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Test 17

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  • stburk <sb@bioinf.uni-sb.de>
    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
    Message 1 of 2 , Jan 24, 2003
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      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
    • Will Spooner
      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
      Message 2 of 2 , Jan 24, 2003
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        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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