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bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
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terminate called after throwing an instance of 'std::runtrime_error' #172

Closed drhoads closed 3 years ago

drhoads commented 3 years ago

Installed Poppunk in WSL2 and used it many times. Needed to run some new data and WSL2 suggested to run sudo apt update. When I was done then poppunk won't finish a run $ poppunk --create-db --output SaureusPoultryGenomes --r-files r-list.txt --qc-filter continue --threads 8 ' terminate called after throwing an instance of 'std::runtrime_error' terminate called recursively terminate called recursively Aborted (core dumped) Poppunk 2.3.0 sketchlib v1.6.2 I tried reinstalling poppunk and no solution.

johnlees commented 3 years ago

This looks like it probably can't find the files listed in r-list.txt, or they don't contain sequence. Could you double-check that? You may want to upgrade sketchlib to v1.7.3 if you can, as that reports this error in a more helpful way.

If that's not it, can you paste the whole output you get from running the command

drhoads commented 3 years ago

If I leave out the '--qc-filter continue' then I do get reports saying that certain files contain no sequence, but these are all downloaded directly from NCBI and I can guarantee they all have sequence in them. I have built blast databases from these same files and completed tblastn searches. I will try to upgrade sketchlib.

drhoads commented 3 years ago

Wait, I figured it out. Problem is using windows listings for the path to the files. Silly mistake, I have to convert to Linux format in WSL2. Stupid me I had the full dos path to the genome files (e.g., e:\DNAwork\Saureus....), and forgot this is a Linux shell and needed it to be /mnt/e/DNAwork/Saureus/.... Sorry about that.

johnlees commented 3 years ago

Ah no problem, I appreciate that the old error message wasn't very clear about this being a data/file access issue!