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Old 07-08-2014, 09:19 AM   #1
jellybaby83
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Default Segmentation fault (core dumped) in Velvet

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.

Code:
[email protected]:~$ 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:

Code:
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.
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Old 07-08-2014, 09:54 AM   #2
GenoMax
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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
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Old 07-08-2014, 10:01 AM   #3
jellybaby83
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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.
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Old 07-08-2014, 10:21 AM   #4
GenoMax
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Does the seg fault occur right away or the program runs for some time before crashing?

If you just run

Code:
$velveth -h
do you get the help output?
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Old 07-08-2014, 10:29 AM   #5
jellybaby83
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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.
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Old 07-08-2014, 10:39 AM   #6
GenoMax
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Do you have any other data you can use to test the velvet install?
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Old 07-08-2014, 10:56 AM   #7
jellybaby83
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Quote:
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.
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Old 07-08-2014, 11:02 AM   #8
GenoMax
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Quote:
Originally Posted by jellybaby83 View Post
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
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Old 07-08-2014, 11:08 AM   #9
jellybaby83
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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:

Code:
velveth test_21 21 -short -fastq SRR642626.filt.fastq
Segmentation fault (core dumped)
But still have the same error message
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Old 07-08-2014, 11:19 AM   #10
GenoMax
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I am going to suggest that you download velvet source code and compile the program yourself.
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Old 07-08-2014, 11:49 AM   #11
jellybaby83
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Ok thanks for all your help
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