Starting /dee2/code/volunteer_pipeline.sh SRR7172080 current disk space = 3088232243200 free memory = 1448576380 SRR7172080 SRAfilesize 9e2226db1f5b7145beb73be4822bde6c SRR7172080.sra SRR7172080.sra file validated SRR7172080 is paired end SRR7172080 is conventional basespace SRR7172080 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172080_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 43 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.661 32.0 32.0 33.0 25.0 33.0 2 22.7145 18.0 18.0 29.0 18.0 33.0 3 30.47925 32.0 27.0 32.0 27.0 33.0 4 30.143 32.0 30.0 33.0 25.0 33.0 5 30.9095 32.0 32.0 33.0 25.0 33.0 6 35.781 37.0 36.0 38.0 31.0 38.0 7 36.69675 38.0 37.0 38.0 34.0 38.0 8 37.3285 38.0 38.0 38.0 36.0 38.0 9 37.43775 38.0 38.0 38.0 37.0 38.0 10-14 37.535700000000006 38.0 38.0 38.0 37.0 38.0 15-19 37.596199999999996 38.0 38.0 38.0 37.8 38.0 20-24 37.6513 38.0 38.0 38.0 38.0 38.0 25-29 37.63955 38.0 38.0 38.0 38.0 38.0 30-34 37.58965 38.0 38.0 38.0 38.0 38.0 35-39 37.58155 38.0 38.0 38.0 38.0 38.0 40-44 37.5565 38.0 38.0 38.0 38.0 38.0 45-49 37.48755 38.0 38.0 38.0 37.6 38.0 50-54 37.4071 38.0 38.0 38.0 37.0 38.0 55-59 37.32854999999999 38.0 38.0 38.0 37.0 38.0 60-64 37.280300000000004 38.0 38.0 38.0 36.8 38.0 65-69 37.212399999999995 38.0 38.0 38.0 36.2 38.0 70-74 37.2122 38.0 38.0 38.0 36.0 38.0 75-79 37.1413 38.0 38.0 38.0 36.0 38.0 80-84 37.118900000000004 38.0 38.0 38.0 36.0 38.0 85-89 37.0056 38.0 38.0 38.0 36.0 38.0 90-94 36.9039 38.0 38.0 38.0 35.4 38.0 95-99 36.768150000000006 38.0 38.0 38.0 35.0 38.0 100-104 36.576100000000004 38.0 38.0 38.0 34.0 38.0 105-109 36.40565 38.0 37.4 38.0 34.0 38.0 110-114 36.297450000000005 38.0 37.2 38.0 34.0 38.0 115-119 36.09545000000001 38.0 37.0 38.0 32.8 38.0 120-124 36.0198 38.0 37.0 38.0 32.6 38.0 125-129 35.73315 38.0 36.2 38.0 31.0 38.0 130-134 35.504900000000006 38.0 36.0 38.0 30.6 38.0 135-139 35.052949999999996 38.0 35.2 38.0 28.0 38.0 140-144 34.89905 38.0 35.2 38.0 28.8 38.0 145-149 34.205200000000005 38.0 35.0 38.0 25.6 38.0 150-151 30.427500000000002 36.0 29.0 38.0 11.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 7 1.0 8 0.0 9 1.0 10 1.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 0.0 19 2.0 20 0.0 21 6.0 22 1.0 23 6.0 24 6.0 25 8.0 26 11.0 27 14.0 28 16.0 29 29.0 30 22.0 31 42.0 32 61.0 33 74.0 34 160.0 35 318.0 36 1000.0 37 2218.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.68318397469689 19.74169741697417 12.836056931997891 34.73906167633105 2 17.60440110027507 27.981995498874717 36.40910227556889 18.00450112528132 3 17.45 32.725 26.325 23.5 4 20.05 39.25 20.825 19.875 5 19.075 40.0 22.475 18.45 6 15.55 37.6 24.875 21.975 7 12.3 20.325 45.6 21.775 8 17.150000000000002 21.275 28.675 32.9 9 17.65 21.9 30.049999999999997 30.4 10-14 19.18 29.909999999999997 26.875 24.035 15-19 19.42 29.075 27.62 23.885 20-24 19.314999999999998 29.299999999999997 28.21 23.175 25-29 19.259999999999998 29.14 27.875 23.724999999999998 30-34 19.705000000000002 28.970000000000002 27.91 23.415 35-39 19.645000000000003 29.549999999999997 27.944999999999997 22.86 40-44 18.93 29.24 27.935 23.895 45-49 19.475 29.03 27.889999999999997 23.605 50-54 19.759999999999998 28.725 27.88 23.635 55-59 19.585 28.389999999999997 28.18 23.845 60-64 19.97 28.575 27.83 23.625 65-69 19.384999999999998 29.205 27.655 23.755000000000003 70-74 19.900000000000002 28.050000000000004 28.22 23.830000000000002 75-79 19.785 29.080000000000002 27.27 23.865 80-84 19.650000000000002 29.14 27.229999999999997 23.98 85-89 20.24 28.535 28.225 23.0 90-94 19.63 28.76 27.650000000000002 23.96 95-99 19.62 28.595 28.07 23.715 100-104 19.794999999999998 28.37 28.315 23.52 105-109 20.135 28.249999999999996 28.29 23.325000000000003 110-114 19.825 28.660000000000004 27.925 23.59 115-119 20.21 28.444999999999997 27.339999999999996 24.005000000000003 120-124 20.41 28.615000000000002 27.715 23.26 125-129 20.465 28.749999999999996 27.355 23.43 130-134 20.765 28.685 27.275 23.275000000000002 135-139 21.07 28.310000000000002 27.465 23.155 140-144 20.52 29.035 26.950000000000003 23.494999999999997 145-149 20.535 28.715000000000003 27.025 23.724999999999998 150-151 20.200000000000003 28.5875 27.375 23.8375 >>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 0.5 8 0.5 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 1.5 20 1.0 21 0.5 22 1.5 23 3.0 24 2.5 25 3.0 26 8.0 27 9.5 28 13.0 29 17.5 30 23.5 31 28.0 32 40.0 33 60.0 34 67.5 35 81.5 36 109.0 37 133.5 38 147.5 39 178.0 40 211.5 41 235.5 42 262.0 43 278.0 44 280.0 45 264.5 46 246.0 47 226.0 48 206.5 49 186.0 50 156.5 51 136.5 52 111.5 53 74.5 54 49.5 55 34.5 56 26.5 57 23.0 58 15.5 59 11.0 60 10.0 61 6.5 62 6.0 63 4.5 64 1.0 65 0.0 66 1.0 67 1.0 68 1.5 69 1.5 70 0.0 71 0.0 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 warn #Base N-Count 1 5.1499999999999995 2 0.025 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 99.775 #Duplication Level Percentage of deduplicated Percentage of total 1 99.77449260836883 99.55000000000001 2 0.22550739163117012 0.44999999999999996 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 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.025 0.0 0.0 0.0 0.0 92-93 0.0875 0.0 0.0 0.0 0.0 94-95 0.16249999999999998 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.2 0.0 0.0 0.0 0.0 102-103 0.3125 0.0 0.0 0.0 0.0 104-105 0.4375 0.0 0.0 0.0 0.0 106-107 0.5375000000000001 0.0 0.0 0.0 0.0 108-109 0.625 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.8125 0.0 0.0 0.0 0.0 114-115 1.075 0.0 0.0 0.0 0.0 116-117 1.325 0.0 0.0 0.0 0.0 118-119 1.6 0.0 0.0 0.0 0.0 120-121 1.8624999999999998 0.0 0.0 0.0 0.0 122-123 2.0875 0.0 0.0 0.0 0.0 124-125 2.3 0.0 0.0 0.0 0.0 126-127 2.4749999999999996 0.0 0.0 0.0 0.0 128-129 2.625 0.0 0.0 0.0 0.0 130-131 2.8625 0.0 0.0 0.0 0.0 132-133 3.275 0.0 0.0 0.0 0.0 134-135 3.7750000000000004 0.0 0.0 0.0 0.0 136-137 4.4 0.0 0.0 0.0 0.0 138-139 4.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTATTTA 10 0.006841402 144.925 3 TATTTAA 10 0.006841402 144.925 4 AAAAAAA 130 6.1509846E-4 10.033269 95-99 >>END_MODULE SRR7172080 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172080_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.31975 34.0 33.0 34.0 33.0 34.0 2 33.408 34.0 33.0 34.0 33.0 34.0 3 33.4275 34.0 33.0 34.0 33.0 34.0 4 33.404 34.0 33.0 34.0 33.0 34.0 5 33.433 34.0 33.0 34.0 33.0 34.0 6 37.60975 38.0 38.0 38.0 38.0 38.0 7 37.60625 38.0 38.0 38.0 38.0 38.0 8 37.6 38.0 38.0 38.0 38.0 38.0 9 37.64375 38.0 38.0 38.0 38.0 38.0 10-14 37.56975 38.0 38.0 38.0 38.0 38.0 15-19 37.5788 38.0 38.0 38.0 38.0 38.0 20-24 37.557950000000005 38.0 38.0 38.0 38.0 38.0 25-29 37.56245 38.0 38.0 38.0 38.0 38.0 30-34 37.524150000000006 38.0 38.0 38.0 38.0 38.0 35-39 37.50695 38.0 38.0 38.0 38.0 38.0 40-44 37.4751 38.0 38.0 38.0 38.0 38.0 45-49 37.4371 38.0 38.0 38.0 37.6 38.0 50-54 37.429100000000005 38.0 38.0 38.0 37.8 38.0 55-59 37.4111 38.0 38.0 38.0 37.0 38.0 60-64 37.299350000000004 38.0 38.0 38.0 37.0 38.0 65-69 37.24935000000001 38.0 38.0 38.0 37.0 38.0 70-74 37.2475 38.0 38.0 38.0 37.0 38.0 75-79 37.10095 38.0 38.0 38.0 36.4 38.0 80-84 37.0619 38.0 38.0 38.0 36.0 38.0 85-89 36.98025 38.0 38.0 38.0 36.0 38.0 90-94 36.9371 38.0 38.0 38.0 36.0 38.0 95-99 36.783300000000004 38.0 38.0 38.0 35.8 38.0 100-104 36.7575 38.0 38.0 38.0 35.0 38.0 105-109 36.7056 38.0 38.0 38.0 34.8 38.0 110-114 36.513149999999996 38.0 38.0 38.0 34.4 38.0 115-119 36.357600000000005 38.0 38.0 38.0 34.0 38.0 120-124 36.13995 38.0 37.6 38.0 33.4 38.0 125-129 35.87215 38.0 36.8 38.0 32.6 38.0 130-134 35.6237 38.0 36.0 38.0 31.6 38.0 135-139 35.316500000000005 38.0 36.0 38.0 30.6 38.0 140-144 34.94825 38.0 36.0 38.0 28.2 38.0 145-149 34.27425 38.0 34.6 38.0 26.8 38.0 150-151 30.625 36.5 29.0 38.0 12.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 1.0 4 2.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 4.0 13 3.0 14 1.0 15 3.0 16 2.0 17 1.0 18 1.0 19 2.0 20 0.0 21 4.0 22 0.0 23 8.0 24 16.0 25 10.0 26 8.0 27 9.0 28 19.0 29 16.0 30 26.0 31 43.0 32 53.0 33 69.0 34 105.0 35 197.0 36 589.0 37 2807.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.975 15.575 15.325 30.125 2 22.85 23.05 35.5 18.6 3 19.900000000000002 26.325 32.425 21.349999999999998 4 23.825 34.775 22.425 18.975 5 23.125 38.175 22.400000000000002 16.3 6 18.6 38.275 23.375 19.75 7 17.525 15.525 45.15 21.8 8 20.1 22.2 27.825 29.875 9 22.425 24.025 28.425 25.124999999999996 10-14 22.919999999999998 28.655 26.69 21.735 15-19 23.549999999999997 28.21 27.91 20.330000000000002 20-24 23.16 28.744999999999997 27.805000000000003 20.29 25-29 22.384999999999998 29.085 27.529999999999998 21.0 30-34 22.79 28.555000000000003 27.83 20.825 35-39 22.939999999999998 28.51 28.23 20.32 40-44 22.86 28.065 28.410000000000004 20.665 45-49 22.865 27.98 28.395 20.76 50-54 22.785 28.360000000000003 28.62 20.235 55-59 23.09 28.29 28.555000000000003 20.064999999999998 60-64 23.044999999999998 28.105000000000004 28.449999999999996 20.4 65-69 23.86 28.27 27.88 19.99 70-74 24.044999999999998 28.110000000000003 27.73 20.115 75-79 23.445 28.244999999999997 27.865000000000002 20.445 80-84 23.445 28.560000000000002 27.560000000000002 20.435 85-89 23.41 28.12 28.02 20.45 90-94 23.715 28.985 27.415 19.885 95-99 23.41 28.375 27.85 20.365 100-104 24.005000000000003 28.084999999999997 27.805000000000003 20.105 105-109 23.215 28.084999999999997 28.365000000000002 20.335 110-114 23.645 28.13 28.134999999999998 20.09 115-119 23.11 27.965 28.544999999999998 20.380000000000003 120-124 23.855 28.355000000000004 28.08 19.71 125-129 24.099999999999998 28.060000000000002 27.955000000000002 19.885 130-134 23.59 28.134999999999998 28.499999999999996 19.775000000000002 135-139 24.099999999999998 28.310000000000002 28.055000000000003 19.535 140-144 24.48 27.43 27.665 20.424999999999997 145-149 25.11 27.675 27.744999999999997 19.470000000000002 150-151 24.5 28.15 28.1875 19.162499999999998 >>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 0.0 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 0.0 22 0.5 23 1.5 24 3.0 25 5.0 26 3.5 27 2.5 28 7.5 29 16.0 30 23.0 31 20.5 32 21.5 33 30.5 34 52.5 35 78.5 36 94.0 37 118.5 38 140.5 39 161.0 40 201.0 41 238.0 42 272.5 43 292.5 44 269.0 45 268.0 46 287.5 47 253.5 48 221.0 49 194.0 50 160.5 51 132.5 52 102.5 53 77.0 54 59.0 55 46.0 56 33.0 57 30.0 58 25.5 59 18.5 60 12.0 61 7.5 62 6.0 63 4.5 64 2.0 65 2.0 66 1.0 67 0.5 68 0.5 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.5 76 0.5 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 99.6 #Duplication Level Percentage of deduplicated Percentage of total 1 99.67369477911646 99.275 2 0.30120481927710846 0.6 3 0.0 0.0 4 0.0 0.0 5 0.0251004016064257 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 AGCAAATTCAGTTTCTAAGCAAAAGCTTTCCAGGCCCCTTTATCCTATTT 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.025 0.0 0.0 0.0 0.0 92-93 0.0875 0.0 0.0 0.0 0.0 94-95 0.16249999999999998 0.0 0.0 0.0 0.0 96-97 0.175 0.0 0.0 0.0 0.0 98-99 0.175 0.0 0.0 0.0 0.0 100-101 0.2 0.0 0.0 0.0 0.0 102-103 0.3125 0.0 0.0 0.0 0.0 104-105 0.4375 0.0 0.0 0.0 0.0 106-107 0.5375000000000001 0.0 0.0 0.0 0.0 108-109 0.625 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.8125 0.0 0.0 0.0 0.0 114-115 1.075 0.0 0.0 0.0 0.0 116-117 1.325 0.0 0.0 0.0 0.0 118-119 1.6124999999999998 0.0 0.0 0.0 0.0 120-121 1.8875000000000002 0.0 0.0 0.0 0.0 122-123 2.1125 0.0 0.0 0.0 0.0 124-125 2.325 0.0 0.0 0.0 0.0 126-127 2.5 0.0 0.0 0.0 0.0 128-129 2.6500000000000004 0.0 0.0 0.0 0.0 130-131 2.875 0.0 0.0 0.0 0.0 132-133 3.275 0.0 0.0 0.0 0.0 134-135 3.7875 0.0 0.0 0.0 0.0 136-137 4.375 0.0 0.0 0.0 0.0 138-139 4.8375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTTAT 10 0.006830828 145.0 1 AATTCAG 10 0.006830828 145.0 5 >>END_MODULE Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537799 spots for SRR7172080.sra Written 537799 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra Read 537796 spots for SRR7172080.sra Written 537796 spots for SRR7172080.sra SRR ids: ['SRR7172080.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v4pk2qdb SRR7172080.sra spots: 10755923 blocks: [[1, 537796], [537797, 1075592], [1075593, 1613388], [1613389, 2151184], [2151185, 2688980], [2688981, 3226776], [3226777, 3764572], [3764573, 4302368], [4302369, 4840164], [4840165, 5377960], [5377961, 5915756], [5915757, 6453552], [6453553, 6991348], [6991349, 7529144], [7529145, 8066940], [8066941, 8604736], [8604737, 9142532], [9142533, 9680328], [9680329, 10218124], [10218125, 10755923]] SRR7172080 file size 3623129 SRR7172080 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 SRR7172080 SRR7172080_1.fastq SRR7172080_2.fastq Input file: SRR7172080_1.fastq Paired file: SRR7172080_2.fastq trimmed: SRR7172080-trimmed-pair1.fastq, SRR7172080-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 Fri Feb 14 03:32:26 2025 >> started Fri Feb 14 03:32:38 2025 >> done (11.906s) 10755923 read pairs processed; of these: 4975 ( 0.05%) short read pairs filtered out after trimming by size control 3752 ( 0.03%) empty read pairs filtered out after trimming by size control 10747196 (99.92%) read pairs available; of these: 5237484 (48.73%) trimmed read pairs available after processing 5509712 (51.27%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 4 0.00% 20 1 0.00% 21 2 0.00% 22 5 0.00% 23 2 0.00% 24 6 0.00% 25 3 0.00% 26 5 0.00% 27 5 0.00% 28 3 0.00% 29 4 0.00% 30 3 0.00% 31 2 0.00% 32 7 0.00% 33 9 0.00% 34 7 0.00% 35 5 0.00% 36 8 0.00% 37 5 0.00% 38 7 0.00% 39 5 0.00% 40 3 0.00% 41 6 0.00% 42 5 0.00% 43 10 0.00% 44 3 0.00% 45 16 0.00% 46 11 0.00% 47 8 0.00% 48 10 0.00% 49 14 0.00% 50 20 0.00% 51 17 0.00% 52 18 0.00% 53 23 0.00% 54 24 0.00% 55 34 0.00% 56 37 0.00% 57 24 0.00% 58 36 0.00% 59 48 0.00% 60 45 0.00% 61 69 0.00% 62 71 0.00% 63 65 0.00% 64 93 0.00% 65 114 0.00% 66 120 0.00% 67 133 0.00% 68 160 0.00% 69 159 0.00% 70 164 0.00% 71 236 0.00% 72 269 0.00% 73 290 0.00% 74 342 0.00% 75 372 0.00% 76 489 0.00% 77 501 0.00% 78 534 0.00% 79 618 0.01% 80 751 0.01% 81 840 0.01% 82 890 0.01% 83 1051 0.01% 84 1282 0.01% 85 1665 0.02% 86 1829 0.02% 87 2093 0.02% 88 2311 0.02% 89 2352 0.02% 90 2637 0.02% 91 2907 0.03% 92 3069 0.03% 93 3357 0.03% 94 3607 0.03% 95 4026 0.04% 96 4182 0.04% 97 4320 0.04% 98 4834 0.04% 99 5111 0.05% 100 5378 0.05% 101 5887 0.05% 102 6313 0.06% 103 6879 0.06% 104 7076 0.07% 105 7730 0.07% 106 8113 0.08% 107 8531 0.08% 108 9156 0.09% 109 9446 0.09% 110 10047 0.09% 111 10511 0.10% 112 11284 0.10% 113 11932 0.11% 114 12591 0.12% 115 13053 0.12% 116 13878 0.13% 117 14442 0.13% 118 14982 0.14% 119 15588 0.15% 120 16229 0.15% 121 16937 0.16% 122 17826 0.17% 123 18920 0.18% 124 19769 0.18% 125 20649 0.19% 126 21931 0.20% 127 22623 0.21% 128 23341 0.22% 129 24926 0.23% 130 26143 0.24% 131 27213 0.25% 132 28853 0.27% 133 30560 0.28% 134 32986 0.31% 135 34693 0.32% 136 36647 0.34% 137 39520 0.37% 138 41808 0.39% 139 45587 0.42% 140 49415 0.46% 141 54759 0.51% 142 61881 0.58% 143 70307 0.65% 144 84110 0.78% 145 103602 0.96% 146 134541 1.25% 147 193620 1.80% 148 316755 2.95% 149 665179 6.19% 150 2694913 25.08% 151 5509712 51.27% 10747196 reads passed initial QC criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=3.90 fanout-score-rank=23 prefix-density=0.33 prefix-fanout=3.3 sequence=CCACATTTGCAGCCA criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=151.63 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=13.4 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATA criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.22 fanout-score-rank=33 prefix-density=0.49 prefix-fanout=2.2 sequence=GGCAGTGGCTGCAA criterion=fanout-score sequence-density=0.07 sequence-density-rank=31 fanout-score=26.99 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=3.0 sequence=CTGCAAATGAGAAAAC SRR7172080 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 03:33:28 Started mapping on | Feb 14 03:33:28 Finished on | Feb 14 03:35:06 Mapping speed, Million of reads per hour | 394.79 Number of input reads | 10747196 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 9997886 Uniquely mapped reads % | 93.03% Average mapped length | 295.30 Number of splices: Total | 9811992 Number of splices: Annotated (sjdb) | 9616753 Number of splices: GT/AG | 9646025 Number of splices: GC/AG | 126335 Number of splices: AT/AC | 8006 Number of splices: Non-canonical | 31626 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 2.20 Insertion rate per base | 0.03% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 282853 % of reads mapped to multiple loci | 2.63% Number of reads mapped to too many loci | 40177 % of reads mapped to too many loci | 0.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.86% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 472159 472159 472159 N_multimapping 282853 282853 282853 N_noFeature 339075 9885770 401063 N_ambiguous 104687 566 54360 UnstrandedReadsAssigned:9554124 PositiveStrandReadsAssigned:111550 NegativeStrandReadsAssigned:9542463 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7172080 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: SRR7172080-trimmed-pair1.fastq SRR7172080-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,747,196 reads, 9,439,440 reads pseudoaligned [quant] estimated average fragment length: 253.909 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 970 rounds 52401 SRR7172080.ke.tsv 34699 SRR7172080.se.tsv 87100 total ==> SRR7172080.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1765.09 751 45.2344 Potri.005G024800.1.v4.1 1035 782.091 69 9.37968 Potri.004G059700.1.v4.1 961 708.112 15 2.25209 Potri.007G009000.2.v4.1 1416 1163.09 0 0 Potri.003G141000.2.v4.1 2943 2690.09 306.136 12.0988 Potri.016G087400.1.v4.1 270 76.7918 723 1000.97 Potri.015G069301.1.v4.1 564 317.967 0 0 Potri.010G195200.1.v4.1 1773 1520.09 288 20.1428 Potri.012G127500.1.v4.1 977 724.096 3242 476.007 ==> SRR7172080.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 54 Potri.001G233950.v4.1 2 Potri.001G122700.v4.1 229 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 321 SRR7172080 completed mapping pipeline successfully