refresh-bio / KMC

Fast and frugal disk based k-mer counter
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Space shortage for output not reported #211

Open jamshed opened 1 year ago

jamshed commented 1 year ago

Hi @marekkokot:

During execution, if kmc observes disk-space shortage in its working directory (for temporary files), then it reports such and exits. But, if enough space is not available in the disk for the final output, this isn't reported. Instead, a partial output database is written as much as possible until the space runs out, and kmc finishes the stage 2. As such, the output is corrupted.

It will be quite helpful if some error is mentioned in this scenario and kmc exits, instead of a graceful completion.

Regards.