Question: Metavelvet stops at Scaffolding
0
gravatar for biotacg
3.2 years ago by
biotacg0
biotacg0 wrote:

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?

ADD COMMENTlink modified 7 months ago by RamRS21k • written 3.2 years ago by biotacg0
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