Open glaudelrio opened 1 month ago
Hi Frank! Any idea why vcf2gwas is breaking at this point?
Starting genotype Quality Control.. QC for Chromosome: hicscaffold_000001 QC for Chromosome: hicscaffold_000000 Quality control successful (Duration: 3 minutes, 31.8 seconds)
Filtering SNPs.. Minor allele frequency: 0.01 Traceback (most recent call last): File "/blue/g.delrio/g.delrio/envs/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/starter.py", line 632, in Converter.filter_snps(min_af, snp_file2_org, snp_file2, chr2) File "/blue/g.delrio/g.delrio/envs/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/utils.py", line 1346, in filter_snps filtered.check_returncode() File "/blue/g.delrio/g.delrio/envs/vcf2gwas/lib/python3.9/subprocess.py", line 456, in check_returncode raise CalledProcessError(self.returncode, self.args, self.stdout, subprocess.CalledProcessError: Command '['bcftools', 'view', '-m2', '-M2', '-v', 'snps', '-q', '0.01:minor', '/blue/g.delrio/g.delrio/vcfs/large_mac3_biallelic_maf02_miss095_m$
vcf2gwas v0.8.9
Initialising..
I appreciate any help you can provide! Thanks
Hi Frank! Any idea why vcf2gwas is breaking at this point?
Starting genotype Quality Control.. QC for Chromosome: hicscaffold_000001 QC for Chromosome: hicscaffold_000000 Quality control successful (Duration: 3 minutes, 31.8 seconds)
Filtering SNPs.. Minor allele frequency: 0.01 Traceback (most recent call last): File "/blue/g.delrio/g.delrio/envs/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/starter.py", line 632, in
Converter.filter_snps(min_af, snp_file2_org, snp_file2, chr2)
File "/blue/g.delrio/g.delrio/envs/vcf2gwas/lib/python3.9/site-packages/vcf2gwas/utils.py", line 1346, in filter_snps
filtered.check_returncode()
File "/blue/g.delrio/g.delrio/envs/vcf2gwas/lib/python3.9/subprocess.py", line 456, in check_returncode
raise CalledProcessError(self.returncode, self.args, self.stdout,
subprocess.CalledProcessError: Command '['bcftools', 'view', '-m2', '-M2', '-v', 'snps', '-q', '0.01:minor', '/blue/g.delrio/g.delrio/vcfs/large_mac3_biallelic_maf02_miss095_m$
vcf2gwas v0.8.9
Initialising..
I appreciate any help you can provide! Thanks