0 45-49 37.17715 38.0 38.0 38.0 37.0 38.0 50-54 37.15644999999999 38.0 38.0 38.0 36.4 38.0 55-59 37.112 38.0 38.0 38.0 36.2 38.0 60-64 37.071600000000004 38.0 38.0 38.0 36.2 38.0 65-69 37.0385 38.0 38.0 38.0 36.0 38.0 70-74 36.98205 38.0 38.0 38.0 36.0 38.0 75-79 36.92725 38.0 38.0 38.0 36.0 38.0 80-84 36.8043 38.0 38.0 38.0 35.4 38.0 85-89 36.69715 38.0 38.0 38.0 35.0 38.0 90-94 36.60355 38.0 38.0 38.0 34.8 38.0 95-99 36.562599999999996 38.0 38.0 38.0 34.6 38.0 100-104 36.42909999999999 38.0 38.0 38.0 34.2 38.0 105-109 36.288500000000006 38.0 38.0 38.0 34.0 38.0 110-114 36.18545 38.0 38.0 38.0 34.0 38.0 115-119 35.9446 38.0 37.0 38.0 33.0 38.0 120-124 35.7399 38.0 36.6 38.0 31.8 38.0 125-129 35.460699999999996 38.0 36.0 38.0 30.6 38.0 130-134 35.2992 38.0 36.0 38.0 30.6 38.0 135-139 35.05015 38.0 35.8 38.0 29.2 38.0 140-144 34.681799999999996 38.0 35.0 38.0 27.6 38.0 145-149 34.22085 38.0 34.6 38.0 26.0 38.0 150-151 30.557375 36.5 29.0 38.0 11.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 2.0 4 1.0 5 0.0 6 2.0 7 1.0 8 1.0 9 2.0 10 1.0 11 2.0 12 0.0 13 0.0 14 2.0 15 0.0 16 3.0 17 2.0 18 3.0 19 5.0 20 7.0 21 3.0 22 6.0 23 5.0 24 12.0 25 5.0 26 15.0 27 15.0 28 24.0 29 28.0 30 33.0 31 51.0 32 67.0 33 92.0 34 148.0 35 241.0 36 637.0 37 2583.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.25 15.85 16.525000000000002 29.375 2 22.825 23.974999999999998 36.0 17.2 3 22.025 26.625 29.475 21.875 4 24.725 34.9 21.4 18.975 5 24.3 35.65 22.375 17.675 6 18.025 37.45 24.725 19.8 7 17.8 17.575 42.75 21.875 8 20.925 23.425 27.975 27.675 9 22.775000000000002 25.5 28.199999999999996 23.525 10-14 22.770000000000003 29.225 26.44 21.565 15-19 22.845 28.03 27.76 21.365000000000002 20-24 22.54 28.325 27.705000000000002 21.43 25-29 22.28 28.439999999999998 27.42 21.86 30-34 22.968374699759806 28.25760608486789 27.56705364291433 21.206965572457968 35-39 22.789252055343894 28.06296370563465 27.807298977341087 21.34048526168037 40-44 23.068044961862704 27.915495784825374 28.15636290646327 20.860096346848657 45-49 22.85 27.715 27.950000000000003 21.485000000000003 50-54 23.169999999999998 27.229999999999997 28.375 21.224999999999998 55-59 22.634999999999998 28.384999999999998 27.744999999999997 21.235 60-64 23.150000000000002 27.994999999999997 27.944999999999997 20.91 65-69 23.505000000000003 27.435 27.985 21.075 70-74 23.265 28.055000000000003 27.655 21.025 75-79 23.39 27.715 27.615000000000002 21.279999999999998 80-84 23.630000000000003 27.42 28.27 20.68 85-89 23.369999999999997 27.975 27.255000000000003 21.4 90-94 23.494999999999997 28.01 27.465 21.029999999999998 95-99 22.75 28.134999999999998 27.805000000000003 21.310000000000002 100-104 23.565 28.199999999999996 27.139999999999997 21.095 105-109 23.43 28.134999999999998 27.589999999999996 20.845 110-114 23.544999999999998 27.779999999999998 27.52 21.154999999999998 115-119 23.995 27.96 27.224999999999998 20.82 120-124 23.49 27.639999999999997 28.110000000000003 20.76 125-129 23.07 28.7 27.49 20.74 130-134 23.845 28.335 27.295 20.525 135-139 23.82 26.895000000000003 28.155 21.13 140-144 23.98 27.525 27.96 20.535 145-149 23.855 27.965 27.79 20.39 150-151 24.625 27.537499999999998 27.8625 19.975 >>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 0.0 6 0.0 7 0.0 8 0.0 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 1.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.0 23 0.0 24 0.0 25 0.0 26 0.5 27 4.0 28 9.0 29 9.5 30 12.0 31 15.0 32 17.5 33 29.0 34 43.5 35 61.5 36 75.0 37 101.5 38 133.5 39 155.0 40 199.0 41 243.5 42 269.0 43 268.5 44 262.5 45 273.0 46 285.5 47 284.5 48 249.0 49 199.5 50 157.0 51 135.0 52 118.5 53 91.5 54 72.0 55 63.5 56 44.5 57 27.0 58 24.5 59 19.5 60 14.0 61 8.5 62 4.0 63 3.0 64 4.0 65 2.5 66 1.0 67 1.0 68 1.0 69 0.5 70 1.0 71 1.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 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 0.08 35-39 0.26 40-44 0.36 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 99.8 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79959919839679 99.6 2 0.2004008016032064 0.4 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 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 pass >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0125 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.0625 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.075 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.175 0.0 0.0 0.0 0.0 94-95 0.1875 0.0 0.0 0.0 0.0 96-97 0.25 0.0 0.0 0.0 0.0 98-99 0.25 0.0 0.0 0.0 0.0 100-101 0.25 0.0 0.0 0.0 0.0 102-103 0.275 0.0 0.0 0.0 0.0 104-105 0.375 0.0 0.0 0.0 0.0 106-107 0.475 0.0 0.0 0.0 0.0 108-109 0.5375 0.0 0.0 0.0 0.0 110-111 0.6375 0.0 0.0 0.0 0.0 112-113 0.725 0.0 0.0 0.0 0.0 114-115 0.8125 0.0 0.0 0.0 0.0 116-117 0.8875 0.0 0.0 0.0 0.0 118-119 1.0625 0.0 0.0 0.0 0.0 120-121 1.1125 0.0 0.0 0.0 0.0 122-123 1.1875 0.0 0.0 0.0 0.0 124-125 1.4625 0.0 0.0 0.0 0.0 126-127 1.5750000000000002 0.0 0.0 0.0 0.0 128-129 1.7 0.0 0.0 0.0 0.0 130-131 1.85 0.0 0.0 0.0 0.0 132-133 2.0375 0.0 0.0 0.0 0.0 134-135 2.3 0.0 0.0 0.0 0.0 136-137 2.4875 0.0 0.0 0.0 0.0 138-139 2.75 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCGTGAG 10 0.006830828 145.0 145 >>END_MODULE Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708628 spots for SRR7171870.sra Written 708628 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra Read 708617 spots for SRR7171870.sra Written 708617 spots for SRR7171870.sra SRR ids: ['SRR7171870.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dvgobr93 SRR7171870.sra spots: 14172351 blocks: [[1, 708617], [708618, 1417234], [1417235, 2125851], [2125852, 2834468], [2834469, 3543085], [3543086, 4251702], [4251703, 4960319], [4960320, 5668936], [5668937, 6377553], [6377554, 7086170], [7086171, 7794787], [7794788, 8503404], [8503405, 9212021], [9212022, 9920638], [9920639, 10629255], [10629256, 11337872], [11337873, 12046489], [12046490, 12755106], [12755107, 13463723], [13463724, 14172351]] SRR7171870 file size 4780844 SRR7171870 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 SRR7171870 SRR7171870_1.fastq SRR7171870_2.fastq Input file: SRR7171870_1.fastq Paired file: SRR7171870_2.fastq trimmed: SRR7171870-trimmed-pair1.fastq, SRR7171870-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 Thu Feb 13 22:49:31 2025 >> started Thu Feb 13 22:49:46 2025 >> done (15.504s) 14172351 read pairs processed; of these: 11986 ( 0.08%) short read pairs filtered out after trimming by size control 9504 ( 0.07%) empty read pairs filtered out after trimming by size control 14150861 (99.85%) read pairs available; of these: 5916695 (41.81%) trimmed read pairs available after processing 8234166 (58.19%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 4 0.00% 21 1 0.00% 22 0 0.00% 23 3 0.00% 24 3 0.00% 25 3 0.00% 26 8 0.00% 27 4 0.00% 28 4 0.00% 29 2 0.00% 30 2 0.00% 31 0 0.00% 32 6 0.00% 33 2 0.00% 34 1 0.00% 35 2 0.00% 36 2 0.00% 37 2 0.00% 38 8 0.00% 39 7 0.00% 40 5 0.00% 41 7 0.00% 42 9 0.00% 43 2 0.00% 44 10 0.00% 45 8 0.00% 46 11 0.00% 47 8 0.00% 48 15 0.00% 49 14 0.00% 50 10 0.00% 51 16 0.00% 52 28 0.00% 53 28 0.00% 54 30 0.00% 55 33 0.00% 56 36 0.00% 57 40 0.00% 58 44 0.00% 59 40 0.00% 60 59 0.00% 61 72 0.00% 62 79 0.00% 63 69 0.00% 64 89 0.00% 65 105 0.00% 66 125 0.00% 67 137 0.00% 68 152 0.00% 69 171 0.00% 70 201 0.00% 71 250 0.00% 72 283 0.00% 73 316 0.00% 74 311 0.00% 75 386 0.00% 76 530 0.00% 77 546 0.00% 78 652 0.00% 79 674 0.00% 80 688 0.00% 81 926 0.01% 82 934 0.01% 83 1181 0.01% 84 1755 0.01% 85 2230 0.02% 86 2389 0.02% 87 2772 0.02% 88 2968 0.02% 89 2914 0.02% 90 3069 0.02% 91 3347 0.02% 92 3661 0.03% 93 3959 0.03% 94 4086 0.03% 95 4286 0.03% 96 4700 0.03% 97 4909 0.03% 98 5174 0.04% 99 5705 0.04% 100 5996 0.04% 101 6345 0.04% 102 6863 0.05% 103 7244 0.05% 104 7815 0.06% 105 8369 0.06% 106 8843 0.06% 107 9138 0.06% 108 9720 0.07% 109 10340 0.07% 110 10736 0.08% 111 11568 0.08% 112 11860 0.08% 113 12817 0.09% 114 13605 0.10% 115 14327 0.10% 116 15318 0.11% 117 15587 0.11% 118 16051 0.11% 119 16754 0.12% 120 17415 0.12% 121 18262 0.13% 122 19201 0.14% 123 20129 0.14% 124 21170 0.15% 125 22137 0.16% 126 23214 0.16% 127 24286 0.17% 128 25107 0.18% 129 26137 0.18% 130 27623 0.20% 131 28787 0.20% 132 30788 0.22% 133 32830 0.23% 134 34822 0.25% 135 36549 0.26% 136 39059 0.28% 137 41809 0.30% 138 45100 0.32% 139 48578 0.34% 140 52659 0.37% 141 59308 0.42% 142 65360 0.46% 143 74513 0.53% 144 87539 0.62% 145 106920 0.76% 146 137660 0.97% 147 193001 1.36% 148 307667 2.17% 149 650236 4.60% 150 3312214 23.41% 151 8234166 58.19% 14150861 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=2.88 fanout-score-rank=28 prefix-density=0.35 prefix-fanout=2.1 sequence=CACTTGCAGCCATTCTCAGCACCAGAGTTCATCTCAGACC criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=84.73 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=11.7 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCAT criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=3.07 fanout-score-rank=25 prefix-density=0.34 prefix-fanout=3.0 sequence=ATGTACCCTGACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=31.26 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.1 sequence=GAAGGATCTGTTTAATTTGAGACAGAAAACATGAAATCCTCCTACACTTTCTTCATTCTTTTCTCACTCTTTTCGTTTGCTAACGTGATCGGTGCTAGAAAAGACACTGGAGAGTATTGGAGAGCTGTCATGAAAGATCAGCCCATGCCAGAAGCAATACA SRR7171870 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 22:50:32 Started mapping on | Feb 13 22:50:33 Finished on | Feb 13 22:52:25 Mapping speed, Million of reads per hour | 454.85 Number of input reads | 14150861 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 13104276 Uniquely mapped reads % | 92.60% Average mapped length | 296.45 Number of splices: Total | 13243253 Number of splices: Annotated (sjdb) | 12988565 Number of splices: GT/AG | 13041706 Number of splices: GC/AG | 158074 Number of splices: AT/AC | 9792 Number of splices: Non-canonical | 33681 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.53 Insertion rate per base | 0.02% Insertion average length | 2.61 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 361262 % of reads mapped to multiple loci | 2.55% Number of reads mapped to too many loci | 79949 % of reads mapped to too many loci | 0.56% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.17% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 697281 697281 697281 N_multimapping 361262 361262 361262 N_noFeature 291639 12980043 348731 N_ambiguous 144818 860 77080 UnstrandedReadsAssigned:12667819 PositiveStrandReadsAssigned:123373 NegativeStrandReadsAssigned:12678465 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7171870 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: SRR7171870-trimmed-pair1.fastq SRR7171870-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,150,861 reads, 12,554,160 reads pseudoaligned [quant] estimated average fragment length: 254.837 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,113 rounds 52401 SRR7171870.ke.tsv 34699 SRR7171870.se.tsv 87100 total ==> SRR7171870.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1764.16 1321 53.9913 Potri.005G024800.1.v4.1 1035 781.163 1129 104.211 Potri.004G059700.1.v4.1 961 707.181 12 1.22352 Potri.007G009000.2.v4.1 1416 1162.16 0 0 Potri.003G141000.2.v4.1 2943 2689.16 643 17.2406 Potri.016G087400.1.v4.1 270 70.2564 941.172 965.922 Potri.015G069301.1.v4.1 564 313.876 0 0 Potri.010G195200.1.v4.1 1773 1519.16 259 12.2929 Potri.012G127500.1.v4.1 977 723.169 3315 330.524 ==> SRR7171870.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 106 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 313 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 6 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 34 SRR7171870 completed mapping pipeline successfully