metaeuk fails

[metalichen]

Hi there!

I ran into an issue while trying to run EukCC via singularity.

I pulled the image and downloaded the database (tried both versions 1.1 and 1.2 with the same result):

wget http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/eukcc2_db_ver_1.1.tar.gz
tar -xzvf eukcc2_db_ver_1.1.tar.gz
singularity pull docker://quay.io/microbiome-informatics/eukcc
singularity exec eukcc_latest.sif eukcc single -h

But, when I tried to run EukCC with a genome, metaeuk immideatly fails:

>singularity exec ../singularity/eukcc.sif eukcc single --db /path/to/eukccdb/eukcc2_db_ver_1.1 ../path/to/MAG.fa 
18-05-2023 16:49:36:  EukCC version 2.1.2
18-05-2023 16:49:36:  #####################################
If you publish using EukCC please make sure to also cite:
18-05-2023 16:49:36:  
eukcc:
Saary, Paul, Alex L. Mitchell, and Robert D. Finn. "Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC." Genome biology 21.1 (2020): 1-21.

18-05-2023 16:49:36:  
hmmer:
Eddy, Sean R. "Accelerated profile HMM searches." PLoS Comput Biol 7.10 (2011): e1002195.

18-05-2023 16:49:36:  
pplacer:
Matsen, Frederick A., Robin B. Kodner, and E. Virginia Armbrust. "pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree." BMC bioinformatics 11.1 (2010): 1-16.

18-05-2023 16:49:36:  
epa-ng:
Barbera, Pierre, et al. "EPA-ng: massively parallel evolutionary placement of genetic sequences." Systematic biology 68.2 (2019): 365-369.

18-05-2023 16:49:36:  
metaEuk:
Levy Karin, Eli, Milot Mirdita, and Johannes Söding. "MetaEuk—Sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics." Microbiome 8 (2020): 1-15.

18-05-2023 16:49:36:  ####################################
18-05-2023 16:49:38:  Set sequence type to DNA
18-05-2023 16:49:39:  metaeuk failed, check logfile /tsl/scratch/gol22pin/01_Xanthoria_metagenomics/workdir/metaeuk/metaeuk.stout

And when I read the metaeuk.stout file, it only says "Illegal instruction"

Would appreciate any direction! Thanks

[metalichen]

Oh, forgot to mention: --debug flag doesn't work either. Here's what I get:

> singularity exec ../singularity/eukcc.sif eukcc single --db /path/to/eukccdb/eukcc2_db_ver_1.1 --debug ../path/to/MAG.fa 

usage: eukcc [-h] [--quiet] [--debug] [-v] {single,folder,define_set,ncbi_update} ...
eukcc: error: unrecognized arguments: --debug

[yan1365]

same error here, any updates?

Thanks

[metalichen]

I eventually got it to run. I am working on a cluster, and have to use slurm. When I tried to run EukCC inside an interactive job, I was getting the error I described above. But when I submitted the job via sbatch, it worked fine and produced the output. I don't know enough about slurm to tell why it was so, but maybe this info will be helpful for you!

[yan1365]

Thank you for your reply. I was actually submitting the job via sbatch but still had the error. Thanks anyway.

[jorondo1]

Hi ! I started getting this error when submitting to slurm instead of running directly from the interactive node, so more similar to @yan1365 's case. Did you manage to solve this ? The error log only contains:

Illegal instruction (core dumped)
Illegal instruction (core dumped)