Bus Error From Fastx Toolkit'S Fastq_Quality_Filter
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9.5 years ago

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!

fastx fastq short error fastq filter • 2.6k views
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Entering edit mode
9.5 years ago

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.

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

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