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Orthofinder failure when running test dataset #37

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devonorourke opened this issue Mar 25, 2020 · 0 comments
Open

Orthofinder failure when running test dataset #37

devonorourke opened this issue Mar 25, 2020 · 0 comments

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@devonorourke
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Hi,
I've tried running ORP through the Conda installation method proposed here, as well as an alternative installation where I manually installed each piece separately following the same steps offered in this repo's Makefile. In each case I get the same error such that the program completes all steps through the spades and transabyss assemblies, but fails once OrthoFinder gets rolling. Then I get this error message:

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Assembly generated with Trans-ABySS 2.0.1 :)
Final assembly: /scratch/dro49/myluwork/rnaome/orpwork/assemblies/test.transabyss/test.transabyss.fasta-final.fa
Total wallclock run time: 0 h 0 m 9 s

OrthoFinder version 2.3.9 Copyright (C) 2014 David Emms

2020-03-18 11:27:24 : Starting OrthoFinder
8 thread(s) for highly parallel tasks (BLAST searches etc.)
8 thread(s) for OrthoFinder algorithm

Checking required programs are installed
----------------------------------------
Test can run "mcl -h" - failed

stdout:

stderr:
b"mcl: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by mcl)\n"
ERROR: Cannot run MCL with the command "mcl -h"
Please check MCL is installed and in the system path

ERROR: An error occurred, please review error messages for more information.
make: *** [/scratch/dro49/conda/Oyster_River_Protocol/oyster.mk:267: /scratch/dro49/myluwork/rnaome/orpwork/orthofuse/test/orthofuser.done] Error 1

What's confusing is that MCL is indeed accessible:

$ which mcl

/scratch/dro49/conda/envs/orp/bin/mcl

and MCL can indeed access the help menu (thus the ERROR: Cannot run MCL with the command "mcl -h" is very confusing!

$ mcl -h

________ mcl verbosity modes
--show ....... print MCL iterands (small graphs only)
-v all ....... turn on all -v options
________ on multi-processor systems
-te <i> ...... number of threads to use                                  [0]

further, I know I've loaded the missing glibc module...

$module list

Currently Loaded Modulefiles:
  1) git/2.16.3          2) anaconda3/2019.10   3) binutils/2.28       4) glibc/2.14

Any ideas what could be breaking here?
Thanks!

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