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loneknightpy / idba

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logic_error: ShortSequence: Sequence is too long. #52

Closed ReneKat closed 5 years ago

ReneKat commented 5 years ago

Hello, I am new to IDBA and the genomics world, so I am hoping to get some help to resolve this error. My command is: idba_ud -r db.fa.gz -o /Results/ After a split second I get the following logic error: terminate called after throwing an instance of 'std::logic_error' what(): ShortSequence: Sequence is too long.

My sequencing reads are in an interleaved gzipped fasta file; between 100-200bp. In the manual, it is written that the -r accepts fasta read file (<=600). I'm assuming this is 600bp? So, I'm unsure how my reads are too long.

Thanks for any guidance!

jvollme commented 5 years ago

Hi renekat, I'm not sure IDBA can handle gzip compressed files. Maybe that's the problem? Try decompressing your input file with "gunzip db.fa.gz" and then running idba again with "-r db.fa"

ReneKat commented 5 years ago

Hi jvollme, That was exactly the problem. Thanks so much for your quick reply!