Re: [Seqan-dev] Memory allocation error with globalAlignmentScore() and globalAlignment()

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Hi Johannes,

we will investigate this problem.

Meanwhile, you could use the globalAlignment() function without a tag. We do not have current benchmarks for MyerHirschberg vs. our new NeedlemanWunsch implementation but the latter is definitely more used and then less error prone.

HTH
Manuel
________________________________________
From: Johannes Dröge [johdro@mpi-inf.mpg.de]
Sent: Wednesday, August 21, 2013 12:54 PM
To: SeqAn Development
Subject: [Seqan-dev] Memory allocation error with globalAlignmentScore() and    globalAlignment()

Hello Seqan developers,

I just ported my software, which was using globalAlignment() extensively without problems, from a Seqan version from 2011 to the recent headers. I had to change the syntax related to the scoring until it compiled well. Anyway, now I got a segfault when running globalAlignment(). I then changed the code to use globalAlignmentsScore(), because I don't actually need the explicit alignment. The error is still persists and seems to be related to the data/types or similar.

1) Here is the original code fragment:

const seqan::Dna5String qseq = ...
seqan::Dna5String rseq = ...
seqan::Align< seqan::Dna5String > aln;
seqan::resize( seqan::rows( aln ), 2);
seqan::assignSource( seqan::row( aln, 0 ), qseq );
seqan::assignSource( seqan::row( aln, 1 ), rseq );
const int score = -seqan::globalAlignment( aln, seqan::SimpleScore(), seqan::MyersHirschberg() );

2) Here is the intermediate code:

const seqan::Dna5String qseq = ...
seqan::Dna5String rseq = ...
seqan::Align< seqan::Dna5String > aln;
seqan::resize( seqan::rows( aln ), 2);
seqan::assignSource( seqan::row( aln, 0 ), qseq );
seqan::assignSource( seqan::row( aln, 1 ), rseq );
const int score = -seqan::globalAlignment( aln, seqan::MyersHirschberg() );

3) Here is the current code:

const seqan::Dna5String qseq = ...
seqan::Dna5String rseq = ...
const int score = -seqan::globalAlignmentScore( qseq, rseq, seqan::MyersHirschberg() );

----------

This is what I get from (2) and (3):

aligning two sequences globally:
seq1: TAGCACTCAGGGAGAATGAGTGCTAAAACATAGAATGAGAAATGGAGGCGAGAGTATGGAGCTGACCAATCGAAAAAAGCGAATCCTGCGGGCCATTGTTGAGATCTATATCTCCACCGCGGAACCGGTAGGTTCCAAGGCCGTGGCAGAGCAGGCCGGACTGGACATCTCCACCGCCACCATACGAAATGAGATGGCCGACCTCACCGAACTGGGCTATCTGGAGCAGCCCCACACCTCGGCCGGACGGATTCCGTCCCCCATGGGCTACCGGCTCTACGTCAACGAGCTCATGGGTGAGCACCAGCTGACCATGCAGGAGACCCAGCGCATCAACGACGCGCTGAACCTGAAAATGGAGGAGCTGGACCGGGTCATCGACCGGGCGGGCAAGGTGCTCTCCCAGATCAGCGACTACCCCGTCTTTACCATGGCCCAGCCCAAGCAGCGGGTGACGGTAAAGCGGTACGACCTGCTGATGGTAGAGGAAAACGCCTTTATCGCTGTGGTGATGACCGACAACTCGGTGGTGCGCAACAAGCTTATCCACCTGTCCGATGAGCTTTCCGACACCCAGCTGCAGCTGCTGTCCACCGTTTTGAACAGCTCCTTTGTAGGTCTGACCGTGGAGGAAATGGAACAG
seq2: TATATTAGCACTCGGAAAGCGAGAGTGCCAACAGTCCGAAGCGGAGAGTGCTAACATGGCAATCAGTGAGAGGAAAAAGAAAATACTGGCGGCGGTGGTGGATGAATACATCCGCACGGCAGAGCCGGTAGGCAGCAAGGCCATCGCCCAGAGCGGCGGGCTGAACTGCTCCTCGGCCACCATCCGCAACGAGCTGGCGGAGCTGGTCGCCATGGGCTATCTGGAGCAGCCCCACACCTCTGCGGGCCGGGTGCCCACCCCCATGGGCTACCGCATGTACGTCAACGAGCTCATGGAGAAGCAGAAGATGAGCCTGGAGGAGACGGAGGAGATGAACCGCCGCCTGAACCAGAAGCTCCAGGAGCTGGACGACACCATCCGGGACGTGAGCAAGCTGGCTTCCCAGCTGACGAATTATCCCGCCCTGGCCCTGACGGCCCAGAGCTCCGTCACGGTAAAGCGCTTCGACCTGATCTATGTGGACGCCAACAACTTCATCATCGTGCTGATGCTGTCCAACAACAGCGTAAAGAGCAAGCTGGTGCATCTGCCGGTGTCCGTGGACCAGGACATGATCAAGCGCCTTTCCACCCTCTTCAACGCCAGCTTTACCGGCGTGGAGGATCAGCAGATCACGCCG
prog: malloc.c:4631: _int_malloc: Assertion `(unsigned long)(size) >= (unsigned long)(nb)' failed.

----------

GDB backtrace:

0x00007ffff6a7d1b5 in raise () from /lib/libc.so.6
(gdb) bt
#0  0x00007ffff6a7d1b5 in raise () from /lib/libc.so.6
#1  0x00007ffff6a7ffc0 in abort () from /lib/libc.so.6
#2  0x00007ffff6ab35bb in ?? () from /lib/libc.so.6
#3  0x00007ffff6abce16 in ?? () from /lib/libc.so.6
#4  0x00000000004f13ce in seqan::deallocate<seqan::String<unsigned int, seqan::Alloc<void> >, unsigned int, unsigned long, seqan::AllocateStorage_> (data=0x832831460)
     at seqan/basic/allocator_interface.h:329
#5  0x00000000004ecc09 in seqan::_deallocateStorage<unsigned int, void, unsigned int, unsigned long> (me=..., ptr=0x832831460, capacity=32)
     at seqan/sequence/string_alloc.h:402
#6  0x00000000004e76d6 in ~String (this=0x7fffede12e80, __in_chrg=<value optimized out>)
     at seqan/sequence/string_alloc.h:177
#7  0x00000000004e1ebd in seqan::_globalAlignment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_> > (gapsH=..., gapsV=..., algorithmTag=...)
     at seqan/align/global_alignment_myers_hirschberg_impl.h:745
#8  0x00000000004df9ea in seqan::_globalAlignment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_>, seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_> > (gapsH=..., gapsV=..., algorithmTag=...)
     at seqan/align/global_alignment_myers_hirschberg_impl.h:183
#9  0x00000000004db18c in seqan::globalAlignment<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<void> >, seqan::Tag<seqan::ArrayGaps_> > (align=...,
     algorithmTag=...) at seqan/align/global_alignment_specialized.h:93
#...

Could this be related to the differing sequence lengths or am I doing something else wrong?

Gruß Johannes

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