Re: [Seqan-dev] RazerS3: store_io_sam.h:293 Assertion failed

[Uwe Appelt <uappelt@clcbio.com>]

Hi David,

thanks for the fix, works fine now.

Cheers,
Uwe


On 28/08/2012 23:48, Weese, David wrote:

Hi Uwe,

I could reproduce your bug. The yesterday ntroduced --dont-shrink option wasn't working correctly. If you now update your svn-trunk, it should be fine.

Cheers,

David

--
David Weese weese@inf.fu-berlin.de
Freie Universität Berlin http://www.inf.fu-berlin.de/
Institut für Informatik Phone: +49 30 838 75137
Takustraße 9 Algorithmic Bioinformatics
14195 Berlin Room 020

Am 28.08.2012 um 14:06 schrieb Uwe Appelt <uappelt@clcbio.com>:

Hi all,

received a failed assertion from a RazerS3 run in a Rabema scenario. Fresh trunk checkout from today (~9:00am, Berlin time). Could someone advise me on that, please?

Command line was:
../bin/rabema/razers3 -v -tc 32 -of sam -rr 100 -i 90 -m 1000000 -ds -o ./rabema/NA18507_1_1e5complex.sam ../ref_genomes/hg19.fa ../reads/NA18507_1_1e5complex.fastq

The following excerpt from stderr lacks only redundant lines, such as some progress information and the timing-paragraphs for all individual threads:

___SETTINGS____________
Genome file:                         ../ref_genomes/hg19.fa
Read file:                           ../reads/NA18507_1_1e5complex.fastq
Compute forward matches:             YES
Compute reverse matches:             YES
Allow Indels:                        YES
Error rate:                          0.1
Pigeonhole mode with overlap:        0
Shape:                               11111111111
Repeat threshold:                    1000
Overabundance threshold:             1
Program PID:                         25972

9950400 bps of 100000 reads loaded.
Loading reads took                   0.175637 seconds

Number of threads:                   32

Initialization took                  0.0466482 seconds

Process genome seq #0[fwd]...
Process genome seq #0[rev]...
...many more similar lines...
Process genome seq #24[fwd]
Process genome seq #24[rev]useExternalSort == 0
useSequentialCompaction == 0
length(threadLocalStorages[0].matches) == 486517
length(store.alignedReadStore) == 15855239
Thread #0
  Masking duplicates took            0.234666 seconds
  Compacting matches took            1.24819e-312 seconds
  Time for filtration                704.828 seconds
  Time for verifications             4751.59 seconds
...many more similar lines...
Thread #31
  Masking duplicates took            0.266166 seconds
  Compacting matches took            1.24819e-312 seconds
  Time for filtration                707.064 seconds
  Time for verifications             4731.22 seconds
Time for copying back                1.84491 seconds

Finding reads took                   5619.52 seconds

___FILTRATION_STATS____
Filtration counter:      171112671856
Successful verfications: 47445773
/home/uappelt/MapperBenchmarks/bin/rabema/seqan-trunk/core/include/seqan/store/store_io_sam.h:293 Assertion failed : atEnd(it1) == atEnd(it2) should be true but was 0 (Cannot get CIGAR from invalid pairwise alignment!)

stack trace:
  0          [0x526eee]  seqan::ClassTest::fail() + 0xe
  1          [0x5adae9]  void seqan::getCigarString<seqan::String<char, seqan::Alloc<void> >, seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::AnchorGaps<seqan::String<seqan::GapAnchor<long>, seqan::Alloc<void> > > >, seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::AnchorGaps<seqan::String<seqan::GapAnchor<long>, seqan::Alloc<void> > > >, int>(seqan::String<char, seqan::Alloc<void> >&, seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::AnchorGaps<seqan::String<seqan::GapAnchor<long>, seqan::Alloc<void> > > >&, seqan::Gaps<seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5Q_>, seqan::Alloc<void> >, seqan::AnchorGaps<seqan::String<seqan::GapAnchor<long>, seqan::Alloc<void> > > >&, int) + 0x3d9
  2          [0x626219]  void seqan::_writeAlignments<std::basic_ofstream<char, std::char_traits<char> >, MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig>, seqan::False>(std::basic_ofstream<char, std::char_traits<char> >&, seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >&, seqan::Tag<seqan::Sam_>, seqan::False) + 0xb39
  3          [0x6e78ac]  int seqan::dumpMatches<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig>, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false>, seqan::RazerSMode<seqan::RazerSGlobal, seqan::RazerSGapped, seqan::RazerSErrors, seqan::NMatchesNone_> >(seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >&, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> >, seqan::RazerSOptions<seqan::RazerSSpec<false, false> >&, seqan::RazerSMode<seqan::RazerSGlobal, seqan::RazerSGapped, seqan::RazerSErrors, seqan::NMatchesNone_> const&) + 0x8bc
  4          [0x6e9b6d]  int seqan::dumpMatches<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig>, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false>, seqan::RazerSGlobal, seqan::RazerSGapped, seqan::NMatchesNone_>(seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >&, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> >, seqan::RazerSOptions<seqan::RazerSSpec<false, false> >&, seqan::RazerSMode<seqan::RazerSGlobal, seqan::RazerSGapped, seqan::Nothing, seqan::NMatchesNone_>) + 0x6d
  5          [0x6faad7]  int seqan::dumpMatches<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig>, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >, seqan::RazerSSpec<false, false> >(seqan::FragmentStore<MyFragStoreConfig, seqan::FragmentStoreConfig<MyFragStoreConfig> >&, seqan::String<seqan::String<unsigned short, seqan::Alloc<void> >, seqan::Alloc<void> >&, seqan::String<char, seqan::Alloc<void> >, seqan::RazerSOptions<seqan::RazerSSpec<false, false> >&) + 0x237
  6          [0x72863b]  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::RazerSOptions<seqan::RazerSSpec<false, false> >&) + 0xb0b
  7          [0x4da270]  main + 0x870
  8      [0x3ad241ecdd]  __libc_start_main + 0xfd
  9          [0x4cbff9]  __gxx_personality_v0 + 0x1a1

The assertion mumbles something about invalid paired-end data!? That might be correct, since the reads are single-end, 100nt Illumina GAII reads. HG19.fa is certainly the latest human genome, including chrM.

Cheers,
Uwe

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