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loneknightpy / idba

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IDBA_UD 'std::logic_error' #60

Open lijie04 opened 3 years ago

lijie04 commented 3 years ago

Different dataset with exactly same parameters set, sometimes I got error message as below, but still get a contig.fa file.

terminate called after throwing an instance of 'std::logic_error' what(): SequenceReader::SequenceReader() istream is invalid.

Do you have suggestions about it?

jvollme commented 3 years ago

My first suggestion would be, that possibly your input-fastqs are corrupted at some point? But a second suggestion would be: is there any particular reason you HAVE to use idba_ud? It does not really seem to be maintained anymore. You might be better off trying megahit (very easy to use) or perhaps spades (somewhat a bit more complicated to use and uses more resources, but arguably the best and most flexible genome assembler for single cell amplifications, isolate genomes and metagenomes)

lijie04 commented 3 years ago

Thank u so much @jvollme , i just curious about what result idba_ud will return me. I have already tried MetaSPAdes and MEGAHIT, just want to do some test on this one.