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IDEELResearch / vcfdo

Some tools for processing and annotating VCF files, with focus on Plasmodium spp
MIT License
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Command required error #8

Open jkreinz opened 3 years ago

jkreinz commented 3 years ago

I've trying to use the polarize command but regardless of whether I pipe in the vcf or use the -i option, I always get the same error:

polarize: error: the following arguments are required: command

in this case, I used the command bcftools view pseudo_qual_dust_indel_fixedmissing_nodups_resorted_nodups2.vcf.gz | vcfdo polarize -f path/to/AMATA_finishedtohypo_renamedfinal_doubleAAmod.fasta

However I noticed this error occurs regardless of what command I try and use (e.g. treemix, pca, etc.). I'm wondering if it's an install issue because I initially had a NumPy version issue but I uninstall and reinstalled everything with pip and it seemed to install fine.

Thanks!

andrewparkermorgan commented 3 years ago

I think this was due to an error in specifying inheritance of command-line arguments to the various vcfdo subcommands. I just pushed a small change that should fix the problem

jkreinz commented 3 years ago

thanks! that did the trick!

jkreinz commented 3 years ago

I'm running into another error when I execute vcfdo sfs after having successfully polarized my vcf:

Traceback (most recent call last):
  File "/ohta1/julia.kreiner/software/miniconda3/lib/python3.8/site-packages/vcfdo/core.py", line 138, in fetch_region
    next_site = VcfSite( next(site_iter), self.assume_ref_ancestral )
  File "cyvcf2/cyvcf2.pyx", line 436, in __call__
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ohta1/julia.kreiner/software/miniconda3/lib/python3.8/site-packages/vcfdo/core.py", line 165, in fetch_region
    raise StopIteration
StopIteration
diogofclima5 commented 8 months ago

Hi, jkreinz Were you able to solve this problem?

I'm running into another error when I execute vcfdo sfs after having successfully polarized my vcf:

Traceback (most recent call last):
  File "/ohta1/julia.kreiner/software/miniconda3/lib/python3.8/site-packages/vcfdo/core.py", line 138, in fetch_region
    next_site = VcfSite( next(site_iter), self.assume_ref_ancestral )
  File "cyvcf2/cyvcf2.pyx", line 436, in __call__
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ohta1/julia.kreiner/software/miniconda3/lib/python3.8/site-packages/vcfdo/core.py", line 165, in fetch_region
    raise StopIteration
StopIteration