soedinglab
Why my metaeuk search is very slow?
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
Expected Behavior
Current Behavior
Steps to Reproduce (for bugs)
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MetaEuk Output (for bugs)
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Context
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Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used (The string after "MetaEuk Version:" when you execute MetaEuk without any parameters):
- Which MetaEuk version was used (Statically-compiled, self-compiled, Homebrew, etc.):
- For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
- Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
- Operating system and version:
What kind of machine are you running metaeuk on? There is no output at all?
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?
