Do you have the Illumina reads? You can just map those directly to the
reference instead of the contigs. Are you mapping two different
strains...what are you trying to do?
On Mon, Jun 29, 2015 at 8:22 AM, Bleker, Carissa R. <blekercr@xxxxxxxx>
wrote:
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!
