Question: Help needed using FastX toolkit: Segmentation fault
gravatar for Angelo Victoria
4.0 years ago by
Philippines/University of the Philippines Diliman
Angelo Victoria30 wrote:

Hi. Novice question here.

I have been practicing a very basic exercise for a project in one of my introductory courses and I have been doing fine with the quality trimming and filtering of a set of reads. However, when I used the data provided by our course facilitators, the quality filtering step in FastX Toolkit outputs "Segmentation Fault". 


I have been looking elsewhere in the internet for answers to this error and the most common would be that the computer runs out of memory. However, when I asked our core facility where we have remote access, they told me that I should not be getting this Segmentation Fault because we are supposed to assemble and verify an E. coli genome that they have curated already for this exercise and they have provided us with more than enough memory. I really have no idea what goes wrong with my data seeing that all my file and tool paths are correctly typed.


P.S. I haven't had the chance to talk personally to the core facility since I've been processing the data on a conference out of town.

quality-control fastx • 2.2k views
ADD COMMENTlink modified 4.0 years ago by p.papathanos0 • written 4.0 years ago by Angelo Victoria30

Fastx toolkit should be retired, really. Nowadays, there are a lot of better and much faster tools for quality filtering.

ADD REPLYlink written 4.0 years ago by lh331k

It's an introductory exercise so I guess it's all right for training. I'm sure we would be introduced to more recent and efficient tools later on. 

ADD REPLYlink written 4.0 years ago by Angelo Victoria30
gravatar for p.papathanos
4.0 years ago by
p.papathanos0 wrote:

Have you checked whether you have enough disk space?

ADD COMMENTlink written 4.0 years ago by p.papathanos0

Hi! I found the fix just now. Apparently, I was using "-Q 33" which is intended for Illumina 1.8 reads. I noticed in FastQC reports that my data are encoded (is that the correct term?) in Illumina 1.3 so I have to use "-Q 64". :)

ADD REPLYlink written 4.0 years ago by Angelo Victoria30
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