Eggnog emapper.py error

Question

[yp19]

Hi guys,

I'm trying to run eggnog to annotate some proteins. I followed the exact instructions found on their wiki page for downloading and basic usage. It runs for a few minutes then I get an error.

$ python emapper.py -i proteins.faa --output emapper_output -m diamond

Traceback (most recent call last):
  File "emapper.py", line 1001, in <module>
    main(args)
  File "emapper.py", line 216, in main
    dump_diamond_matches(args.input, seed_orthologs_file, args)
  File "emapper.py", line 353, in dump_diamond_matches
    raise e
subprocess.CalledProcessError: Command returned non-zero exit status -9

Anyone know what is causing this error?

Thank you

[h.mon]

Probably related to the version of diamond: diamond sometimes changes its database format, and a new version of the software may be incompatible with an old database.

What diamond version are you using? How did you install the eggnog databases?

[yp19]

I installed eggnog by downloading this file (1.03.tar.gz) found here: https://github.com/jhcepas/eggnog-mapper/releases and then running download_eggnog_data.py (to get the databases, took a long time)

That is all I did, I did not install diamond separately as I thought it came with the package above.

[h.mon]

My bad, you are right: it seems eggnog-mapper uses an "internal" diamond. Try running it directly from the command-line to see if there is some problem with it:

/path/to/eggnog_base/bin/diamond

Or maybe you have a local diamond with precedence over eggnog-mapper's diamond. What is the result of which diamond?

[yp19]

Thanks for your help, I tried running it directly, got this

Error: Syntax: diamond COMMAND [OPTIONS]. To print help message: diamond help

which diamond results in

/usr/bin/which: no diamond in (/cvmfs/home/etc..etc)

[AK]

Try doing export PATH="/path/to/eggnog-mapper-version/bin":$PATH before python emapper.py (replace /path/to/eggnog-mapper-version/bin to yours)?

[yp19]

Thank you. Just tried this, no luck unfortunately

[h.mon]

My final guess is the diamond database was prepared under a newer diamond than the one from eggnog-mapper 1.0.3 (which bundles diamond 0.8.22), as an eggnog-mapper 2.0 (which bundles diamond 0.9.24) is almost released. Try manually replacing diamond, or try to install eggnog-mapper directly from the git repo with git clone.

[yp19]

I will try that and report back. Thank you for the help!

[yp19]

Tried installing eggnog-mapper directly from git repo, it ran for ~30mins then the same kind of error:

Building reference index... Traceback (most recent call last):
  File "emapper.py", line 1210, in <module>
    main(args)
  File "emapper.py", line 226, in main
    dump_diamond_matches(args.input, seed_orthologs_file, args)
  File "emapper.py", line 380, in dump_diamond_matches
    raise e
subprocess.CalledProcessError: Command returned non-zero exit status -9

Answer 1

[yp19]

In case this happens to anyone else, it turned out it was just a memory issue! Just ran it with more memory and it now runs fine. Thanks for your input everyone.

[h.mon]

How did you run with more memory? Did you change computers?

Or were you using a resource manager such as SLURM or SGE, and you changed the queue or memory settings?

[yp19]

SLURM, and I just requested a node with more memory