Question: Metavelvet segmentation fault
0
gravatar for makisthegreat
2.1 years ago by
makisthegreat0 wrote:

Hello all,

I've been using the latest version of Velvet (1.2.10) and the latest version of Metavelvet (1.2.02) to assemble metagenomic datasets of pair-end reads of about 120 bp length.

I use Velvetoptimiser to choose the appropriate k-mer then run vevleth again (as for some reason velvetoptimiser doesn't produce the Roadmaps file) and then try to run metavelvet. But when I do so I get a segmentation fault error like this:

[126.515876] Starting pebble resolution...
Segmentation fault (core dumped)

It's not a memory problem as I am running into a 512GB RAM machine (64 cpus) and the process is quite quick. (I've also checked with free -m)

I've compiled both velvet and metavelvet at 'MAKMERLENGTH=101', 'OPENMP=1'.

My server is running on CentOS 7.1.1503 with g++  version 4.8.5.

Any ideas anyone?

Oh and Merry Christmas!

 

 

ADD COMMENTlink modified 12 days ago by yanhuihui0 • written 2.1 years ago by makisthegreat0

Bumping for any answers... I could use any suggestions...

ADD REPLYlink written 2.0 years ago by makisthegreat0

Did you get any further with this problem? I'm also running into segmentation faults and tried everything I could imagine but nothing seems to work.

ADD REPLYlink written 23 months ago by rwinand0
0
gravatar for cclaing
2.0 years ago by
cclaing0
University of Alberta
cclaing0 wrote:

I'm not particularly familiar with metavelvet, but a SegFault is caused when a program tries to read and write memory outside of the bounds it has allocated for itself. 

Have you compiled it with "MAKMERLENGTH=101" or "MAXKMERLENGTH=101"? Maybe missing the X could cause it not to be flagged by the program causing undocumented behavior?

 

 

 

ADD COMMENTlink written 2.0 years ago by cclaing0
0
gravatar for makisthegreat
24 months ago by
makisthegreat0 wrote:

No it was just a typo in my post. I compiled it with "MAXKMERLENGTH=101". Is there a way to check what memory bounds the executables have allocated for itselfs? I've never heard that before.

Thank you,

ADD COMMENTlink written 24 months ago by makisthegreat0
0
gravatar for karishma.guru
23 months ago by
karishma.guru0 wrote:

Hello all,

I am facing the same issue  of Segmentation fault (core dumped) when running meta-velvetg.

My data is size R1 and R2 being 5.2 GB each. What could be a possible solutions?

1) Can I subsample the data and run it?

2) Can I  select contigs greater than 500bp from contig.fa file generated from velvetg and then run meta-velvetgI will have to make changes to the Graph files also I think.

 

Please let me know how to go about this.

Regards

KKumar

 

ADD COMMENTlink written 23 months ago by karishma.guru0
0
gravatar for yanhuihui
12 days ago by
yanhuihui0
yanhuihui0 wrote:

I have come across the same problem, I run the metavelvet1.2.02 in Centos7 with memory of 256G,gcc-4.8.5, and I have got the same error [126.515876] Starting pebble resolution... Segmentation fault (core dumped)

However, I have googled a lot, there's somebody advice to downgrade the gcc-4.8.5 to gcc-4.6.2 to compile the Metavelvet. Then copy the whole folder to the new environment with gcc-4.8.5, then it may worked. But I am sticking at the stage of install gcc-4.6.2, It's really hard to make. So, I am not sure if this method really worked.

ADD COMMENTlink written 12 days ago by yanhuihui0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1337 users visited in the last hour