[Seqan-dev] bug report readSequence()

[Eik Dahms <eik.dahms@gmail.com>]

Dear all,

i recently upgraded sequan from 1.4.0 to 2.0.0. I did not change my code. 

When i now try to run the program  i get the following allocation error when i try to read a sequence via readSequence() from a FaiIndex:

/seqan/basic/basic_exception.h:368 FAILED!  (Uncaught exception of type std::bad_alloc: std::bad_alloc)

This error occurs only on my laptop with 4GB RAM. When i run the program on a Server with 500GB RAM - it works.

It seems that the memory that is allocated, for the string that the sequence is read in, is to high.

I appended the stacktrace from gnu debugger.  

Thanks in advance !

Eik

#0  0x00007ffff676ecc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
#1  0x00007ffff67720d8 in __GI_abort () at abort.c:89
#2  0x000000000043bbdc in fail () at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/basic/debug_test_system.h:1715
#3  seqan::globalExceptionHandler () at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/basic/basic_exception.h:368
#4  0x00007ffff7078836 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#5  0x00007ffff7078863 in std::terminate() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#6  0x00007ffff7078aa2 in __cxa_throw () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#7  0x00007ffff7078f8d in operator new(unsigned long) () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6
#8  0x000000000043b9b0 in allocate<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::SimpleType<unsigned char, seqan::Dna5_>, long unsigned int, seqan::AllocateStorage_> (
    count=<optimized out>, data=@0x7fffffffcae0: 0x0) at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/basic/allocator_interface.h:227
#9  _allocateStorage<seqan::SimpleType<unsigned char, seqan::Dna5_>, void, unsigned long> (new_capacity=14865477993, me=...) at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/sequence/string_alloc.h:360
#10 _reallocateStorage<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<>, long unsigned int> (new_capacity=14865477993, me=...)
    at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/sequence/string_base.h:1509
#11 _reallocateStorage<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<>, long unsigned int> (new_capacity=<optimized out>, me=...)
    at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/sequence/string_base.h:1554
#12 seqan::_reserveStorage<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<>, long unsigned int, seqan::TagGenerous_>(seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> > &, unsigned long) (seq=..., new_capacity=<optimized out>, tag=...) at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/sequence/string_base.h:1656
#13 0x0000000000465001 in reserve<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<>, long unsigned int, seqan::TagGenerous_> (new_capacity=<optimized out>, seq=..., tag=...)
    at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/sequence/string_base.h:1674
#14 reserve<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, long unsigned int> (new_capacity=<optimized out>, me=...)
    at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/sequence/sequence_interface.h:1336
#15 reserveChunk<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<>, long unsigned int> (size=<optimized out>, str=...)
    at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/sequence/string_base.h:1956
#16 _readUntil<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::Iter<const seqan::String<char, seqan::MMap<> >, seqan::AdaptorIterator<char const*, seqan::Tag<seqan::Default_> > >, seqan::CountDownFunctor<seqan::NotFunctor<seqan::OrFunctor<seqan::OrFunctor<seqan::EqualsChar<' '>, seqan::EqualsChar<'\011'> >, seqan::OrFunctor<seqan::EqualsChar<'\012'>, seqan::EqualsChar<'\015'> > > > >, seqan::OrFunctor<seqan::OrFunctor<seqan::EqualsChar<' '>, seqan::EqualsChar<'\011'> >, seqan::OrFunctor<seqan::EqualsChar<'\012'>, seqan::EqualsChar<'\015'> > >, char const, seqan::SimpleType<unsigned char, seqan::Dna5_> > (ignoreFunctor=<synthetischer Zeiger>, stopFunctor=<synthetischer Zeiger>, iter=<synthetischer Zeiger>, target=...)
    at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/stream/tokenization.h:308
#17 readUntil<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >, seqan::Iter<const seqan::String<char, seqan::MMap<> >, seqan::AdaptorIterator<char const*, seqan::Tag<seqan::Default_> > >, seqan::CountDownFunctor<seqan::NotFunctor<seqan::OrFunctor<seqan::OrFunctor<seqan::EqualsChar<' '>, seqan::EqualsChar<'\011'> >, seqan::OrFunctor<seqan::EqualsChar<'\012'>, seqan::EqualsChar<'\015'> > > > >, seqan::OrFunctor<seqan::OrFunctor<seqan::EqualsChar<' '>, seqan::EqualsChar<'\011'> >, seqan::OrFunctor<seqan::EqualsChar<'\012'>, seqan::EqualsChar<'\015'> > > > (ignoreFunctor=<synthetischer Zeiger>, 
    stopFunctor=<synthetischer Zeiger>, iter=<synthetischer Zeiger>, target=...) at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/stream/tokenization.h:331
#18 seqan::readRegion<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void>, unsigned int, int, int> (str=..., index=..., rID=rID@entry=90449, beginPos=<optimized out>, beginPos@entry=1, 
    endPos=<optimized out>, endPos@entry=2) at /home/edahms/AlgBio/taxator-tk/includes-external/seqan/seq_io/fai_index.h:333