Starting /dee2/code/volunteer_pipeline.sh SRR12670989 current disk space = 3051500900352 free memory = 1470261468 SRR12670989 SRAfilesize 7a6e5535877db5d98cac8f148ced449f SRR12670989.sra SRR12670989.sra file validated SRR12670989 is paired end SRR12670989 is conventional basespace SRR12670989 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670989_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 36.4655 37.0 37.0 37.0 37.0 37.0 2 36.4005 37.0 37.0 37.0 37.0 37.0 3 36.4905 37.0 37.0 37.0 37.0 37.0 4 36.5735 37.0 37.0 37.0 37.0 37.0 5 36.6355 37.0 37.0 37.0 37.0 37.0 6 36.653 37.0 37.0 37.0 37.0 37.0 7 36.573 37.0 37.0 37.0 37.0 37.0 8 36.606 37.0 37.0 37.0 37.0 37.0 9 36.597 37.0 37.0 37.0 37.0 37.0 10-14 36.6291 37.0 37.0 37.0 37.0 37.0 15-19 36.583600000000004 37.0 37.0 37.0 37.0 37.0 20-24 36.5486 37.0 37.0 37.0 37.0 37.0 25-29 36.48910000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.4762 37.0 37.0 37.0 37.0 37.0 35-39 36.475100000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.4527 37.0 37.0 37.0 37.0 37.0 45-49 36.4114 37.0 37.0 37.0 37.0 37.0 50-54 36.3947 37.0 37.0 37.0 37.0 37.0 55-59 36.34630000000001 37.0 37.0 37.0 37.0 37.0 60-64 36.3163 37.0 37.0 37.0 37.0 37.0 65-69 36.3254 37.0 37.0 37.0 37.0 37.0 70-74 36.2977 37.0 37.0 37.0 37.0 37.0 75-79 36.249100000000006 37.0 37.0 37.0 37.0 37.0 80-84 36.185199999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.227199999999996 37.0 37.0 37.0 37.0 37.0 90-94 36.17309999999999 37.0 37.0 37.0 37.0 37.0 95-99 36.1221 37.0 37.0 37.0 37.0 37.0 100-104 36.1556 37.0 37.0 37.0 37.0 37.0 105-109 36.0576 37.0 37.0 37.0 37.0 37.0 110-114 36.1053 37.0 37.0 37.0 37.0 37.0 115-119 36.0321 37.0 37.0 37.0 37.0 37.0 120-124 35.957300000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.9711 37.0 37.0 37.0 37.0 37.0 130-134 35.803999999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.87339999999999 37.0 37.0 37.0 37.0 37.0 140-144 35.8776 37.0 37.0 37.0 37.0 37.0 145-149 35.7349 37.0 37.0 37.0 37.0 37.0 150-151 35.562749999999994 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 2.0 23 4.0 24 5.0 25 2.0 26 9.0 27 10.0 28 11.0 29 16.0 30 33.0 31 41.0 32 51.0 33 74.0 34 143.0 35 267.0 36 2710.0 37 619.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.19609804902451 10.25512756378189 7.5037518759379696 40.04502251125563 2 18.825 12.325 37.824999999999996 31.025000000000002 3 18.7 15.45 25.924999999999997 39.925 4 21.6 22.975 24.6 30.825000000000003 5 23.474999999999998 29.275000000000002 26.375 20.875 6 21.175 33.35 22.85 22.625 7 14.899999999999999 27.025 41.175 16.900000000000002 8 16.225 26.825 32.65 24.3 9 16.775000000000002 22.900000000000002 35.725 24.6 10-14 19.57 29.445 28.335 22.650000000000002 15-19 19.79 27.675 28.365000000000002 24.169999999999998 20-24 19.835 27.675 28.235 24.255 25-29 20.169999999999998 27.639999999999997 28.155 24.035 30-34 20.24 28.13 27.465 24.165 35-39 20.23 27.889999999999997 28.08 23.799999999999997 40-44 20.43 28.83 27.185 23.555 45-49 19.54 28.110000000000003 28.035 24.315 50-54 20.25 28.42 27.744999999999997 23.585 55-59 19.6 29.005 27.665 23.73 60-64 20.005 28.244999999999997 27.63 24.12 65-69 19.62 28.405 27.93 24.044999999999998 70-74 20.39 27.42 27.529999999999998 24.66 75-79 20.51 27.345000000000002 27.505000000000003 24.64 80-84 20.185 28.07 27.905 23.84 85-89 20.325 28.575 27.500000000000004 23.599999999999998 90-94 20.215 28.02 27.62 24.145 95-99 20.23 27.97 27.51 24.29 100-104 20.555 28.65 27.55 23.244999999999997 105-109 20.294999999999998 28.23 27.525 23.95 110-114 20.69 27.315 28.299999999999997 23.695 115-119 20.724999999999998 27.815 27.495000000000005 23.965 120-124 21.15 27.134999999999998 27.794999999999998 23.919999999999998 125-129 20.86 27.525 27.560000000000002 24.055 130-134 20.935000000000002 27.705000000000002 27.77 23.59 135-139 21.165 27.97 26.995 23.87 140-144 20.669999999999998 27.875 27.85 23.605 145-149 21.025 28.055000000000003 27.025 23.895 150-151 20.825 28.375 27.0125 23.7875 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.5 3 1.0 4 1.5 5 1.5 6 1.0 7 1.5 8 1.5 9 1.0 10 0.5 11 0.5 12 0.5 13 1.0 14 1.0 15 0.0 16 0.0 17 0.0 18 0.0 19 1.0 20 1.0 21 0.5 22 0.5 23 0.0 24 1.0 25 1.0 26 2.5 27 3.5 28 6.0 29 18.5 30 25.5 31 29.5 32 36.5 33 42.0 34 48.5 35 60.5 36 86.5 37 110.0 38 129.5 39 145.5 40 169.5 41 203.5 42 215.5 43 222.5 44 242.0 45 245.5 46 250.5 47 257.5 48 237.5 49 226.5 50 200.0 51 148.5 52 128.5 53 108.0 54 78.5 55 67.0 56 64.5 57 56.0 58 33.0 59 19.0 60 15.5 61 13.5 62 13.0 63 8.5 64 3.0 65 0.5 66 1.5 67 3.5 68 3.0 69 1.0 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 pass #Base N-Count 1 0.05 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 90.725 #Duplication Level Percentage of deduplicated Percentage of total 1 91.01680903830255 82.575 2 8.046293744833287 14.6 3 0.6888950124001102 1.875 4 0.19289060347203085 0.7000000000000001 5 0.055111600992008826 0.25 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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit GGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGA 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 0.0125 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.07500000000000001 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.1375 0.0 0.0 0.0 0.0 94-95 0.175 0.0 0.0 0.0 0.0 96-97 0.2375 0.0 0.0 0.0 0.0 98-99 0.2625 0.0 0.0 0.0 0.0 100-101 0.36250000000000004 0.0 0.0 0.0 0.0 102-103 0.4375 0.0 0.0 0.0 0.0 104-105 0.55 0.0 0.0 0.0 0.0 106-107 0.6625000000000001 0.0 0.0 0.0 0.0 108-109 0.7625 0.0 0.0 0.0 0.0 110-111 0.825 0.0 0.0 0.0 0.0 112-113 0.8374999999999999 0.0 0.0 0.0 0.0 114-115 0.9375 0.0 0.0 0.0 0.0 116-117 1.025 0.0 0.0 0.0 0.0 118-119 1.1875 0.0 0.0 0.0 0.0 120-121 1.2875 0.0 0.0 0.0 0.0 122-123 1.475 0.0 0.0 0.0 0.0 124-125 1.6625 0.0 0.0 0.0 0.0 126-127 1.8625 0.0 0.0 0.0 0.0 128-129 2.0375 0.0 0.0 0.0 0.0 130-131 2.1500000000000004 0.0 0.0 0.0 0.0 132-133 2.3 0.0 0.0 0.0 0.0 134-135 2.475 0.0 0.0 0.0 0.0 136-137 2.675 0.0 0.0 0.0 0.0 138-139 2.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12670989 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670989_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 36.303 37.0 37.0 37.0 37.0 37.0 2 36.29 37.0 37.0 37.0 37.0 37.0 3 36.3855 37.0 37.0 37.0 37.0 37.0 4 36.318 37.0 37.0 37.0 37.0 37.0 5 36.371 37.0 37.0 37.0 37.0 37.0 6 36.4115 37.0 37.0 37.0 37.0 37.0 7 36.43 37.0 37.0 37.0 37.0 37.0 8 36.4575 37.0 37.0 37.0 37.0 37.0 9 36.471 37.0 37.0 37.0 37.0 37.0 10-14 36.423199999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.466899999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.434099999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.3318 37.0 37.0 37.0 37.0 37.0 30-34 36.3444 37.0 37.0 37.0 37.0 37.0 35-39 36.3183 37.0 37.0 37.0 37.0 37.0 40-44 36.2824 37.0 37.0 37.0 37.0 37.0 45-49 36.2846 37.0 37.0 37.0 37.0 37.0 50-54 36.2421 37.0 37.0 37.0 37.0 37.0 55-59 36.235 37.0 37.0 37.0 37.0 37.0 60-64 36.2368 37.0 37.0 37.0 37.0 37.0 65-69 36.231100000000005 37.0 37.0 37.0 37.0 37.0 70-74 36.2427 37.0 37.0 37.0 37.0 37.0 75-79 36.15 37.0 37.0 37.0 37.0 37.0 80-84 36.1426 37.0 37.0 37.0 37.0 37.0 85-89 36.1 37.0 37.0 37.0 37.0 37.0 90-94 36.128 37.0 37.0 37.0 37.0 37.0 95-99 36.084500000000006 37.0 37.0 37.0 37.0 37.0 100-104 36.118700000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.048500000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.0404 37.0 37.0 37.0 37.0 37.0 115-119 36.0622 37.0 37.0 37.0 37.0 37.0 120-124 35.9202 37.0 37.0 37.0 37.0 37.0 125-129 35.815000000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.8956 37.0 37.0 37.0 37.0 37.0 135-139 35.8498 37.0 37.0 37.0 37.0 37.0 140-144 35.8121 37.0 37.0 37.0 37.0 37.0 145-149 35.689699999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.343 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 0.0 14 2.0 15 2.0 16 2.0 17 1.0 18 0.0 19 2.0 20 2.0 21 2.0 22 2.0 23 3.0 24 5.0 25 5.0 26 6.0 27 14.0 28 16.0 29 18.0 30 26.0 31 25.0 32 34.0 33 79.0 34 143.0 35 368.0 36 2657.0 37 585.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.1 23.3 10.075000000000001 26.525 2 26.8 24.7 32.1 16.400000000000002 3 19.875 25.974999999999998 33.550000000000004 20.599999999999998 4 22.650000000000002 34.425 24.725 18.2 5 24.325 36.525 22.3 16.85 6 20.575 37.574999999999996 23.3 18.55 7 19.75 22.325 39.2 18.725 8 21.025 25.3 27.55 26.125 9 21.275 23.7 30.375000000000004 24.65 10-14 23.46 29.205 26.25 21.085 15-19 23.71 28.139999999999997 27.200000000000003 20.95 20-24 23.155 28.775000000000002 27.155 20.915 25-29 23.425 28.360000000000003 27.750000000000004 20.465 30-34 22.915 28.000000000000004 27.965 21.12 35-39 22.555 28.415000000000003 27.944999999999997 21.085 40-44 22.485 28.744999999999997 28.025 20.745 45-49 23.150000000000002 28.28 27.389999999999997 21.18 50-54 22.89 27.985 27.589999999999996 21.535 55-59 23.06 27.83 27.49 21.62 60-64 22.95 27.834999999999997 28.17 21.044999999999998 65-69 22.825 27.485 27.310000000000002 22.38 70-74 23.035 28.065 27.63 21.27 75-79 22.615 28.185 27.375 21.825 80-84 23.445 28.025 26.61 21.92 85-89 23.080000000000002 28.33 27.295 21.295 90-94 23.47 27.445000000000004 27.755000000000003 21.33 95-99 23.785 27.6 27.355 21.26 100-104 23.580000000000002 28.83 26.985 20.605 105-109 23.315 27.375 28.015 21.295 110-114 23.474999999999998 28.455000000000002 27.229999999999997 20.84 115-119 23.715 28.035 27.445000000000004 20.805 120-124 23.94 28.1 27.46 20.5 125-129 23.78 28.435 26.805 20.979999999999997 130-134 24.055 28.315 26.895000000000003 20.735 135-139 23.22 27.445000000000004 28.044999999999998 21.29 140-144 24.15 27.22 27.735 20.895 145-149 24.759999999999998 28.1 26.939999999999998 20.200000000000003 150-151 24.325 28.3875 26.5375 20.75 >>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 0.5 11 1.0 12 1.0 13 1.0 14 0.5 15 0.5 16 0.5 17 0.5 18 0.5 19 0.0 20 0.0 21 1.0 22 1.0 23 2.5 24 3.0 25 2.5 26 5.0 27 8.0 28 9.5 29 10.5 30 14.5 31 16.5 32 25.5 33 38.5 34 53.0 35 70.5 36 77.0 37 91.0 38 124.0 39 172.5 40 195.5 41 211.0 42 235.5 43 253.0 44 273.5 45 274.5 46 262.0 47 257.5 48 235.0 49 202.5 50 176.0 51 145.0 52 112.5 53 85.5 54 73.0 55 59.0 56 53.0 57 39.0 58 27.0 59 27.0 60 16.5 61 10.0 62 15.0 63 12.0 64 4.0 65 2.5 66 2.0 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 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 1.0 84 1.0 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 0.5 >>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 90.425 #Duplication Level Percentage of deduplicated Percentage of total 1 90.98700580591651 82.27499999999999 2 8.072988664639205 14.6 3 0.6358860934476085 1.725 4 0.2211777716339508 0.8 5 0.0 0.0 6 0.0 0.0 7 0.02764722145424385 0.17500000000000002 8 0.02764722145424385 0.2 9 0.02764722145424385 0.22499999999999998 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 9 0.22499999999999998 No Hit CACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATC 8 0.2 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 7 0.17500000000000002 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 0.0125 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.1 0.0 0.0 0.0 0.0 88-89 0.125 0.0 0.0 0.0 0.0 90-91 0.125 0.0 0.0 0.0 0.0 92-93 0.1625 0.0 0.0 0.0 0.0 94-95 0.2 0.0 0.0 0.0 0.0 96-97 0.2625 0.0 0.0 0.0 0.0 98-99 0.2875 0.0 0.0 0.0 0.0 100-101 0.38749999999999996 0.0 0.0 0.0 0.0 102-103 0.4625 0.0 0.0 0.0 0.0 104-105 0.575 0.0 0.0 0.0 0.0 106-107 0.6875 0.0 0.0 0.0 0.0 108-109 0.8125 0.0 0.0 0.0 0.0 110-111 0.875 0.0 0.0 0.0 0.0 112-113 0.8875 0.0 0.0 0.0 0.0 114-115 0.9875 0.0 0.0 0.0 0.0 116-117 1.0750000000000002 0.0 0.0 0.0 0.0 118-119 1.2374999999999998 0.0 0.0 0.0 0.0 120-121 1.3375 0.0 0.0 0.0 0.0 122-123 1.525 0.0 0.0 0.0 0.0 124-125 1.7125 0.0 0.0 0.0 0.0 126-127 1.9125 0.0 0.0 0.0 0.0 128-129 2.0875 0.0 0.0 0.0 0.0 130-131 2.2 0.0 0.0 0.0 0.0 132-133 2.35 0.0 0.0 0.0 0.0 134-135 2.525 0.0 0.0 0.0 0.0 136-137 2.725 0.0 0.0 0.0 0.0 138-139 2.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACCACAG 10 0.006830828 145.0 5 CACCACA 10 0.006830828 145.0 4 AAAAAAA 40 0.0076550315 18.125 1 >>END_MODULE Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580619 spots for SRR12670989.sra Written 580619 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra Read 580616 spots for SRR12670989.sra Written 580616 spots for SRR12670989.sra SRR ids: ['SRR12670989.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9w6vlda0 SRR12670989.sra spots: 11612323 blocks: [[1, 580616], [580617, 1161232], [1161233, 1741848], [1741849, 2322464], [2322465, 2903080], [2903081, 3483696], [3483697, 4064312], [4064313, 4644928], [4644929, 5225544], [5225545, 5806160], [5806161, 6386776], [6386777, 6967392], [6967393, 7548008], [7548009, 8128624], [8128625, 8709240], [8709241, 9289856], [9289857, 9870472], [9870473, 10451088], [10451089, 11031704], [11031705, 11612323]] SRR12670989 file size 3924675 SRR12670989 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 SRR12670989 SRR12670989_1.fastq SRR12670989_2.fastq Input file: SRR12670989_1.fastq Paired file: SRR12670989_2.fastq trimmed: SRR12670989-trimmed-pair1.fastq, SRR12670989-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 Feb 11 11:40:17 2025 >> started Tue Feb 11 11:40:30 2025 >> done (13.329s) 11612323 read pairs processed; of these: 40 ( 0.00%) short read pairs filtered out after trimming by size control 1735 ( 0.01%) empty read pairs filtered out after trimming by size control 11610548 (99.98%) read pairs available; of these: 503866 ( 4.34%) trimmed read pairs available after processing 11106682 (95.66%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 1 0.00% 21 3 0.00% 22 6 0.00% 23 1 0.00% 24 3 0.00% 25 2 0.00% 26 2 0.00% 27 2 0.00% 28 6 0.00% 29 4 0.00% 30 4 0.00% 31 8 0.00% 32 8 0.00% 33 4 0.00% 34 7 0.00% 35 8 0.00% 36 4 0.00% 37 9 0.00% 38 10 0.00% 39 10 0.00% 40 6 0.00% 41 11 0.00% 42 10 0.00% 43 5 0.00% 44 8 0.00% 45 12 0.00% 46 9 0.00% 47 12 0.00% 48 12 0.00% 49 20 0.00% 50 19 0.00% 51 19 0.00% 52 33 0.00% 53 28 0.00% 54 22 0.00% 55 36 0.00% 56 35 0.00% 57 29 0.00% 58 51 0.00% 59 47 0.00% 60 56 0.00% 61 64 0.00% 62 68 0.00% 63 80 0.00% 64 88 0.00% 65 89 0.00% 66 98 0.00% 67 106 0.00% 68 126 0.00% 69 136 0.00% 70 194 0.00% 71 198 0.00% 72 206 0.00% 73 265 0.00% 74 296 0.00% 75 357 0.00% 76 359 0.00% 77 376 0.00% 78 424 0.00% 79 488 0.00% 80 522 0.00% 81 656 0.01% 82 672 0.01% 83 735 0.01% 84 879 0.01% 85 901 0.01% 86 1017 0.01% 87 1091 0.01% 88 1228 0.01% 89 1286 0.01% 90 1415 0.01% 91 1591 0.01% 92 1621 0.01% 93 1777 0.02% 94 1928 0.02% 95 2239 0.02% 96 2266 0.02% 97 2405 0.02% 98 2482 0.02% 99 2645 0.02% 100 2965 0.03% 101 3007 0.03% 102 3147 0.03% 103 3318 0.03% 104 3579 0.03% 105 3828 0.03% 106 3966 0.03% 107 4254 0.04% 108 4446 0.04% 109 4496 0.04% 110 4724 0.04% 111 4909 0.04% 112 5224 0.04% 113 5253 0.05% 114 5557 0.05% 115 5848 0.05% 116 6281 0.05% 117 6666 0.06% 118 6749 0.06% 119 6891 0.06% 120 7396 0.06% 121 7419 0.06% 122 7701 0.07% 123 7981 0.07% 124 8260 0.07% 125 8564 0.07% 126 9026 0.08% 127 9306 0.08% 128 9718 0.08% 129 9714 0.08% 130 10327 0.09% 131 10522 0.09% 132 10662 0.09% 133 11091 0.10% 134 11159 0.10% 135 11693 0.10% 136 11923 0.10% 137 12394 0.11% 138 12682 0.11% 139 13564 0.12% 140 13492 0.12% 141 14161 0.12% 142 14638 0.13% 143 15141 0.13% 144 15364 0.13% 145 15529 0.13% 146 16225 0.14% 147 16427 0.14% 148 17247 0.15% 149 17273 0.15% 150 18199 0.16% 151 11106682 95.66% 11610548 reads passed initial QC criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=23 prefix-density=0.60 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=fanout-score sequence-density=0.20 sequence-density-rank=16 fanout-score=12.22 fanout-score-rank=1 prefix-density=0.41 prefix-fanout=6.1 sequence=TTCTTTCCAATGCT criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=2.25 fanout-score-rank=27 prefix-density=0.56 prefix-fanout=2.2 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=29.05 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=4.6 sequence=GGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAT SRR12670989 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 11:41:24 Started mapping on | Feb 11 11:41:25 Finished on | Feb 11 11:42:55 Mapping speed, Million of reads per hour | 464.42 Number of input reads | 11610548 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 10421462 Uniquely mapped reads % | 89.76% Average mapped length | 295.42 Number of splices: Total | 10559422 Number of splices: Annotated (sjdb) | 10335705 Number of splices: GT/AG | 10355298 Number of splices: GC/AG | 165471 Number of splices: AT/AC | 6444 Number of splices: Non-canonical | 32209 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.87 Insertion rate per base | 0.02% Insertion average length | 2.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 291990 % of reads mapped to multiple loci | 2.51% Number of reads mapped to too many loci | 150369 % of reads mapped to too many loci | 1.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.19% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 897096 897096 897096 N_multimapping 291990 291990 291990 N_noFeature 411473 10231677 452601 N_ambiguous 240127 939 90923 UnstrandedReadsAssigned:9769862 PositiveStrandReadsAssigned:188846 NegativeStrandReadsAssigned:9877938 Dataset is classified negative stranded MeadianReadLen=147 20thPercentileLength=147 echo kmer=143 SRR12670989 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: SRR12670989-trimmed-pair1.fastq SRR12670989-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,610,548 reads, 10,217,538 reads pseudoaligned [quant] estimated average fragment length: 287.847 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,026 rounds 52401 SRR12670989.ke.tsv 34699 SRR12670989.se.tsv 87100 total ==> SRR12670989.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1731.15 433 18.7092 Potri.005G024800.1.v4.1 1035 748.153 204 20.3959 Potri.004G059700.1.v4.1 961 674.339 5 0.554618 Potri.007G009000.2.v4.1 1416 1129.15 0 0 Potri.003G141000.2.v4.1 2943 2656.15 672 18.9242 Potri.016G087400.1.v4.1 270 71.3395 510 534.74 Potri.015G069301.1.v4.1 564 294.045 0 0 Potri.010G195200.1.v4.1 1773 1486.15 165 8.30467 Potri.012G127500.1.v4.1 977 690.255 92 9.96966 ==> SRR12670989.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 144 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 196 Potri.001G212900.v4.1 11 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 13 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 0 SRR12670989 completed mapping pipeline successfully