Velvet: Segmentation fault (core dumped)

Question

[second_exon]

I compiled Velvet 1.2.10 in my Ububtu desktop based on User Manual as follows

make
make color
make 'CATEGORIES=57'
make 'MAXKMERLENGTH=61'
make 'OPENMP=1'

After compiling, I could run one of my paired mi-seq reads,

./velveth output1 31 -fastq -shortPaired ./shuffled/W2_Shuffled.fastq

But couldn't able to run other sequences, I hit with the error

Segmentation fault (core dumped)

​Please, help me, how to overcome this?

[Ram]

I hope you've read through all the segfault posts here. Word of caution: velvet is a memory hog, you better have a high config machine.

Answer 1

[SES]

This may not be the issue given your command to velveth, but your method for compiling velvet doesn't look correct. I would run make clean, followed by make ... with all your compilation options in one go. Then, try again and see if you have the same issue.

Also, you may find it helpful to run a small sample of data to see if this error has something to do with the parameters or compilation settings. If not, you can watch the resource usage with top or qstat/bstat (or similar) to see if this is an issue with memory.

[second_exon]

Thank you for your response and time.

I have tried your suggestions but ended up in same error message. I strongly believe, error may be due to compilation problem not memory issue. Top command tells, CPU: 12% and Mem: 45%. FastQC reports, total sequences: 463023, and sequence length: 30-301. I believe, I can run this stuff in my desktop with 4GB RAM.

[SES]

Just because the program didn't use all the memory doesn't rule out a memory issue, it could be that it could not allocate memory. I think the issue may be with your read lengths and whether you are specifying long or short, since you have a mixture of both. I would take a subset of short reads and retry the assembly with the '-short' option to velveth.

Answer 2

[rafael.d.macho]

I had the same problem about "core dump" or similar and it was that you need to locate the sequences within the same folder as the software to make it run, despite you had written the very path towards the file wherever you may left it.

Here is my example:

Computer@Computer:~/Descargas/velvet_1.2.10$ ./velveth velvet5 31 -fastq.gz -shortPaired ~/Descargas/SRR292770_1.fastq.gz ~/Descargas/SRR292770_2.fastq.gz