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Difficulty Using FastX Toolkit on Mac

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?

mac unix ngs fastx executable
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updated by ATpoint ATpoint • written by mfrenkel • mfrenkel

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.

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written by ATpoint ATpoint

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.

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written by mfrenkel • mfrenkel

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.

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written by ATpoint ATpoint

1 answer

I don't have a Mac, but my recollection is that recent OS versions don't work with 32-bit binaries. It seems to be what you have downloaded - at least it says so in the file name. I think you will either need to download 64-bit binaries or re-compile.

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written by Mensur Dlakic Mensur Dlakic

I think you're right; do you know how I would go about re-compiling?

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written by mfrenkel • mfrenkel

Follow a link on the same page from which you downloaded to GitHub sources, and there you will find compilation instructions.

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written by Mensur Dlakic Mensur Dlakic

I've tried that in the past. ./configure worked but then the command "make" threw an error for which there seems to be little documentation or help:

fastx.c:29:10: error: the current #pragma pack aligment value is modified in the included file [-Werror,-Wpragma-pack]

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written by mfrenkel • mfrenkel

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