Hi,
I was trying to map Illumina contigs to a mira assembled Pacbio referene.
My config looks like:
'''
project = glycomyces_mapping_try1
job = genome,mapping,accurate
# parameter settings
parameters = COMMON_SETTINGS -GE:not=8, -DI:trt=/tmp/
parameters = -NW:cmrnl=no
# since no fasta qualtity file for illumina
parameters = SOLEXA_SETTINGS --noqualities
# reference sequence
readgroup = GlycomycesPacbio
is_reference
data = /path/to/file/glycomyces_assembly_pacbio_try1_out.caf
# illumina sequences
readgroup = GlyvomyceseIllumina
data = /path/to/file/glycomyces_illumina.fasta.fna
technology = solexa
default_qual = 30 # fake quality value
'''
After running for a few hours I get the error:
'''
Internal logic/programming/debugging error (*sigh* this should not have
happened)
********************************************************************************
* from + len > size of contig? *
********************************************************************************
->Thrown: void Contig::updateCountVectors(const int32 from, const int32 len,
vector<char>::const_iterator updateI, const uint32 seqtype, const bool
addiftrue, int32 coveragemultiplier)
->Caught: void Contig::stripToBackbone()
Aborting process, probably due to an internal error.
'''
I noticed a previous problem like this in the mailing list and a recommendation
was to use only one thread, however this gave exactly the same error at the
some point in the mapping. I also tried both the CAF and MAF files from the
initial Pacbio denovo assembly.
This is my first time doing an assembly, so any and all advice is welcome!
