Hello,
I'm trying to run Dtrios on a subset of samples (8/433) using genotype likelihoods:
~/Dsuite/Build/Dsuite Dtrios -g prairie-grouse-w-outgroup.vcf.recode.vcf SUB.txt
The SUB.txt file has many sample ignored to try and get this to run, as below:
Slurm standard error file produces the following:
_Going to calculate D and f4-ratio values for 4 trios
Done permutations
The VCF contains 37330031 variants
Going to use block size of 1866500 variants to get 20 Jackknife blocks
Processed 100000 variants (0.267881%) in 641.53secs
Processed 200000 variants (0.535762%) in 1281.3secs
Processed 300000 variants (0.803643%) in 1903.02secs
NW_026294618.1 6533503 . A G nan PASS . GL:PL:GP -2.79699,0,-6.49696:28,0,65:0.000842934,0.999157,1.50474e-07 -2.79699,0,-6.49696:28,0,65:0.000842934,0.999157,1.50474e-07 -21.6181,0,-0.690064:216,0,7:1.16164e-22,0.911956,0.0880438
. . .
setInfo.populations[i] xxx
allPs[i] -6.3004e-08
allSplit1Ps[i] -6.3004e-08
allSplit2Ps[i] -6.3004e-08
Dsuite: Dmin.cpp:440: int DminMain(int, char**): Assertion `pS3a >= 0' failed.
Any recommendations / solutions?
Thank you,
-Andrew
Hello, I'm trying to run Dtrios on a subset of samples (8/433) using genotype likelihoods: ~/Dsuite/Build/Dsuite Dtrios -g prairie-grouse-w-outgroup.vcf.recode.vcf SUB.txt
The SUB.txt file has many sample ignored to try and get this to run, as below:
_../final_bams/F1259_ACTTGTTATC-TCTAGGCGCG_L001_filt.bam Allopatric ../final_bams/F1260_CGTGTACCAG-AACTTATCCT_L001_filt.bam Allopatric ../final_bams/F1261_TTAACCTTCG-TGTCTGGCCT_L001_filt.bam xxx ../final_bams/F1263_GTTGGATGAA-TTACCTGGAA_L001_filt.bam xxx ../final_bams/F1268_AGCCTATGAT-GTAGGTGGTG_L001_filt.bam xxx ../final_bams/F1281_CTAGATTGCG-CGCCATATCT_L001_filt.bam xxx ../final_bams/F1282_CGATGCGGTT-ACCAAGCAGG_L001_filt.bam xxx ../final_bams/F1283_TCCGGACTAG-ATTGTTCGTC_L001_filt.bam xxx ../final_bams/F1293_GTGACGGAGC-TGGACCGCCA_L001_filt.bam xxx ../final_bams/F327_AATTCCATCT-GTAACTGAAG_L001filt.bam Northern
Slurm standard error file produces the following: _Going to calculate D and f4-ratio values for 4 trios Done permutations The VCF contains 37330031 variants Going to use block size of 1866500 variants to get 20 Jackknife blocks Processed 100000 variants (0.267881%) in 641.53secs Processed 200000 variants (0.535762%) in 1281.3secs Processed 300000 variants (0.803643%) in 1903.02secs NW_026294618.1 6533503 . A G nan PASS . GL:PL:GP -2.79699,0,-6.49696:28,0,65:0.000842934,0.999157,1.50474e-07 -2.79699,0,-6.49696:28,0,65:0.000842934,0.999157,1.50474e-07 -21.6181,0,-0.690064:216,0,7:1.16164e-22,0.911956,0.0880438 . . . setInfo.populations[i] xxx allPs[i] -6.3004e-08 allSplit1Ps[i] -6.3004e-08 allSplit2Ps[i] -6.3004e-08 Dsuite: Dmin.cpp:440: int DminMain(int, char**): Assertion `pS3a >= 0' failed.
Any recommendations / solutions? Thank you, -Andrew