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unicycler.vcf_func.CannotMakeVcf: #259

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hafizmtalha opened this issue Apr 14, 2021 · 1 comment
Closed

unicycler.vcf_func.CannotMakeVcf: #259

hafizmtalha opened this issue Apr 14, 2021 · 1 comment

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@hafizmtalha
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I'm running the unicycler with --vcf option enabled. assembly step works fine but error comes at vcf building step. any idea how to resolve this?
Traceback (most recent call last):
File "/usr/bin/unicycler", line 11, in
load_entry_point('unicycler==0.4.8', 'console_scripts', 'unicycler')()
File "/usr/lib/python3/dist-packages/unicycler/unicycler.py", line 227, in main
make_vcf(final_assembly_vcf, args, final_assembly_fasta, insert_size_1st, insert_size_99th)
File "/usr/lib/python3/dist-packages/unicycler/vcf_func.py", line 110, in make_vcf
raise CannotMakeVcf('mpileup/bcftools encountered an error: ' + err.decode())
unicycler.vcf_func.CannotMakeVcf: 'mpileup/bcftools encountered an error: /bin/sh: 1: Syntax error: "(" unexpected\n'

@rrwick
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rrwick commented Jan 19, 2022

Sorry, but --vcf is being removed from Unicycler (see #271) so I'm going to close this issue.

@rrwick rrwick closed this as completed Jan 19, 2022
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