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marbl / merqury

k-mer based assembly evaluation
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completeness file is empty #64

Closed cell-c closed 2 years ago

cell-c commented 2 years ago

Hi Thanks for the good evaluation tool for genome assembly .

When I run merqury, it gave rise to error "Error: Unable to access jarfile /eval/kmerHistToPloidyDepth.jar" in spectra-cn.log. All results work well except that kmer completeness file is empty.

What do you think the issue could be?

Thank you,

Chuang

brianwalenz commented 2 years ago

Looks like the MERQURY environment variable isn't set. See step two in https://github.com/marbl/merqury#direct-installation. This should be the location of the merqury install; ls -l $MERQURY/eval/kmerHistToPloidyDepth.jar should show the file.

cell-c commented 2 years ago

Many thanks for your suggestion. I resolved it. I checked files and found that $MERQURY was not set in a shell file.