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eblerjana / pangenie

Pangenome-based genome inference
MIT License
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.cereal cannot be opened #66

Closed dmjask closed 4 months ago

dmjask commented 9 months ago

I'm trying to genotype a limited region with short reads - I know this is not what pangenie was directly designed for, but I have followed your recommendations for this attempt.

After running a successful indexing step I have proceeded with the genotyping as described, but the job fails with this error:

terminate called after throwing an instance of 'std::runtime_error'
  what():  /path/to/output/for/pangenie/six6_UniqueKmersMap.cereal cannot be opened.

Upon inspection of dir, the .cereal does not exist. At dir of sbatch of pangenie there is a .cereal file from indexing, but this remains empty. Any idea or suggestion what may be the issue or fix? Thanks in advance!

dmjask commented 9 months ago

I re ran the indexing and genotyping, which resulted in no .cereal files as well as no .tsv.gz. The path_segments.fasta is output, along with a genotyping.vcf and histogram.histo.