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100Re: Error running latest ssaha

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  • coxtonyj
    Aug 23, 2007
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      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.

      Cheers


      Tony




      --- 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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