Tophat2 Error running 'long_spanning_reads' on M1 Mac
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12 weeks ago
riboseq938 • 0

Hi everyone,

I am trying to perform Tophat2 based genome alignment (I understand there are alternative tools out there, but for this purpose it needs to be Tophat2), but I keep running into issues at the 'long_spanning_reads' stage. I'm new to bioinformatics.

I used the precompiled x86_64 binaries for mac because I couldn't compile from source because of problems with libomp. I'm running under arch x86_64 so that I can install matching architecture Boost libraries.

The error message when I attempt to run tophat2 is: Error running 'long_spanning_reads':dyld[17776]: missing symbol called

I think it's a problem with the way in which I installed Tophat2 but I'm really not sure how to fix it.

Please let me know if there is a better way to run tophat2 on an M1 pro mac or if this has already been covered elsewhere, thank you.

Tophat2 Boost RiboSeq M1-Mac • 247 views
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Entering edit mode
12 weeks ago

use micromamba to install tophat2 (the x86_64 version not arm64) that should take care of installing the correct libraries

https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html

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