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60Re: [ssahausers] ssaha-hash: crashes when pathchange?

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  • Adam Spargo
    Feb 2, 2006
    • 0 Attachment
      Hi,
      The error message is saying that a sequence name check failed, that the
      name didn't start with either a '>' or a '@', ie fasta or fastq format.

      All I can say is are you sure?
      If you can't resolve the problem then you can make the files available for
      me to download and I will try to recreate the problem.

      Adam.


      On Thu, 2 Feb 2006, MaximilianHaeussler wrote:

      > Hi,
      >
      > I have a very very weird problem here. Isolating it took me a couple
      > of hours:
      >
      > I have to put the hashfiles and the query file in two different
      > directories.
      >
      > a) When I run ssaha from the directory where the hash files are
      > located, everything works fine.
      >
      > b) when I run ssaha from the directory where the query file is
      > located, it crashes with the following (not very informative) error
      > message:
      > -
      > ssaha: ..//SequenceReader/SequenceReader.cpp:305: const char *
      > SourceReaderIndex::extractName(unsigned int): Assertion
      > `(nameBuffer_[0]=='>')||(nameBuffer_[0]=='@')' failed.
      > -
      >
      > It's a standard debian linux box (colinux'ed though), with an ext2
      > filesystem. Here are the two command lines:
      >
      > a) "ssaha ~/usr/genotrace/odmrna.fa hash.fasta.oikopleura_dioica.001
      > -sf hash -ph"
      > ----> OK
      >
      > b) "ssaha odmrna.fa
      > ~/tracedb/od/ssaha/hash.fasta.oikopleura_dioica.001 -sf hash -ph "
      > ---> ERROR MESSAGE
      >
      > Any ideas on this?!?!
      >
      > Thanks,
      > Max
      >
      >
      >
      >
      >
      >
      >
      > Yahoo! Groups Links
      >
      >
      >
      >
      >
      >
      >

      --
      Dr Adam Spargo
      High Performance Assembly Group email: aws@...
      Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
      Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919
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