Hi All,
I am trying to generate the allele counts file using the following line in in momi2: python -m momi.read_vcf --no_aa --verbose sorex.vcf.gz sorex_pops.txt sorex_allele_counts.gz --bed sorex.bed.
I am getting the following value Error:
Traceback (most recent call last):
File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/site-packages/momi/read_vcf.py", line 45, in
info_aa_field=args.info_aa_field).dump(args.out_file)
File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/site-packages/momi/data/snps.py", line 96, in read_vcf
bcf_in.subset_samples(list(ind2pop.keys()))
File "pysam/cbcf.pyx", line 2407, in pysam.cbcf.VariantFile.subset_samples (pysam/cbcf.c:32879)
ValueError: I/O operation on closed file
Can someone help in solving this issue?
Thanks,
Tobit
Hi All, I am trying to generate the allele counts file using the following line in in momi2: python -m momi.read_vcf --no_aa --verbose sorex.vcf.gz sorex_pops.txt sorex_allele_counts.gz --bed sorex.bed. I am getting the following value Error: Traceback (most recent call last): File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/site-packages/momi/read_vcf.py", line 45, in
info_aa_field=args.info_aa_field).dump(args.out_file)
File "/home/tliyandja/miniconda3/envs/momi-py36/lib/python3.6/site-packages/momi/data/snps.py", line 96, in read_vcf
bcf_in.subset_samples(list(ind2pop.keys()))
File "pysam/cbcf.pyx", line 2407, in pysam.cbcf.VariantFile.subset_samples (pysam/cbcf.c:32879)
ValueError: I/O operation on closed file
Can someone help in solving this issue?
Thanks,
Tobit