Entering edit mode
2.7 years ago
mfrenkel
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0
I downloaded the FastX toolkit precomplied binaries for "MacOS X 10.5.8 (32-bit)" (http://hannonlab.cshl.edu/fastx_toolkit/download.html). However, when I cd into the directory with the tools and try to execute any of them, I get the error:
-bash: /usr/local/bin/fastq_quality_filter: cannot execute binary file
I'm not positive but it seems like it might be because the file kinds are "Unix executable" which might not be compatible with Mac (though I downloaded the binaries that were supposedly for Mac). I've tried chmod + x but the files already have execution permission so that didn't help. Any other ideas?
fastx is a super-old tool that (by best knowledge) has no support for paired-end data and simply is deprecated imho, so I would not use it anymore. Depending on what you want to do use something like
seqtk. What do you want to do? I am sure there are more recent and better replacements.All I want to do is preprocess my FASTQ files with a quality filter before downstream analysis. FASTX seemed like the main hit when looking for tools to do quality filtering.
If this is paired-end data this will not work. As said the tool is anciently-old. Try something recent and well-maintained such as https://github.com/OpenGene/fastp
In general, you can use package managers such as conda to get software rather than compiling from source, that is easier as it takes care of all dependencies and does not run into any compilation errors/troubles.