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ssaha-hash: crashes when pathchange?

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  • MaximilianHaeussler
    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.
    Message 1 of 2 , Feb 2 1:32 AM
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      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
    • Adam Spargo
      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
      Message 2 of 2 , Feb 2 1:48 AM
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        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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