Starting /dee2/code/volunteer_pipeline.sh SRR1797577 current disk space = 1525258645504 free memory = 1579609888 SRR1797577 SRAfilesize 89bb16a1dc127187d7be8bbdc03f7b50 SRR1797577.sra SRR1797577.sra file validated SRR1797577 is paired end SRR1797577 is conventional basespace SRR1797577 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797577_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 54 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.01275 34.0 34.0 34.0 31.0 34.0 2 32.83025 34.0 34.0 34.0 31.0 34.0 3 33.36075 34.0 34.0 34.0 31.0 34.0 4 36.73825 37.0 37.0 37.0 35.0 37.0 5 36.754 37.0 37.0 37.0 37.0 37.0 6 36.7515 37.0 37.0 37.0 37.0 37.0 7 36.7455 37.0 37.0 37.0 37.0 37.0 8 36.7705 37.0 37.0 37.0 37.0 37.0 9 38.728 39.0 39.0 39.0 39.0 39.0 10-14 38.9886 39.4 39.2 39.4 38.4 39.4 15-19 40.25750000000001 41.0 40.2 41.0 38.8 41.0 20-24 40.1545 41.0 40.0 41.0 38.4 41.0 25-29 39.7191 41.0 39.8 41.0 37.4 41.0 30-34 39.58364999999999 41.0 39.8 41.0 36.2 41.0 35-39 39.203700000000005 41.0 39.0 41.0 35.0 41.0 40-44 38.810950000000005 40.8 38.0 41.0 35.0 41.0 45-49 38.2022 40.0 36.0 41.0 34.6 41.0 50-54 37.55050000000001 39.6 35.0 41.0 33.4 41.0 55-59 36.76985 38.2 35.0 41.0 33.0 41.0 60-64 36.194849999999995 36.6 35.0 40.0 32.8 41.0 65-69 35.622949999999996 35.4 35.0 39.0 32.6 41.0 70-74 34.944199999999995 35.0 35.0 37.2 32.4 39.8 75-79 33.89635 35.0 34.0 36.0 30.8 38.0 80-84 33.719950000000004 35.0 34.0 35.0 31.0 36.6 85-89 33.34485 35.0 34.0 35.0 30.8 36.0 90-94 32.889599999999994 35.0 34.0 35.0 29.6 35.0 95-99 32.49159999999999 35.0 33.4 35.0 28.2 35.0 100-104 31.989650000000005 35.0 33.0 35.0 26.2 35.0 105-109 31.82405 35.0 33.0 35.0 25.4 35.0 110-114 31.2354 35.0 32.2 35.0 24.0 35.0 115-119 30.583500000000004 34.0 31.0 35.0 21.2 35.0 120-124 29.80885 34.0 30.0 35.0 16.2 35.0 125-129 29.29215 34.0 29.2 35.0 9.2 35.0 130-134 28.192049999999995 33.6 27.4 35.0 2.0 35.0 135-139 27.11395 33.0 24.8 35.0 2.0 35.0 140-144 26.27895 33.0 24.0 35.0 2.0 35.0 145-149 24.578500000000002 32.0 12.2 34.6 2.0 35.0 150 17.42875 20.0 2.0 29.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 2.0 7 3.0 8 5.0 9 8.0 10 2.0 11 3.0 12 7.0 13 7.0 14 9.0 15 5.0 16 11.0 17 9.0 18 13.0 19 22.0 20 11.0 21 15.0 22 31.0 23 30.0 24 26.0 25 51.0 26 39.0 27 54.0 28 79.0 29 79.0 30 97.0 31 127.0 32 183.0 33 278.0 34 376.0 35 640.0 36 1046.0 37 728.0 38 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.61493950552341 11.204629142556549 12.572330352446082 44.60810099947396 2 29.825000000000003 10.325 24.349999999999998 35.5 3 24.7 11.0 18.175 46.125 4 29.65 14.85 17.575 37.925 5 30.975 20.925 20.325 27.775 6 32.425 22.275 19.075 26.224999999999998 7 20.125 27.950000000000003 30.775000000000002 21.15 8 23.225 23.025000000000002 28.299999999999997 25.45 9 22.975 20.150000000000002 28.65 28.225 10-14 24.2 24.565 24.825 26.41 15-19 25.009999999999998 22.955000000000002 24.62 27.415 20-24 25.36126806340317 23.50117505875294 23.77618880944047 27.36136806840342 25-29 25.545 23.145 23.605 27.705000000000002 30-34 25.319999999999997 23.165 23.16 28.355000000000004 35-39 25.330000000000002 23.21 23.31 28.15 40-44 25.8 23.1 23.455000000000002 27.644999999999996 45-49 25.83 22.75 23.355 28.065 50-54 25.695 22.915 22.775000000000002 28.615000000000002 55-59 25.45 22.865 23.119999999999997 28.565 60-64 26.040000000000003 22.830000000000002 22.720000000000002 28.410000000000004 65-69 26.284999999999997 22.89 22.85 27.975 70-74 25.929999999999996 22.400000000000002 23.155 28.515 75-79 25.840000000000003 22.814999999999998 23.200000000000003 28.144999999999996 80-84 26.505000000000003 22.31 22.405 28.78 85-89 26.205000000000002 22.439999999999998 22.395 28.96 90-94 26.5 22.27 22.715 28.515 95-99 26.889999999999997 22.439999999999998 22.585 28.084999999999997 100-104 26.590000000000003 22.455 22.634999999999998 28.32 105-109 26.47 22.189999999999998 22.96 28.38 110-114 27.169999999999998 21.560000000000002 22.075 29.195 115-119 27.189999999999998 21.975 22.3 28.535 120-124 26.91 22.52 21.46 29.110000000000003 125-129 27.089999999999996 21.795 21.975 29.14 130-134 27.095000000000002 21.490000000000002 22.225 29.189999999999998 135-139 28.13 21.445 22.005 28.42 140-144 27.705000000000002 22.189999999999998 21.375 28.73 145-149 27.839999999999996 21.43 22.13 28.599999999999998 150 28.175 21.75 18.5 31.574999999999996 >>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 0.0 24 0.0 25 0.0 26 0.0 27 0.5 28 0.5 29 1.5 30 3.5 31 4.5 32 7.5 33 12.5 34 17.0 35 21.0 36 27.0 37 34.5 38 55.0 39 74.5 40 82.5 41 102.5 42 116.0 43 131.0 44 143.0 45 140.0 46 151.5 47 157.5 48 144.5 49 131.0 50 137.0 51 135.5 52 122.0 53 113.0 54 111.0 55 115.0 56 102.0 57 83.0 58 78.0 59 81.5 60 79.0 61 82.0 62 87.5 63 81.5 64 76.0 65 79.5 66 84.5 67 80.5 68 75.0 69 76.5 70 75.0 71 69.0 72 61.5 73 54.5 74 54.0 75 50.5 76 46.5 77 38.0 78 28.0 79 21.5 80 14.0 81 11.0 82 9.5 83 11.0 84 8.5 85 4.5 86 2.0 87 0.0 88 0.5 89 0.5 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 4.95 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 0.005 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57318604067285 99.15 2 0.42681395932714034 0.8500000000000001 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 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0125 0.0 0.0 0.0 0.0 106-107 0.05 0.0 0.0 0.0 0.0 108-109 0.05 0.0 0.0 0.0 0.0 110-111 0.075 0.0 0.0 0.0 0.0 112-113 0.0875 0.0 0.0 0.0 0.0 114-115 0.1 0.0 0.0 0.0 0.0 116-117 0.175 0.0 0.0 0.0 0.0 118-119 0.175 0.0 0.0 0.0 0.0 120-121 0.175 0.0 0.0 0.0 0.0 122-123 0.25 0.0 0.0 0.0 0.0 124-125 0.2625 0.0 0.0 0.0 0.0 126-127 0.3625 0.0 0.0 0.0 0.0 128-129 0.45 0.0 0.0 0.0 0.0 130-131 0.6375 0.0 0.0 0.0 0.0 132-133 0.8125 0.0 0.0 0.0 0.0 134-135 1.075 0.0 0.0 0.0 0.0 136-137 1.3 0.0 0.0 0.0 0.0 138 1.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR1797577 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797577_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 55 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.11 34.0 33.0 34.0 31.0 34.0 2 33.318 34.0 34.0 34.0 31.0 34.0 3 33.302 34.0 34.0 34.0 31.0 34.0 4 36.605 37.0 37.0 37.0 35.0 37.0 5 36.68125 37.0 37.0 37.0 37.0 37.0 6 36.61775 37.0 37.0 37.0 36.0 37.0 7 36.527 37.0 37.0 37.0 35.0 37.0 8 36.60375 37.0 37.0 37.0 35.0 37.0 9 38.5205 39.0 39.0 39.0 38.0 39.0 10-14 38.85525 39.4 39.4 39.4 38.2 39.4 15-19 39.9352 41.0 40.2 41.0 38.2 41.0 20-24 39.79935 41.0 40.0 41.0 38.0 41.0 25-29 39.3917 41.0 39.8 41.0 36.4 41.0 30-34 38.8228 40.6 38.6 41.0 35.0 41.0 35-39 38.77465000000001 41.0 38.4 41.0 35.0 41.0 40-44 38.1835 40.0 36.4 41.0 34.8 41.0 45-49 37.5401 39.6 35.0 41.0 33.2 41.0 50-54 36.497049999999994 38.2 34.8 40.4 32.4 41.0 55-59 36.233050000000006 36.6 35.0 40.8 32.8 41.0 60-64 35.90795 35.4 35.0 39.6 33.0 41.0 65-69 35.2057 35.0 35.0 38.4 32.4 40.8 70-74 34.5324 35.0 35.0 36.6 32.0 39.2 75-79 33.815250000000006 35.0 34.6 35.4 30.8 37.4 80-84 33.2034 35.0 33.8 35.0 29.8 36.2 85-89 32.81745 35.0 34.0 35.0 29.0 35.4 90-94 32.5012 35.0 33.2 35.0 28.2 35.0 95-99 32.12285000000001 35.0 33.0 35.0 26.6 35.0 100-104 31.766949999999998 35.0 33.0 35.0 25.0 35.0 105-109 31.319300000000005 35.0 32.4 35.0 23.6 35.0 110-114 30.60855 34.4 31.2 35.0 21.0 35.0 115-119 30.155700000000003 34.0 30.8 35.0 18.0 35.0 120-124 29.419549999999997 34.0 29.4 35.0 9.6 35.0 125-129 28.805149999999998 34.0 28.8 35.0 3.2 35.0 130-134 28.356749999999998 33.8 28.2 35.0 2.0 35.0 135-139 27.126599999999996 33.0 25.0 35.0 2.0 35.0 140-144 26.018700000000003 32.6 23.0 35.0 2.0 35.0 145-149 24.21835 31.6 9.8 34.0 2.0 35.0 150 18.20325 24.0 2.0 30.0 2.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 2.0 4 1.0 5 4.0 6 3.0 7 8.0 8 8.0 9 5.0 10 9.0 11 4.0 12 6.0 13 6.0 14 4.0 15 7.0 16 14.0 17 9.0 18 18.0 19 16.0 20 20.0 21 27.0 22 32.0 23 30.0 24 32.0 25 40.0 26 45.0 27 67.0 28 65.0 29 86.0 30 105.0 31 138.0 32 188.0 33 272.0 34 394.0 35 694.0 36 1043.0 37 588.0 38 4.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 27.925 17.849999999999998 10.875 43.35 2 35.708927231807955 24.956239059764943 16.829207301825456 22.50562640660165 3 24.675 26.924999999999997 20.225 28.175 4 28.7 25.074999999999996 20.424999999999997 25.8 5 32.375 25.974999999999998 18.3 23.35 6 27.125 31.974999999999998 18.175 22.725 7 24.375 17.9 29.95 27.775 8 27.3 20.974999999999998 21.2 30.525000000000002 9 26.0 20.65 23.275000000000002 30.075000000000003 10-14 28.494999999999997 23.995 20.244999999999997 27.265 15-19 28.125 23.175 21.905 26.795 20-24 28.49 23.315 21.47 26.724999999999998 25-29 28.985 22.6 20.825 27.589999999999996 30-34 28.575 22.74 21.575 27.11 35-39 28.155 22.985 21.495 27.365000000000002 40-44 28.64 22.685 21.240000000000002 27.435 45-49 28.744999999999997 22.785 21.72 26.75 50-54 28.78 22.82 21.27 27.13 55-59 28.95 22.705000000000002 21.395 26.950000000000003 60-64 27.87 22.435 22.235 27.46 65-69 28.749999999999996 22.825 21.584999999999997 26.840000000000003 70-74 29.075 22.685 21.584999999999997 26.655 75-79 28.74 22.564999999999998 22.205 26.490000000000002 80-84 29.125 22.455 22.055 26.365 85-89 29.49 22.27 21.46 26.779999999999998 90-94 29.125 22.63 21.78 26.465 95-99 28.735 22.275 22.345000000000002 26.645000000000003 100-104 29.265 22.27 21.905 26.56 105-109 28.610000000000003 22.25 22.54 26.6 110-114 29.335 22.235 22.005 26.424999999999997 115-119 29.535 22.14 22.03 26.295 120-124 29.439999999999998 22.74 21.675 26.145000000000003 125-129 29.085 22.91 22.225 25.779999999999998 130-134 29.156457822891145 22.856142807140355 21.826091304565228 26.161308065403272 135-139 29.82 22.07 21.88 26.229999999999997 140-144 29.520000000000003 23.035 21.58 25.865 145-149 30.36 21.91 21.54 26.19 150 30.025000000000002 22.675 19.825 27.474999999999998 >>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 0.5 20 0.5 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.5 28 1.5 29 1.5 30 2.0 31 4.0 32 6.0 33 7.0 34 9.0 35 15.5 36 26.0 37 33.5 38 38.0 39 52.0 40 66.0 41 89.0 42 102.0 43 98.0 44 122.5 45 144.0 46 142.0 47 137.0 48 134.0 49 127.5 50 130.0 51 136.5 52 126.0 53 111.0 54 104.5 55 101.5 56 102.0 57 106.0 58 98.0 59 94.0 60 85.0 61 88.5 62 88.5 63 81.0 64 87.5 65 89.0 66 90.5 67 91.5 68 89.0 69 89.0 70 90.0 71 83.5 72 78.5 73 69.5 74 64.0 75 58.0 76 44.5 77 32.0 78 25.5 79 27.0 80 26.0 81 15.5 82 10.0 83 8.0 84 4.0 85 3.5 86 2.5 87 1.5 88 1.5 89 1.0 90 1.0 91 1.0 92 1.0 93 0.5 94 0.5 95 1.0 96 0.5 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.025 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 0.005 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.6 #Duplication Level Percentage of deduplicated Percentage of total 1 99.59839357429718 99.2 2 0.4016064257028112 0.8 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 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0125 0.0 0.0 0.0 0.0 106-107 0.05 0.0 0.0 0.0 0.0 108-109 0.05 0.0 0.0 0.0 0.0 110-111 0.075 0.0 0.0 0.0 0.0 112-113 0.0875 0.0 0.0 0.0 0.0 114-115 0.1 0.0 0.0 0.0 0.0 116-117 0.175 0.0 0.0 0.0 0.0 118-119 0.175 0.0 0.0 0.0 0.0 120-121 0.175 0.0 0.0 0.0 0.0 122-123 0.25 0.0 0.0 0.0 0.0 124-125 0.2875 0.0 0.0 0.0 0.0 126-127 0.4 0.0 0.0 0.0 0.0 128-129 0.48750000000000004 0.0 0.0 0.0 0.0 130-131 0.6499999999999999 0.0 0.0 0.0 0.0 132-133 0.8375 0.0 0.0 0.0 0.0 134-135 1.1 0.0 0.0 0.0 0.0 136-137 1.35 0.0 0.0 0.0 0.0 138 1.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGGGGG 115 0.002704152 10.01739 130-134 >>END_MODULE Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265721 spots for SRR1797577.sra Written 1265721 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra Read 1265709 spots for SRR1797577.sra Written 1265709 spots for SRR1797577.sra SRR ids: ['SRR1797577.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rl5fy77c SRR1797577.sra spots: 25314192 blocks: [[1, 1265709], [1265710, 2531418], [2531419, 3797127], [3797128, 5062836], [5062837, 6328545], [6328546, 7594254], [7594255, 8859963], [8859964, 10125672], [10125673, 11391381], [11391382, 12657090], [12657091, 13922799], [13922800, 15188508], [15188509, 16454217], [16454218, 17719926], [17719927, 18985635], [18985636, 20251344], [20251345, 21517053], [21517054, 22782762], [22782763, 24048471], [24048472, 25314192]] SRR1797577 file size 8507006 SRR1797577 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 SRR1797577 SRR1797577_1.fastq SRR1797577_2.fastq Input file: SRR1797577_1.fastq Paired file: SRR1797577_2.fastq trimmed: SRR1797577-trimmed-pair1.fastq, SRR1797577-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 Mon Dec 9 13:16:58 2024 >> started Mon Dec 9 13:18:46 2024 >> done (107.821s) 25314192 read pairs processed; of these: 56962 ( 0.23%) short read pairs filtered out after trimming by size control 41104 ( 0.16%) empty read pairs filtered out after trimming by size control 25216126 (99.61%) read pairs available; of these: 18335286 (72.71%) trimmed read pairs available after processing 6880840 (27.29%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 39 0.00% 20 72 0.00% 21 110 0.00% 22 174 0.00% 23 248 0.00% 24 287 0.00% 25 377 0.00% 26 503 0.00% 27 621 0.00% 28 724 0.00% 29 881 0.00% 30 1024 0.00% 31 1165 0.00% 32 1305 0.01% 33 1381 0.01% 34 1591 0.01% 35 1653 0.01% 36 1770 0.01% 37 1991 0.01% 38 2106 0.01% 39 2325 0.01% 40 2463 0.01% 41 2624 0.01% 42 2751 0.01% 43 2918 0.01% 44 3081 0.01% 45 3243 0.01% 46 3380 0.01% 47 3713 0.01% 48 3686 0.01% 49 3856 0.02% 50 4317 0.02% 51 4381 0.02% 52 4699 0.02% 53 5015 0.02% 54 5063 0.02% 55 5492 0.02% 56 5731 0.02% 57 6058 0.02% 58 6201 0.02% 59 6477 0.03% 60 6806 0.03% 61 7198 0.03% 62 7515 0.03% 63 7862 0.03% 64 8322 0.03% 65 8848 0.04% 66 9184 0.04% 67 9639 0.04% 68 10133 0.04% 69 10471 0.04% 70 11161 0.04% 71 11774 0.05% 72 12462 0.05% 73 12952 0.05% 74 13706 0.05% 75 14432 0.06% 76 15360 0.06% 77 16011 0.06% 78 17129 0.07% 79 18133 0.07% 80 19491 0.08% 81 20503 0.08% 82 21954 0.09% 83 23980 0.10% 84 28014 0.11% 85 29933 0.12% 86 31539 0.13% 87 33379 0.13% 88 35142 0.14% 89 36703 0.15% 90 37966 0.15% 91 39896 0.16% 92 41412 0.16% 93 42574 0.17% 94 44621 0.18% 95 46302 0.18% 96 48258 0.19% 97 49784 0.20% 98 52177 0.21% 99 54350 0.22% 100 55584 0.22% 101 57357 0.23% 102 59599 0.24% 103 62430 0.25% 104 65805 0.26% 105 69484 0.28% 106 73228 0.29% 107 78244 0.31% 108 82989 0.33% 109 87544 0.35% 110 91593 0.36% 111 96416 0.38% 112 100585 0.40% 113 104496 0.41% 114 112522 0.45% 115 120662 0.48% 116 126094 0.50% 117 131505 0.52% 118 136899 0.54% 119 144965 0.57% 120 151648 0.60% 121 162644 0.64% 122 171163 0.68% 123 182537 0.72% 124 192084 0.76% 125 197917 0.78% 126 210965 0.84% 127 221944 0.88% 128 235709 0.93% 129 248806 0.99% 130 264314 1.05% 131 282299 1.12% 132 300979 1.19% 133 318514 1.26% 134 326116 1.29% 135 339014 1.34% 136 358384 1.42% 137 376362 1.49% 138 396152 1.57% 139 422555 1.68% 140 452376 1.79% 141 483576 1.92% 142 521455 2.07% 143 562925 2.23% 144 622142 2.47% 145 715683 2.84% 146 850522 3.37% 147 1074148 4.26% 148 1494865 5.93% 149 3266898 12.96% 150 6880840 27.29% 25216126 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=4.10 fanout-score-rank=33 prefix-density=0.30 prefix-fanout=3.7 sequence=TGCCGCACTTGCAG criterion=fanout-score sequence-density=0.05 sequence-density-rank=37 fanout-score=366.47 fanout-score-rank=1 prefix-density=1.02 prefix-fanout=17.9 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=149.43 fanout-score-rank=8 prefix-density=1.61 prefix-fanout=21.8 sequence=CGGCGGCGGCGG criterion=fanout-score sequence-density=0.12 sequence-density-rank=30 fanout-score=299.43 fanout-score-rank=1 prefix-density=1.61 prefix-fanout=21.8 sequence=CGGCGGCGGCGC SRR1797577 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 13:20:54 Started mapping on | Dec 09 13:21:01 Finished on | Dec 09 13:23:20 Mapping speed, Million of reads per hour | 653.08 Number of input reads | 25216126 Average input read length | 277 UNIQUE READS: Uniquely mapped reads number | 23908500 Uniquely mapped reads % | 94.81% Average mapped length | 277.39 Number of splices: Total | 18722139 Number of splices: Annotated (sjdb) | 17707609 Number of splices: GT/AG | 18482207 Number of splices: GC/AG | 199271 Number of splices: AT/AC | 11210 Number of splices: Non-canonical | 29451 Mismatch rate per base, % | 0.27% Deletion rate per base | 0.02% Deletion average length | 2.70 Insertion rate per base | 0.01% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 369904 % of reads mapped to multiple loci | 1.47% Number of reads mapped to too many loci | 89055 % of reads mapped to too many loci | 0.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.85% % of reads unmapped: other | 2.52% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 964738 964738 964738 N_multimapping 369904 369904 369904 N_noFeature 579263 23148619 991509 N_ambiguous 398917 2832 53829 UnstrandedReadsAssigned:22930320 PositiveStrandReadsAssigned:757049 NegativeStrandReadsAssigned:22863162 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=142 echo kmer=137 SRR1797577 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: SRR1797577-trimmed-pair1.fastq SRR1797577-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 25,216,126 reads, 23,022,489 reads pseudoaligned [quant] estimated average fragment length: 212.023 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,163 rounds 52973 SRR1797577.ke.tsv 35125 SRR1797577.se.tsv 88098 total ==> SRR1797577.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 725.132 0 0 PNS24247 1044 832.977 33.7375 2.4626 PNS24249 1928 1716.98 396.323 14.0345 PNS24246 1044 832.977 33.7375 2.4626 PNS24248 1044 832.977 33.7375 2.4626 PNS24244 1471 1259.98 61.4648 2.96604 PNS24243 293 92.5451 0 0 KQK14069 1603 1391.98 1798.79 78.5708 KQK14071 474 264.638 57.5383 13.2196 ==> SRR1797577.se.tsv <== BRADI_1g14170v3 1886 BRADI_1g53295v3 186 BRADI_1g59795v3 312 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 573 BRADI_1g74790v3 414 BRADI_1g09890v3 0 BRADI_1g77505v3 198 BRADI_1g48960v3 9 SRR1797577 completed mapping pipeline successfully