Exception while indexing large psuedomolecule

BBMap short read aligner, and other bioinformatic tools.

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Exception while indexing large psuedomolecule

Forum: General Discussion

Creator: Nathan S. Watson-Haigh

Created: 2015-06-22

Updated: 2015-07-22

Nathan S. Watson-Haigh - 2015-06-22

I have a single large pseuomolecule in FASTA format which I'm trying to index with bbmap (v34.86). However it is throwing this exception and I don't know what the possible problem might be:

Exception in thread "main" java.lang.AssertionError: Genome 1: numChroms=0
at dna.Data.setGenome2(Data.java:875)
at dna.Data.setGenome(Data.java:778)
at align2.BBMap.loadIndex(BBMap.java:302)
at align2.BBMap.main(BBMap.java:32)

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Nathan S. Watson-Haigh - 2015-06-22

Confirmed an exception is raised for the latest version v35.10:

Exception in thread "main" java.lang.AssertionError: Genome 1: numChroms=0
at dna.Data.setGenome2(Data.java:860)
at dna.Data.setGenome(Data.java:763)
at align2.BBMap.loadIndex(BBMap.java:306)
at align2.BBMap.main(BBMap.java:32)

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Brian Bushnell - 2015-07-22

Hi! Apologies for not noticing this earlier; I mainly watch SeqAnswers.

Would it be possible for you to email me the fasta file causing the problem? It sounds like the error is because either there's nothing in the file or it is improperly formatted, but I'm not really sure...

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