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101Re: Error running latest ssaha

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  • sraxylan
    Aug 23, 2007
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      --- In ssahausers@yahoogroups.com, "coxtonyj" <anthony.j.cox@...> wrote:
      >
      > Hi
      >
      > Your command should work if test.fa is in valid fasta format.
      > However the file needs to be in UNIX text file format - ie
      > just one character at each linebreak. I managed to replicate
      > this error by giving it a fasta file in DOS text file format.
      >
      > Try 'dos2unix test.fa' and rerunning the query.

      Tony,

      Thanks for the reply. I've checked, and test.fa is definitely using
      unix line endings already.

      Having played with this a bit more it seems this is something to do
      with using absolute paths. If I run a search where the query and the
      hash are in the same folder then it works. If I leave the hash in one
      folder and move the query to another and then run a command which uses
      an absolute path to the hash then it fails. Am I missing something in
      my setup which would allow me to run searches from a directory which
      doesn't contain the search database?

      Cheers

      Simon.


      >
      > --- In ssahausers@yahoogroups.com, "sraxylan" <sraxylan@> wrote:
      > >
      > > I'm trying to run ssaha on a fedora 7 (32bit) system and it's dying
      > > with an error every time I run it.
      > >
      > > I'm running the latest v33 version of ssaha, but I've also tried
      > v31c
      > > which also fails.
      > >
      > > I can successfully compute the hashtable from my subject fasta
      > files,
      > > but when I try to search against this with a short test sequence
      > ssaha
      > > dies.
      > >
      > > /usr/local/bin/ssaha test.fa
      > > /data/public/DNA/Genomes/NCBIM36/Current/ncbi36_1 -qf fasta -sf hash
      > >
      > > [snip lots of output]
      > >
      > > Info: running DNA query against DNA hash table.
      > > ssaha:
      > > /home/andrewss/SSAHA/SSAHA/SequenceReader/SequenceReader.cpp:305:
      > > const char* SourceReaderIndex::extractName(SequenceNumber):
      > Assertion
      > > `(nameBuffer_[0]=='>')||(nameBuffer_[0]=='@')' failed.
      > > Aborted
      > >
      > > Any ideas about how to make this work?
      > >
      >
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