Bus Error From Fastx Toolkit'S Fastq_Quality_Filter

Question

[Behindtherabbit]

I am trying to filter reads on sequence quality, using the command line version of fastqqualityfilter (fastx 0.0.13 for OS X 10.5.8; I am running OS X 10.6.7). I have already trimmed these reads using the trimmer:

fastx_trimmer -f 30 -l 600 -i myreads.fq -o myreads.trimmed.fq -Q 33

and checked quality using fastqc. both of these operations ran without error. but, when I try to filter the trimmed fq file:

fastq_quality_filter -q 20 -p 50 -i myreads.trimmed.fq -o myreads.filtered.fq -Q 33

Bus error

Has anyone encountered this error from fastqqualityfilter before? Any thoughts why this is happening?

Thanks for any suggestions!

Answer 1

[Istvan Albert]

The precompiled fastx toolkit is for 32 bit Mac and is dynamically linking to other libraries. The type of error indicates that you may be using it on a 64 bit Mac. Utilities that do not call into other libraries will still work.

[Behindtherabbit]

yes, I was using it on a 64bit Mac. thanks for the help!