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Error when running vg construct command.
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Entering edit mode
6 months ago

When running the command vg construct -r x.fa -v x.vcf >x.vg in Linux, it throws an error "Bad Argument. Usage: vg[-l] number". How to resolve this error?

vg • 166 views
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Entering edit mode
6 months ago

there is the problem with your $PATH. Either vg is not installed and or it is at the end of your $PATH .

You're currently calling another vg: https://www.unix.com/man-page/debian/1/cg/

cg - Recursively grep for a pattern and store it.

find where is installed the correct vg and prepend it to the PATH.

export PATH=/path/to/executable/vg/directory:${PATH}
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Thank you, Pierre Lindenbaum. vg was not installed properly. I installed it again and ran the command, it worked.

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