[Seqan-dev] SplazerS crash

[Felix Heeger <fheeger@mi.fu-berlin.de>]

Hi,

I am trying to use SplazerS for RNA read mapping.

For certain input files I get the following error:
"/home/heeger/seqan/core/include/seqan/sequence/segment_infix.h:722
Assertion failed : pos < static_cast<TPos>(length(me)) was: 0 >= 0
(Trying to acces an element behind the last one!)"

This is compiled from the head version of the svn. I am running on
Debian 64.

The input files I used for this are here:
reference: http://page.mi.fu-berlin.de/heeger/problem.fa
reads: http://page.mi.fu-berlin.de/heeger/reads.fa

I am running the following command line:
splazers -vv -m1 -id -i95 problem.fa reads.fa

I will attach the complete output at the bottom.

I tired to download the release version of SplazerS, but the download
does not work (probably due to changes in the homepage).

Thanks in advance,
felix

Complete output of SplazerS:

bin/splazers -vv -m1 -id -i95 problem.fa reads.fas 

Read length      = 18bp
Max num errors   = 1
Recognition rate = 99%

--> Reading bin/gapped_params/results_N18_L.dat
Couldn't open file bin/gapped_params/results_N18_L.dat
Couldn't find preprocessed parameter files. Please configure manually
(options --shape and --threshold).
Using default configurations (shape = 11111111111 and q-gram lemma).

___PARAMETER_CHOOSING__

Read length      = 18bp
Max num errors   = 1
Recognition rate = 99%

--> Reading bin/gapped_params/results_N18_L.dat
Couldn't open file bin/gapped_params/results_N18_L.dat
Couldn't find preprocessed parameter files. Please configure manually
(options --shape and --threshold).
Using default configurations (shape = 11111111111 and q-gram lemma).

___SETTINGS____________
Genome file:                     	problem.fa
Read file:                       	reads.fasta
Compute forward matches:         	YES
Compute reverse matches:         	YES
Error rate:                      	0.05
Minimal threshold:               	1
Shape:                           	11111111111
Suffix Minimal threshold:        	1
Suffix Shape:                    	11111111111
Repeat threshold:                	1000
Overabundance threshold:         	1
Taboo length:                    	1

Ignoring 202 low quality reads.
26734561 bps of 356659 reads loaded.
Loading reads took               	6.10979 seconds
Expected number of random deletion-indicating matches: 7.98111e-19
Expected number of random insertion-indicating matches: 0.000145028
Performing spliced mapping.
Make index left right
Patterns created

Process genome seq
#0[fwd]/home/heeger/seqan/core/include/seqan/sequence/segment_infix.h:722 Assertion failed : pos < static_cast<TPos>(length(me)) was: 0 >= 0 (Trying to acces an element behind the last one!)

stack trace:
  0          [0x5c5675]  seqan::ClassTest::fail() + 0xe
  1          [0x601f10]
seqan::Reference<seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>
const>::Type seqan::value<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment,
int>(seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment> const&, int)
+ 0x59
  2          [0x601f49]  seqan::SimpleType<unsigned char,
seqan::Dna5Q_>& seqan::Segment<seqan::String<seqan::SimpleType<unsigned
char, seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::InfixSegment>::operator[]<int>(int) const + 0x1b
  3          [0x601f71]  int seqan::score<int,
seqan::Tag<seqan::Simple_>, int, int,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>
>(seqan::Score<int, seqan::Tag<seqan::Simple_> > const&, int, int,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment> const&,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment> const&) +
0x26
  4          [0x602278]  int
seqan::_extendSeedOneDirection<seqan::Tag<seqan::SeedSimple_> const,
int, seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, int,
int>(seqan::Seed<int, seqan::Tag<seqan::SeedSimple_> const>&,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment> const&,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment> const&, int,
seqan::Score<int, seqan::Tag<seqan::Simple_> > const&, int) + 0x2d0
  5          [0x602cef]  void
seqan::extendSeedScore<seqan::Tag<seqan::SeedSimple_> const, int,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, int,
int>(seqan::Seed<int, seqan::Tag<seqan::SeedSimple_> const>&, int&, int,
seqan::Score<int, seqan::Tag<seqan::Simple_> > const&,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment> const&,
seqan::Segment<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment> const&, int,
seqan::Tag<seqan::ExtendSeedGappedXDrop_>) + 0x285
  6          [0x603a35]  void
seqan::extendMatch<seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >, unsigned int, seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::ReadMatch<long>, seqan::RazerSOptions<seqan::RazerSSpec<false, false> > const>(seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >&, unsigned int, seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>&, seqan::ReadMatch<long>&, seqan::RazerSOptions<seqan::RazerSSpec<false, false> > const&, seqan::LongestPrefix) + 0x204
  7          [0x603f67]  bool seqan::matchVerify<seqan::ReadMatch<long>,
seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>,
seqan::Alloc<void> >,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >,
seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Myers<seqan::FindInfix, seqan::True, void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false>, seqan::LongestPrefix>(seqan::ReadMatch<long>&, seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, unsigned int, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >&, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Myers<seqan::FindInfix, seqan::True, void> >, seqan::Alloc<void> >&, seqan::RazerSOptions<seqan::RazerSSpec<false, false> > const&, seqan::Tag<seqan::SwiftSemiGlobal_<void> >, seqan::LongestPrefix) + 0x42a
  8          [0x6716d3]  void
seqan::mapSplicedReads<seqan::String<seqan::ReadMatch<long>,
seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >,
seqan::Index<seqan::StringSet<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::Tag<seqan::Default_> > >, seqan::Index<seqan::StringSet<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::Tag<seqan::Default_> > >, seqan::Tag<seqan::SwiftSemiGlobal_<void> >, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Myers<seqan::FindInfix, seqan::True, void> >, seqan::Alloc<void> >, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false> >(seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >&, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >&, unsigned int, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::Owner<seqan::ConcatDirect<void> > >&, seqan::String<seqan::Pair<unsigned int, seqan::Pair<unsigned int, long, seqan::BitCompressed<2u, 64u> >, void>, seqan::Alloc<void> >&, seqan::Pattern<seqan::Index<seqan::StringSet<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::Tag<seqan::Default_> > >, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >&, seqan::Pattern<seqan::Index<seqan::StringSet<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>, seqan::UngappedShape<0u> >, seqan::Tag<seqan::Default_> > >, seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > > >&, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Myers<seqan::FindInfix, seqan::True, void> >, seqan::Alloc<void> >&, seqan::String<seqan::Pattern<seqan::Segment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::InfixSegment>, seqan::Myers<seqan::FindInfix, seqan::True, void> >, seqan::Alloc<void> >&, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >&, char, seqan::RazerSOptions<seqan::RazerSSpec<false, false> >&) + 0x110f
  9          [0x673333]  int
seqan::mapSplicedReads<seqan::String<seqan::ReadMatch<long>,
seqan::Alloc<void> >,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >,
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >,
seqan::Alloc<void> >, seqan::RazerSSpec<false, false>,
seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>,
seqan::UngappedShape<0u> >, seqan::Shape<seqan::SimpleType<unsigned
char, seqan::Dna_>, seqan::UngappedShape<0u> >,
seqan::Tag<seqan::SwiftSemiGlobal_<void> >
>(seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >&,
seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&,
seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&, std::map<unsigned int,
std::pair<std::string, unsigned int>, std::less<unsigned int>,
std::allocator<std::pair<unsigned int const, std::pair<std::string,
unsigned int> > > >&,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >&,
seqan::String<seqan::Pair<unsigned int, seqan::Pair<unsigned int, long,
seqan::BitCompressed<2u, 64u> >, void>, seqan::Alloc<void> >&,
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >,
seqan::Alloc<void> >&, seqan::RazerSOptions<seqan::RazerSSpec<false,
false> >&, seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>,
seqan::UngappedShape<0u> > const&,
seqan::Shape<seqan::SimpleType<unsigned char, seqan::Dna_>,
seqan::UngappedShape<0u> > const&,
seqan::Swift<seqan::Tag<seqan::SwiftSemiGlobal_<void> > >) + 0xd98
 10          [0x68dda6]  int
seqan::mapSplicedReads<seqan::String<seqan::ReadMatch<long>,
seqan::Alloc<void> >,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >,
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >,
seqan::Alloc<void> >, seqan::RazerSSpec<false, false>
>(seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >&,
seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&,
seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&, std::map<unsigned int,
std::pair<std::string, unsigned int>, std::less<unsigned int>,
std::allocator<std::pair<unsigned int const, std::pair<std::string,
unsigned int> > > >&,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >&,
seqan::String<seqan::Pair<unsigned int, seqan::Pair<unsigned int, long,
seqan::BitCompressed<2u, 64u> >, void>, seqan::Alloc<void> >&,
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >,
seqan::Alloc<void> >&, seqan::RazerSOptions<seqan::RazerSSpec<false,
false> >&) + 0x703
 11          [0x68e3ed]  int
seqan::mapReads<seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void>
>, seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >,
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >,
seqan::Alloc<void> >, seqan::RazerSSpec<false, false>
>(seqan::String<seqan::ReadMatch<long>, seqan::Alloc<void> >&,
seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&,
seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&, std::map<unsigned int,
std::pair<std::string, unsigned int>, std::less<unsigned int>,
std::allocator<std::pair<unsigned int const, std::pair<std::string,
unsigned int> > > >&,
seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char,
seqan::Dna5Q_>, seqan::Alloc<void> >,
seqan::Owner<seqan::ConcatDirect<void> > >&,
seqan::String<seqan::Pair<unsigned int, seqan::Pair<unsigned int, long,
seqan::BitCompressed<2u, 64u> >, void>, seqan::Alloc<void> >&,
seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >,
seqan::Alloc<void> >&, seqan::RazerSOptions<seqan::RazerSSpec<false,
false> >&) + 0x98
 12          [0x69a4b4]  int mapReads<seqan::RazerSSpec<false, false>
>(seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&,
seqan::StringSet<seqan::String<char, seqan::Alloc<void> >,
seqan::Owner<seqan::Tag<seqan::Default_> > >&, seqan::String<char,
seqan::Alloc<void> >&, seqan::RazerSOptions<seqan::RazerSSpec<false,
false> >&) + 0xbae
 13          [0x56f5c4]  main + 0x8125
 14    [0x7fc1c67591a6]  __libc_start_main + 0xe6
 15          [0x566f59]  std::ios_base::Init::~Init() + 0x41

Aborted