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24Re: [ssahausers] Test 17

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  • Will Spooner
    Jan 24, 2003
    • 0 Attachment
      Hi Stefan,

      We are having problems with the Linux build at the moment. To suppress the
      segfault error, you can either:

      * Run your query with the -da flag set to 0 (this suppresses graphical
      alignments).

      * Prebuild a hash table from your subject sequence (look for the -sn
      flag in the docs), and then run your query with -sf hash.

      SSAHA works perfectly using this second method.

      I'm not sure where the failed assert arises. I've not seen this problem
      before, so if you do track it down and can offer a patch, please let me
      know.

      Kind regards,

      Will

      ---
      Dr William Spooner whs@...
      Ensembl Web Developer http://www.ensembl.org

      On Fri, 24 Jan 2003, stburk <sb@...-sb.de> wrote:

      > Hello!
      >
      > Today i tried to compile and run SSAHA V3.0 on a linux machine
      > using
      > gcc version 2.95.4 20011002 (Debian prerelease)
      >
      > While it compiled fine, running testSequenceReaderFasta resulted
      > in Test 17 failing with:
      >
      > testSequenceReaderFasta:
      > /home/stburk/MPIHOME/SSAHA/SequenceReader/testSequenceReaderFasta.cpp:1017:
      > int main(): Assertion `c1==c2' failed.
      > Aborted
      >
      > Also, if i run testSSAHA.csh it fails during
      > TEST: Checking main runs with default arguments
      > with the output:
      >
      > constructing QueryManager
      > Info: running DNA query against DNA hash table.
      > FF
      > p1_1a788a01.p1c
      > 1
      > 504
      > p1_1a788a01.p1c
      > 1
      > 504
      > 504
      > 100.00
      > Segmentation fault
      >
      > I already started to locate the problem and it appears to occur in
      > void MatchTaskAlign::operator()(MatchStore& store)
      > included from MatchAligner.cpp
      > when calling
      > subjectSource_.extractSource( &pSubject, //subjectData,
      > (*i)->getSubjectNum(),
      > (*i)->getSubjectStart(),
      > (*i)->getSubjectEnd() );
      >
      > Any help would be appreciated (i will try to find out more during the
      > weekend myself).
      >
      > Thanks,
      >
      > Stefan
      >
      >
      >
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