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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