Why my metaeuk search is very slow?

[liuxianghui]

Dear Sir,
Thanks for developing the tool for prediction of euk proteins from contigs.
I downloaded the database for gut microbiome gene catalog amino acid sequences
fasta: humanGut_IGC.11M.pep.fa
from cngb database https://db.cngb.org/microbiome/genecatalog/genecatalog/?gene_name=Human%20Gut%20(11M))
and made it into a mmseq2 database twins_IGC.
11M seems big but shall be big but yours MMETSP_zenodo_3247846_uniclust90_2018_08_seed_valid_taxids seems to be much bigger with ~88 million proteins and I have no problem to use my contigs dataset allDBswabs to query for it (only take several days).

metaeuk easy-predict allDBswabs twins_IGC predsResultProteinsswabs_twins_IGC tmp
metaeuk taxtocontig allDBswabs predsResultProteinsswabs_twins_IGC.fas predsResultProteinsswabs_twins_IGC.fas.headersMap.tsv twins_IGC taxResultswabs_twins_IGC tmp --majority 0.5 --tax-lineage --lca-mode 2
However, the job has been running for weeks and I have no idea about it because there is no output.
Job id Name User Time Use S Queue

---

100780.pbs01 predictIGC xianghui 1888:55: R std
I hope you could kindly suggest,
My query allDBswabs contains 102934 sequences.
Does it help if i try to specify more memory for it or like mmseq2, try to run mpi process? How to run mpi for metaeuk.
Xianghui

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[milot-mirdita]

What kind of machine are you running metaeuk on? There is no output at all?

[liuxianghui]

I am running this on a linux cluster. My job was submitted with 64 cores. It finally came to an end. I am very surprised that it took a lot time. Could the problem caused by any indexing?

[elileka]

Could you please send us the log files produced during the run?
Thank you!