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Re: Error running latest ssaha

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  • coxtonyj
    You re right, there does seem to be an issue when you specify -sf hash - both query and subject need to be in the same directory. Interestingly it always
    Message 1 of 5 , Aug 23 7:19 AM
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      You're right, there does seem to be an issue when you specify '-sf
      hash' - both query and subject need to be in the same directory.
      Interestingly it always seems to be able to load in the hash table
      correctly, even if that is the one with the path. I will try to look
      into it.

      If both query and subject are '-sf fasta' then any combination of
      relative or absolute paths for both query and subject file works OK
      for me.

      --- In ssahausers@yahoogroups.com, "sraxylan" <simon.andrews@...>
      wrote:
      >
      > --- 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?
      > > >
      > >
      >
    • sraxylan
      ... Having looked at this some more I found that if you use a full path to specify the location of the fasta file when you create the hash initially you can
      Message 2 of 5 , Aug 24 3:14 AM
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        --- In ssahausers@yahoogroups.com, "coxtonyj" <anthony.j.cox@...> wrote:
        >
        > You're right, there does seem to be an issue when you specify '-sf
        > hash' - both query and subject need to be in the same directory.
        > Interestingly it always seems to be able to load in the hash table
        > correctly, even if that is the one with the path. I will try to look
        > into it.

        Having looked at this some more I found that if you use a full path to
        specify the location of the fasta file when you create the hash
        initially you can then perform searches from anywhere. This gives me
        a good work round for my problem. It might be a simple fix to expand
        the filename to a full path when saving a hash?

        TTFN

        Simon.
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