Why does Metavelvet stops at "Scaffolding" without error message or at "Starting pebble resolution..." with a Segmentation fault?
I'm using MetaVelvet to analyse ~3million PE Illumina MiSeq reads with an insert length of ~400. The reads were checked for quality and trimmed before assembly. Metavelvet stops at the scaffolding stage.
The commands used to run Metavelvet were:
velveth output 77 -fastq -shortPaired -separate inputR1.fastq inputR2.fastq
velvetg output -exp_cov auto -ins_length 400
meta-velvetg output -ins_length 400 | tee logfile
The script stops either at:
[VelvetGraph] === Scaffolding ===
or at
Starting pebble resolution...
Segmentation fault (core dumped)
Do you know why it stops?
I also tried an -ins_length 300, but without success.
This question has been asked before , but not useful answer has been given so far, so with this post I hope to reopen the discussion and to find a solution to the problem.
I'm running on a 16 CPUs 32GB RAM server and I've installed Metavelvet as described in the following Dockerfile:
FROM fedora:23
RUN dnf -y update && dnf -y install wget tar make zlib-devel gcc-c++
RUN wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
RUN tar zxf velvet_1.2.10.tgz
# install velvet allow for long sequences and multiple threads
RUN cd velvet_1.2.10 && make MAXKMERLENGTH=127 LONGSEQUENCES=1 OPENMP=1
RUN cp velvet_1.2.10/velvet* /usr/bin
RUN wget http://metavelvet.dna.bio.keio.ac.jp/src/MetaVelvet-1.2.02.tgz
RUN tar zxf MetaVelvet-1.2.02.tgz
RUN cd MetaVelvet-1.2.02 && make MAXKMERLENGTH=127
RUN cp MetaVelvet-1.2.02/meta-velvetg /usr/bin
I also tried installing velvet without the LONGSEQUENCES=1 OPENMP=1 options i.e:make MAXKMERLENGTH=127, but this didn't change anything.
How can this problem be solved?
