Segmentation fault (core dumped) in Velvet

[jellybaby83]

Hi all,

I am using MiSeq paired end data which I recived from our sequencing facility, this data had already been cleaned using sythe and sickle. I have put the data through Fastqc to check the quality and revieved the following information:

File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 1270012
Filtered Sequences 0
Sequence length 20-251

I want to use Velvet as it seems to be the program used in most papers from within my field. I have installed Velvet from the ubuntu software center as I am not very skilled in using termial commands. It appeares to be the same version as from the velvet website (1.2.10).

The problem I have is that when I attempt to use velveth I get a segmentation fault.

shell@shell-MS-1727:~$ velveth VPI_21 21 -shortPaired -fastq -separate VPI_R1.fastq VPI_R2.fastq
Segmentation fault (core dumped)

I have reinstalled ubuntu as I read that I might have caused an issue when using a chmod command when following a "teach youself linux" book but this has not helped fix the issue.

I have also tried:

sudo apt-get install velvet
Reading package lists... Done
Building dependency tree       
Reading state information... Done
velvet is already the newest version.
0 to upgrade, 0 to newly install, 0 to remove and 10 not to upgrade.

I have very little linux experiance and so I am not sure:
A) What this error means
B) How to fix it.

Any help would be greatly appreciated.

[GenoMax]

Are you using a virtual machine for running ubuntu? How much memory have you assigned to the VM if this is a virtual machine? Are you running 32-bit or 64-bit version of ubuntu.

Wikipedia has a simple intro for Seg Faults in first paragraph: http://en.wikipedia.org/wiki/Seg_fault

[jellybaby83]

I am not using a vertual machine. I am running 64-bit version 14.04 LTS, with 3.8GiB memory.
Thank you for the link I will have a read over it.

[GenoMax]

Does the seg fault occur right away or the program runs for some time before crashing?

If you just run

$velveth -h

do you get the help output?

[jellybaby83]

The crash occurs right away I get no other outputs only the error message.

If I run "$velveth -h" I do get the help output.

[GenoMax]

Do you have any other data you can use to test the velvet install?

[jellybaby83]

Do you have any other data you can use to test the velvet install?

Unfortunately not, is there anywhere I could get some? I had a quick look on the NCBI ftp website but couldn't see anything that didn't look like it had been assembled already.

[GenoMax]

Unfortunately not, is there anywhere I could get some? I had a quick look on the NCBI ftp website but couldn't see anything that didn't look like it had been assembled already.

There is a test set you can use on this page: http://ged.msu.edu/angus/beacon-2012...vet-ecoli.html

[jellybaby83]

Thank you GenoMax I will try with that.

I found a single read file on

ftp://ftp-trace.ncbi.nih.gov/1000gen...sequence_read/

I used:

velveth test_21 21 -short -fastq SRR642626.filt.fastq
Segmentation fault (core dumped)

But still have the same error message

[GenoMax]

I am going to suggest that you download velvet source code and compile the program yourself.

[jellybaby83]

Ok thanks for all your help