Error with salmon version/libjemalloc.so.2

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Rayana Feltrin

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Mar 9, 2021, 8:40:56 AM3/9/21

to trinityrnaseq-users

Hello!

I have recently installed Trinity v2.6.6... and my salmon version (installed with conda) is 1.4.0. So I've been trying to run the script used to test the Trinity installation, and got stuck in the following error:

Error, cannot determine salmon version installed from (salmon: error while loading shared libraries: libjemalloc.so.2: cannot open shared object file: No such file or directory
) at ../../Trinity line 3697.

Because of that, I have also installed jemalloc 5.2.1 and put its /bin and /lib path in ~./bashrc and ~/.bash_profile, since the file libjemalloc.so.2 is inside /lib. However, it hasn't solved the problem.

Surprisingly, I've also found the file libjemalloc.so.2 inside /lib in my miniconda2/envs/salmon directory. So I tried to put this whole /lib path in my ~/.bashrc and ~/bash_profile, but the same error appears when I try to test the Trinity installation again.

I would appreciate any thoughts on this issue.

Thank you in advance!

Brian Haas

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Mar 9, 2021, 8:54:24 AM3/9/21

to Rayana Feltrin, trinityrnaseq-users

Hi,

I'd recommend using the latest Trinity: https://github.com/trinityrnaseq/trinityrnaseq/releases/tag/v2.12.0

If salmon is giving you any issues, you can just disable it with --no_salmon - it's not essential, I just prefer using it when you can.

best,

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