Nope, I only have the fasta file. They are from the same strain, I'm trying to
a hybrid assembly with the PacBio and Illumina data.
________________________________
From: mira_talk-bounce@xxxxxxxxxxxxx <mira_talk-bounce@xxxxxxxxxxxxx> on behalf
of Chris Hoefler <hoeflerb@xxxxxxxxx>
Sent: Monday, June 29, 2015 10:42 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: from + len > size of contig?
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<mailto: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!
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
