Question: Bus Error From Fastx Toolkit'S Fastq_Quality_Filter
0
gravatar for Behindtherabbit
8.0 years ago by
Blacksburg, VA USA
Behindtherabbit60 wrote:

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!

short filter fastq fastx error • 2.3k views
ADD COMMENTlink written 8.0 years ago by Behindtherabbit60
1
gravatar for Istvan Albert
8.0 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Istvan Albert ♦♦ 81k

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

ADD REPLYlink written 8.0 years ago by Behindtherabbit60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1258 users visited in the last hour