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pmelsted / bifrost

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
BSD 2-Clause "Simplified" License
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bad alloc in v1.0.5 and latest master #54

Closed ptrebert closed 2 years ago

ptrebert commented 3 years ago

Hi,

I get the below error for both the v1.0.5 installed from Conda (with k=31) and the latest master build (with k=63) for the Bifrost build --colors command:

KmerStream::KmerStream(): Start computing k-mer cardinality estimations
CompactedDBG::build(): Estimated number of k-mers occurring at least once: 119170197639
CompactedDBG::build(): Estimated number of minimizer occurring at least once: 25150968762
CompactedDBG::build(): Estimated number of k-mers occurring twice or more: 24926987045
CompactedDBG::build(): Estimated number of minimizers occurring twice or more: 5164277853
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc

The input is a bunch of read files (mixed gzipped fastq and fasta). I tested the same command (using the latest master build) with two small fasta files, and that works. Could that be a simple issue with the input reads (similar to #21)? Any suggestion what to look for?

Thanks!

GuillaumeHolley commented 2 years ago

Hi @ptrebert,

Could you let me know if this is still an issue for you with the latest version of Bifrost? Otherwise, could you send a minimal example to reproduce the issue?

Thanks, Guillaume

GuillaumeHolley commented 2 years ago

Hi @ptrebert,

I am closing for now but feel free to reopen if this is still an issue.

Guillaume