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Re: [Seqan-dev] SplazerS crash

<-- thread -->
<-- date -->
  • From: "Emde, Anne-Katrin" <Anne-Katrin.Emde@fu-berlin.de>
  • To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Date: Thu, 8 Mar 2012 19:45:01 +0000
  • Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Subject: Re: [Seqan-dev] SplazerS crash
Hi Felix,

the crash seems to have something to do with SeqAn's old seeds module. We will fix this problem as quickly as possible.

For now, I would recommend you to run SplazerS in Hamming distance mode (without option -id), i.e. allowing for only one split gap and no additional gaps in read prefix and suffix alignment. Especially as it looks like you are dealing with relatively short Illumina reads (75bp). This can save a lot of runtime while not sacrificing much in terms of sensitivity on Illumina data.

As a side note: by specifying the parameter directory (-pd seqan-trunk/core/apps/splazers/gapped_params/) performance will be optimized, both in terms of sensitivity as well as runtime. Alternatively, you can copy the splazers binary and the gapped_params folder to the same directory, then splazers will locate the folder automatically. Otherwise, splazers may use suboptimal filtering parameters possibly leading to decreased mapping sensitivity. 

Hope this helps for the moment, we will send another email once the problem is fixed.

Best,
Anne-Katrin


-----------------------------------------------
 Anne-Katrin Emde
 +49 30 83875240
 emde@inf.fu-berlin.de

 Algorithmic Bioinformatics
 Department of Computer Science
 Freie Universität Berlin
----------------------------------------------
________________________________________
Von: Felix Heeger [fheeger@mi.fu-berlin.de]
Gesendet: Donnerstag, 8. März 2012 16:51
An: seqan-dev@lists.fu-berlin.de
Betreff: [Seqan-dev] SplazerS crash

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



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  • References:
    • [Seqan-dev] SplazerS crash
      • From: Felix Heeger <fheeger@mi.fu-berlin.de>
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