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wurmlab / flo

Same species annotation lift over pipeline.
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faToTwoBit: cannot execute binary file #23

Closed divyanandu closed 6 years ago

divyanandu commented 6 years ago

I am trying to lift over a viral genome from one version to another. I am getting the following error when doing that. I checked the permissions of the faToTwoBit file and that looks fine. I am running this on a Mac

Error: mkdir run cp /Users/divya/NC_009333.fa run/source.fa cp /Users/divya/GQ994935.fa run/target.fa faToTwoBit run/source.fa run/source.2bit ext/kent/bin/faToTwoBit: ext/kent/bin/faToTwoBit: cannot execute binary file rake aborted! Command failed with status (126): [faToTwoBit run/source.fa run/source.2bit...] /Users/divya/flo/Rakefile:127:in to_2bit' /Users/divya/flo/Rakefile:72:inblock in <top (required)>' /Users/divya/flo/Rakefile:37:in `block in <top (required)>' Tasks: TOP => run/liftover.chn

yeban commented 6 years ago

Is it possible that you downloaded Linux version of the executables on the Mac? This can be the case if you used the install.sh script, which is meant to be for Linux (I realize that's not clear in the README - sorry).

divyanandu commented 6 years ago

Thats exactly what I did. I will try and install the mac version and see if that solved the problem. Thanks!

divyanandu commented 6 years ago

Is there a list of dependencies that I need to install?

yeban commented 6 years ago

Tools listed in install.sh script.

yeban commented 6 years ago

I updated install.sh to download for linux or mac depending on you computer.