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marbl / merqury

k-mer based assembly evaluation
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kmer completeness file empty #45

Closed unnatisonawala closed 3 years ago

unnatisonawala commented 3 years ago

Hello,

When I run merqury, it runs without error, I get all the spectra-cn plots, and the qv file populates okay, I can even see meryl dbs generated for my assemblies, but the kmer completeness file is empty. Also, the asm only wig files are empty as well. What do you think the issue could be?

Thank you, Unnati

arangrhie commented 3 years ago

Hello Unnati,

Can you check or post the spectra-cn log file? Wonder if this step failed: java -jar -Xmx256m $MERQURY/eval/kmerHistToPloidyDepth.jar reads.hist Or meryl ran out of memory or something...

In addition, a spectra-cn plot would help understand what happened.

Thanks, Arang

unnatisonawala commented 3 years ago

Hi Arang,

Thank you for getting back to me. I looked through the spectra-cn log file and it turned out to be something really simple. The way I had named my output for meryl, the read database ended up being named as {reads}.meryl.k18.meryl causing all the issues. Running okay now.

Thanks again, Unnati