Starting /dee2/code/volunteer_pipeline.sh SRR12455390 current disk space = 1524921561088 free memory = 1554989064 SRR12455390 SRAfilesize ef44e49f5b09f1c62213bd09a3d8ed1c SRR12455390.sra SRR12455390.sra file validated SRR12455390 is paired end SRR12455390 is conventional basespace SRR12455390 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12455390_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 57 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.55125 32.0 32.0 32.0 27.0 32.0 2 28.09125 32.0 27.0 32.0 12.0 32.0 3 34.14625 37.0 32.0 37.0 32.0 37.0 4 35.89375 37.0 37.0 37.0 32.0 37.0 5 36.1775 37.0 37.0 37.0 37.0 37.0 6 39.37625 41.0 41.0 41.0 37.0 41.0 7 38.072 41.0 37.0 41.0 32.0 41.0 8 39.48375 41.0 41.0 41.0 37.0 41.0 9 38.5245 41.0 37.0 41.0 32.0 41.0 10-14 39.16295 41.0 40.2 41.0 36.0 41.0 15-19 39.131150000000005 41.0 40.2 41.0 35.0 41.0 20-24 39.4855 41.0 41.0 41.0 37.0 41.0 25-29 39.3994 41.0 41.0 41.0 37.0 41.0 30-34 39.37605 41.0 41.0 41.0 37.0 41.0 35-39 39.08565 41.0 41.0 41.0 35.0 41.0 40-44 36.0134 39.2 34.6 41.0 25.0 41.0 45-49 35.908550000000005 40.2 35.0 41.0 21.0 41.0 50-54 36.387699999999995 40.2 34.0 41.0 26.0 41.0 55-59 33.930749999999996 36.6 29.0 40.2 22.0 41.0 60-64 31.778699999999997 34.8 26.0 39.2 16.0 41.0 65-69 34.82455 40.2 33.0 41.0 15.0 41.0 70-74 30.574149999999996 35.0 19.0 41.0 14.0 41.0 75-79 32.179 33.8 28.0 39.4 21.0 41.0 80-84 34.6381 39.4 30.0 41.0 19.0 41.0 85-89 34.9724 39.4 32.0 41.0 21.0 41.0 90-94 32.15585 36.8 24.0 41.0 15.0 41.0 95-99 32.03995 34.8 24.0 41.0 16.0 41.0 100-104 34.874900000000004 40.2 32.0 41.0 18.0 41.0 105-109 31.6878 35.0 26.0 41.0 14.0 41.0 110-114 31.6433 35.8 23.0 40.2 16.0 41.0 115-119 34.411 38.4 29.0 41.0 20.0 41.0 120-124 34.8678 40.2 32.0 41.0 19.0 41.0 125-129 31.951600000000003 36.0 26.0 41.0 14.0 41.0 130-134 31.7274 36.0 23.0 41.0 12.0 41.0 135-139 28.1855 30.0 20.0 37.6 12.0 41.0 140-144 29.76265 33.0 20.0 40.2 12.0 41.0 145-149 32.149950000000004 36.0 26.0 41.0 12.0 41.0 150 24.92675 27.0 12.0 37.0 12.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 2.0 19 3.0 20 8.0 21 22.0 22 27.0 23 43.0 24 65.0 25 88.0 26 122.0 27 135.0 28 135.0 29 176.0 30 178.0 31 196.0 32 201.0 33 237.0 34 225.0 35 294.0 36 298.0 37 347.0 38 422.0 39 526.0 40 250.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.682590233545646 8.014861995753716 11.093418259023355 34.20912951167728 2 34.300000000000004 17.974999999999998 19.15 28.575 3 35.925000000000004 23.375 14.174999999999999 26.525 4 40.025 26.325 11.625 22.025 5 34.0 29.849999999999998 13.925 22.225 6 26.025 32.5 18.425 23.05 7 26.35 13.825000000000001 33.975 25.85 8 27.700000000000003 17.1 22.725 32.475 9 26.6 17.05 25.95 30.4 10-14 29.409999999999997 21.955 20.380000000000003 28.255000000000003 15-19 29.955 20.64 21.29 28.115000000000002 20-24 30.154999999999998 21.73 20.815 27.3 25-29 29.880000000000003 21.175 20.8 28.144999999999996 30-34 29.110000000000003 21.355 20.865000000000002 28.67 35-39 29.522952295229523 21.51715171517152 20.432043204320433 28.52785278527853 40-44 29.509999999999998 21.525 21.335 27.63 45-49 30.25 21.015 20.575 28.16 50-54 30.793079307930793 21.272127212721273 21.002100210021002 26.932693269326936 55-59 30.19 21.455 20.505000000000003 27.85 60-64 29.854999999999997 22.99 21.195 25.96 65-69 29.895 21.525 20.395 28.185 70-74 31.095 21.61 19.96 27.334999999999997 75-79 29.98 21.865000000000002 20.785 27.37 80-84 30.61806180618062 21.417141714171418 20.547054705470547 27.41774177417742 85-89 29.294999999999998 21.075 20.785 28.845 90-94 29.955 21.565 21.23 27.250000000000004 95-99 29.175 21.67 21.25 27.905 100-104 30.159999999999997 20.955 20.28 28.605000000000004 105-109 29.465000000000003 21.135 21.349999999999998 28.050000000000004 110-114 29.195 21.93 21.17 27.705000000000002 115-119 29.755 21.224999999999998 20.485 28.535 120-124 29.635 21.27 21.02 28.075 125-129 29.225 20.755000000000003 21.625 28.395 130-134 29.81 21.705 20.4 28.084999999999997 135-139 29.154999999999998 22.505 21.46 26.88 140-144 29.17 22.115000000000002 21.125 27.589999999999996 145-149 29.875 21.525 20.62 27.98 150 28.075 25.025 23.849999999999998 23.05 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 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 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 0.5 26 1.5 27 2.5 28 2.5 29 3.0 30 2.5 31 2.0 32 4.5 33 8.5 34 12.0 35 18.5 36 18.5 37 24.0 38 35.5 39 39.0 40 46.0 41 59.0 42 70.5 43 83.0 44 94.0 45 98.0 46 98.0 47 96.5 48 101.0 49 100.0 50 101.5 51 105.0 52 100.0 53 109.5 54 117.5 55 107.0 56 95.5 57 93.0 58 99.5 59 96.0 60 99.0 61 105.0 62 111.0 63 119.5 64 122.5 65 124.5 66 115.0 67 122.5 68 138.5 69 133.5 70 116.0 71 104.0 72 96.5 73 87.0 74 71.0 75 63.5 76 55.0 77 40.5 78 39.5 79 30.0 80 19.5 81 15.5 82 8.5 83 5.0 84 4.5 85 2.5 86 1.0 87 1.0 88 0.5 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 5.800000000000001 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 0.01 40-44 0.0 45-49 0.0 50-54 0.01 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.01 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 96.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 96.18082618862041 92.55 2 3.715250714471291 7.1499999999999995 3 0.10392309690828788 0.3 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 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 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.175 0.0 0.0 0.0 0.0 90-91 0.2375 0.0 0.0 0.0 0.0 92-93 0.2625 0.0 0.0 0.0 0.0 94-95 0.275 0.0 0.0 0.0 0.0 96-97 0.3 0.0 0.0 0.0 0.0 98-99 0.375 0.0 0.0 0.0 0.0 100-101 0.4375 0.0 0.0 0.0 0.0 102-103 0.475 0.0 0.0 0.0 0.0 104-105 0.525 0.0 0.0 0.0 0.0 106-107 0.55 0.0 0.0 0.0 0.0 108-109 0.5625 0.0 0.0 0.0 0.0 110-111 0.6125 0.0 0.0 0.0 0.0 112-113 0.7 0.0 0.0 0.0 0.0 114-115 0.775 0.0 0.0 0.0 0.0 116-117 0.8 0.0 0.0 0.0 0.0 118-119 0.8625 0.0 0.0 0.0 0.0 120-121 1.0125 0.0 0.0 0.0 0.0 122-123 1.1 0.0 0.0 0.0 0.0 124-125 1.175 0.0 0.0 0.0 0.0 126-127 1.2375 0.0 0.0 0.0 0.0 128-129 1.3375 0.0 0.0 0.0 0.0 130-131 1.5 0.0 0.0 0.0 0.0 132-133 1.65 0.0 0.0 0.0 0.0 134-135 1.7000000000000002 0.0 0.0 0.0 0.0 136-137 1.8250000000000002 0.0 0.0 0.0 0.0 138 1.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTATATA 10 0.0069808904 143.95 4 CGACCCA 10 0.0069808904 143.95 8 >>END_MODULE SRR12455390 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12455390_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 56 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.04625 32.0 32.0 32.0 32.0 32.0 2 29.935 32.0 32.0 32.0 27.0 32.0 3 33.64125 37.0 32.0 37.0 32.0 37.0 4 35.01875 37.0 37.0 37.0 32.0 37.0 5 35.39125 37.0 37.0 37.0 32.0 37.0 6 37.751 41.0 37.0 41.0 32.0 41.0 7 31.98375 37.0 27.0 41.0 12.0 41.0 8 37.80075 41.0 37.0 41.0 32.0 41.0 9 28.266 32.0 12.0 41.0 12.0 41.0 10-14 35.1861 39.2 30.8 41.0 23.0 41.0 15-19 36.17035 40.2 34.0 41.0 24.0 41.0 20-24 37.68965 41.0 37.8 41.0 28.0 41.0 25-29 35.5201 39.4 32.8 41.0 23.0 41.0 30-34 34.81175 39.2 31.0 41.0 20.0 41.0 35-39 36.079550000000005 41.0 36.0 41.0 23.0 41.0 40-44 35.128299999999996 40.2 33.0 41.0 21.0 41.0 45-49 29.924950000000003 31.8 21.0 39.4 15.0 41.0 50-54 30.951299999999996 33.8 24.0 39.2 14.0 41.0 55-59 29.8602 33.0 19.0 40.2 14.0 41.0 60-64 26.63485 28.0 17.0 36.6 12.0 40.2 65-69 30.81445 33.8 23.0 41.0 16.0 41.0 70-74 28.4515 30.0 18.0 40.2 12.0 41.0 75-79 31.760450000000002 34.0 24.0 40.2 18.0 41.0 80-84 30.18705 32.8 22.0 40.2 14.0 41.0 85-89 34.38 39.4 30.0 41.0 20.0 41.0 90-94 29.05355 32.0 17.0 40.2 12.0 41.0 95-99 28.344550000000005 30.8 21.0 37.6 16.0 40.2 100-104 31.749450000000003 34.8 25.0 40.2 18.0 41.0 105-109 27.546100000000003 29.0 18.0 39.4 12.0 41.0 110-114 28.471600000000002 30.0 18.0 38.6 12.0 41.0 115-119 26.20525 28.0 14.0 36.4 12.0 39.2 120-124 22.076099999999997 21.0 12.0 31.0 9.6 38.4 125-129 24.924500000000002 28.0 12.0 35.0 10.4 41.0 130-134 27.7848 31.0 16.0 39.4 11.2 41.0 135-139 24.59925 26.0 16.0 34.8 9.6 41.0 140-144 20.8203 18.0 13.2 28.8 9.6 33.8 145-149 21.260699999999996 20.0 12.0 31.0 8.8 37.0 150 25.22275 27.0 12.0 37.0 12.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 2.0 15 17.0 16 38.0 17 50.0 18 74.0 19 98.0 20 106.0 21 115.0 22 149.0 23 164.0 24 150.0 25 176.0 26 172.0 27 170.0 28 161.0 29 172.0 30 176.0 31 197.0 32 218.0 33 244.0 34 271.0 35 270.0 36 253.0 37 262.0 38 188.0 39 98.0 40 8.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 44.05506883604506 9.712140175219023 10.83854818523154 35.39424280350438 2 33.4 18.0 19.475 29.125 3 36.15 25.15 12.950000000000001 25.75 4 38.800000000000004 28.225 11.5 21.475 5 34.375 28.575 15.375 21.675 6 25.874999999999996 32.4 18.8 22.925 7 27.400000000000002 14.475 32.675 25.45 8 27.450000000000003 17.375 21.325 33.85 9 27.85 19.15 26.825 26.174999999999997 10-14 30.2 21.84 20.935000000000002 27.025 15-19 29.641482074103703 20.946047302365116 21.5910795539777 27.821391069553474 20-24 29.93 21.790000000000003 20.715 27.565 25-29 30.464999999999996 22.185 20.875 26.474999999999998 30-34 29.970000000000002 22.295 21.060000000000002 26.674999999999997 35-39 29.965000000000003 21.224999999999998 21.044999999999998 27.765 40-44 29.895 21.790000000000003 20.765 27.55 45-49 31.840000000000003 23.400000000000002 20.135 24.625 50-54 30.630000000000003 22.53 20.7 26.14 55-59 30.995 22.37 20.39 26.245 60-64 31.91 23.935000000000002 20.925 23.23 65-69 30.695 22.13 20.955 26.22 70-74 31.405 22.91 19.835 25.85 75-79 30.070000000000004 21.709999999999997 21.09 27.13 80-84 30.764999999999997 22.495 21.61 25.130000000000003 85-89 29.865000000000002 21.97 19.814999999999998 28.349999999999998 90-94 29.857985798579854 23.307330733073307 20.717071707170717 26.117611761176118 95-99 30.035 23.195 21.57 25.2 100-104 30.768076807680767 21.807180718071805 20.587058705870586 26.837683768376834 105-109 30.395 22.55 21.75 25.305 110-114 30.714999999999996 22.62 20.735 25.929999999999996 115-119 30.31 24.235 20.895 24.560000000000002 120-124 31.369999999999997 23.115 21.060000000000002 24.455 125-129 29.535 24.22 20.465 25.779999999999998 130-134 30.305 21.625 20.985 27.084999999999997 135-139 30.555 22.84 20.775 25.83 140-144 30.020000000000003 24.555 21.365000000000002 24.060000000000002 145-149 30.885 23.485 20.96 24.67 150 29.375 22.7 20.65 27.275 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 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 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.5 25 0.5 26 1.0 27 1.0 28 1.5 29 4.0 30 3.0 31 3.0 32 10.5 33 13.5 34 13.0 35 18.5 36 27.5 37 28.0 38 26.5 39 40.5 40 53.0 41 62.0 42 78.0 43 87.0 44 90.5 45 91.5 46 95.5 47 99.5 48 108.0 49 117.5 50 107.0 51 103.0 52 110.5 53 117.0 54 111.0 55 106.0 56 111.0 57 108.5 58 107.5 59 121.5 60 125.0 61 115.5 62 113.0 63 111.0 64 111.5 65 109.0 66 101.5 67 106.0 68 124.5 69 129.5 70 110.0 71 93.5 72 92.0 73 82.5 74 64.0 75 53.0 76 42.5 77 35.5 78 27.5 79 18.5 80 17.0 81 12.5 82 7.5 83 5.0 84 4.0 85 2.0 86 2.0 87 1.5 88 0.0 89 1.0 90 1.0 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 0.125 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 0.005 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 0.01 95-99 0.0 100-104 0.01 105-109 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 97.775 #Duplication Level Percentage of deduplicated Percentage of total 1 97.80107389414472 95.625 2 2.1477882894400406 4.2 3 0.025568908207619537 0.075 4 0.025568908207619537 0.1 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.05 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.05 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.0625 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.16249999999999998 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 82-83 0.25 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.3 0.0 0.0 0.0 0.0 90-91 0.3125 0.0 0.0 0.0 0.0 92-93 0.3375 0.0 0.0 0.0 0.0 94-95 0.35 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.4375 0.0 0.0 0.0 0.0 100-101 0.5 0.0 0.0 0.0 0.0 102-103 0.525 0.0 0.0 0.0 0.0 104-105 0.575 0.0 0.0 0.0 0.0 106-107 0.625 0.0 0.0 0.0 0.0 108-109 0.6625000000000001 0.0 0.0 0.0 0.0 110-111 0.7 0.0 0.0 0.0 0.0 112-113 0.75 0.0 0.0 0.0 0.0 114-115 0.7875000000000001 0.0 0.0 0.0 0.0 116-117 0.8 0.0 0.0 0.0 0.0 118-119 0.8125 0.0 0.0 0.0 0.0 120-121 0.8875 0.0 0.0 0.0 0.0 122-123 0.9875 0.0 0.0 0.0 0.0 124-125 1.025 0.0 0.0 0.0 0.0 126-127 1.0625 0.0 0.0 0.0 0.0 128-129 1.125 0.0 0.0 0.0 0.0 130-131 1.2374999999999998 0.0 0.0 0.0 0.0 132-133 1.325 0.0 0.0 0.0 0.0 134-135 1.3875 0.0 0.0 0.0 0.0 136-137 1.45 0.0 0.0 0.0 0.0 138 1.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137266 spots for SRR12455390.sra Written 1137266 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra Read 1137251 spots for SRR12455390.sra Written 1137251 spots for SRR12455390.sra SRR ids: ['SRR12455390.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_f055kudj SRR12455390.sra spots: 22745035 blocks: [[1, 1137251], [1137252, 2274502], [2274503, 3411753], [3411754, 4549004], [4549005, 5686255], [5686256, 6823506], [6823507, 7960757], [7960758, 9098008], [9098009, 10235259], [10235260, 11372510], [11372511, 12509761], [12509762, 13647012], [13647013, 14784263], [14784264, 15921514], [15921515, 17058765], [17058766, 18196016], [18196017, 19333267], [19333268, 20470518], [20470519, 21607769], [21607770, 22745035]] SRR12455390 file size 7663633 SRR12455390 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 SRR12455390 SRR12455390_1.fastq SRR12455390_2.fastq Input file: SRR12455390_1.fastq Paired file: SRR12455390_2.fastq trimmed: SRR12455390-trimmed-pair1.fastq, SRR12455390-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 10:12:18 2024 >> started Tue Dec 10 10:12:46 2024 >> done (28.033s) 22745035 read pairs processed; of these: 523 ( 0.00%) short read pairs filtered out after trimming by size control 15536 ( 0.07%) empty read pairs filtered out after trimming by size control 22728976 (99.93%) read pairs available; of these: 2338536 (10.29%) trimmed read pairs available after processing 20390440 (89.71%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 78 0.00% 19 74 0.00% 20 87 0.00% 21 90 0.00% 22 126 0.00% 23 148 0.00% 24 160 0.00% 25 155 0.00% 26 207 0.00% 27 187 0.00% 28 189 0.00% 29 202 0.00% 30 233 0.00% 31 200 0.00% 32 226 0.00% 33 254 0.00% 34 235 0.00% 35 288 0.00% 36 261 0.00% 37 265 0.00% 38 283 0.00% 39 294 0.00% 40 313 0.00% 41 304 0.00% 42 340 0.00% 43 309 0.00% 44 321 0.00% 45 323 0.00% 46 335 0.00% 47 352 0.00% 48 388 0.00% 49 351 0.00% 50 346 0.00% 51 392 0.00% 52 372 0.00% 53 440 0.00% 54 387 0.00% 55 436 0.00% 56 383 0.00% 57 440 0.00% 58 470 0.00% 59 483 0.00% 60 478 0.00% 61 560 0.00% 62 550 0.00% 63 541 0.00% 64 598 0.00% 65 572 0.00% 66 603 0.00% 67 685 0.00% 68 758 0.00% 69 735 0.00% 70 784 0.00% 71 778 0.00% 72 908 0.00% 73 991 0.00% 74 1008 0.00% 75 1057 0.00% 76 1112 0.00% 77 1260 0.01% 78 1271 0.01% 79 1444 0.01% 80 1409 0.01% 81 1583 0.01% 82 1764 0.01% 83 1952 0.01% 84 2019 0.01% 85 2140 0.01% 86 2324 0.01% 87 2498 0.01% 88 2606 0.01% 89 2878 0.01% 90 3023 0.01% 91 3288 0.01% 92 3555 0.02% 93 3806 0.02% 94 3789 0.02% 95 4318 0.02% 96 4385 0.02% 97 4695 0.02% 98 4951 0.02% 99 5186 0.02% 100 5595 0.02% 101 5921 0.03% 102 6077 0.03% 103 6425 0.03% 104 6756 0.03% 105 7056 0.03% 106 7426 0.03% 107 7739 0.03% 108 8077 0.04% 109 8433 0.04% 110 8852 0.04% 111 9155 0.04% 112 9587 0.04% 113 9985 0.04% 114 10725 0.05% 115 10479 0.05% 116 10867 0.05% 117 11294 0.05% 118 11794 0.05% 119 12488 0.05% 120 13339 0.06% 121 13907 0.06% 122 14386 0.06% 123 14765 0.06% 124 15410 0.07% 125 15747 0.07% 126 16346 0.07% 127 16225 0.07% 128 17245 0.08% 129 17844 0.08% 130 18525 0.08% 131 18937 0.08% 132 19933 0.09% 133 20771 0.09% 134 21681 0.10% 135 21681 0.10% 136 22505 0.10% 137 23002 0.10% 138 23084 0.10% 139 24414 0.11% 140 25420 0.11% 141 26605 0.12% 142 27674 0.12% 143 28731 0.13% 144 29665 0.13% 145 31100 0.14% 146 35402 0.16% 147 53214 0.23% 148 154680 0.68% 149 1290978 5.68% 150 20390440 89.71% 22728976 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=6.09 fanout-score-rank=13 prefix-density=0.28 prefix-fanout=4.2 sequence=GAGTTCAGCAAGGTCGGCTTCGTCTTCCGCGAGCACAACAGCTCCCCTGGGTACTATGATGGCAGGTACTG criterion=fanout-score sequence-density=0.07 sequence-density-rank=22 fanout-score=390.81 fanout-score-rank=1 prefix-density=1.29 prefix-fanout=22.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=14.81 fanout-score-rank=11 prefix-density=0.22 prefix-fanout=12.1 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGATGACCACTGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAA criterion=fanout-score sequence-density=0.07 sequence-density-rank=22 fanout-score=402.28 fanout-score-rank=1 prefix-density=1.23 prefix-fanout=23.6 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG SRR12455390 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 10:13:57 Started mapping on | Dec 10 10:13:57 Finished on | Dec 10 10:16:44 Mapping speed, Million of reads per hour | 489.97 Number of input reads | 22728976 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 19057062 Uniquely mapped reads % | 83.84% Average mapped length | 291.86 Number of splices: Total | 13766678 Number of splices: Annotated (sjdb) | 13086944 Number of splices: GT/AG | 13542359 Number of splices: GC/AG | 175820 Number of splices: AT/AC | 6455 Number of splices: Non-canonical | 42044 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.01% Deletion average length | 2.64 Insertion rate per base | 0.01% Insertion average length | 2.51 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 579794 % of reads mapped to multiple loci | 2.55% Number of reads mapped to too many loci | 83635 % of reads mapped to too many loci | 0.37% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.02% % of reads unmapped: other | 5.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3092120 3092120 3092120 N_multimapping 579794 579794 579794 N_noFeature 490186 9634860 9632233 N_ambiguous 349893 37425 37682 UnstrandedReadsAssigned:18216983 PositiveStrandReadsAssigned:9384777 NegativeStrandReadsAssigned:9387147 Dataset is classified unstranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR12455390 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: SRR12455390-trimmed-pair1.fastq SRR12455390-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,728,976 reads, 19,954,432 reads pseudoaligned [quant] estimated average fragment length: 240.789 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,089 rounds 52973 SRR12455390.ke.tsv 35125 SRR12455390.se.tsv 88098 total ==> SRR12455390.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 696.49 0 0 PNS24247 1044 804.211 10.1364 0.733739 PNS24249 1928 1688.21 470.522 16.2248 PNS24246 1044 804.211 10.1364 0.733739 PNS24248 1044 804.211 10.1364 0.733739 PNS24244 1471 1231.21 6.06884 0.286945 PNS24243 293 75.1023 10 7.75126 KQK14069 1603 1363.21 3864.81 165.041 KQK14071 474 236.286 862.586 212.515 ==> SRR12455390.se.tsv <== BRADI_1g14170v3 4752 BRADI_1g53295v3 37 BRADI_1g59795v3 92 BRADI_1g07683v3 0 BRADI_1g00485v3 12 BRADI_1g20270v3 1646 BRADI_1g74790v3 504 BRADI_1g09890v3 12 BRADI_1g77505v3 205 BRADI_1g48960v3 0 SRR12455390 completed mapping pipeline successfully