Segmentation fault from fastx_quality_stats

[shuang]

I was trying to generate a distribution of read quality and length of a fastq which was generated from PacBio.

I used "fastx_quality_stats" in fastx toolkit. However, I received error message of "Segmentation fault". Why?

Below is my command:
fastx_quality_stats -Q 33 -i in.fastq -o out.txt


Segmentation fault

[westerman]

Well, you don't give us much to go on. Could be a problem with fastx_quality_stats. Could be a problem with your data (too many, too long, different Q-scoring, PacBio, etc.). Seg faults are one of the most common type of computer errors. Basically it means that the program is trying to access memory that is should not (out of the program's space, out of the physical memory space, etc.).

I suggest reducing your data down to a single read and trying that. Or post your first several fastq lines and we can take a look at it.

[spacup]

A little bit late....

Check read length.
In fastx_quality_stats, there is a limit at 2000nt.