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soedinglab / metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
GNU General Public License v3.0
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Error in MetaEuk during BUSCO run #45

Open berkelem opened 2 years ago

berkelem commented 2 years ago

We have received a user report of an error thrown by Metaeuk during a BUSCO run. The issue reported is here: https://gitlab.com/ezlab/busco/-/issues/554

The error is

Could not create symlink of /busco_wd/new/run_saccharomycetes_odb10/metaeuk_output/tmp/15269632893279415955/contigs.source!

Can you please advise on what could be causing this problem and how to address it?

milot-mirdita commented 2 years ago

We are not really sure how to tackle this. Were there other users who reported this or a similar issue with metaeuk in BUSCO?

Do you have a minimal example on how to reproduce the issue? This might be a docker on mac only issue?

berkelem commented 2 years ago

You may be right - it could be a Docker on Mac issue. I have been unable to replicate it, and no other users have reported it. I had assumed that because the error was written to stderr by Metaeuk that it was something in the Metaeuk codebase. I'll let you know if it comes up again.

milot-mirdita commented 2 years ago

It's definitely something that happened within MetaEuk. I just have no idea how to trigger the issue and thus how to fix it.

This is the first place in the pipeline where it creates a symlink. It seems like it can't create one for some reason.

tinameiring commented 10 months ago

Hi there, Has this been resolved yet? I get the same error on my linux device: ERROR: Metaeuk did not recognize any genes matching the dataset in the input file. If this is unexpected, check your input file and your installation of Metaeuk

In the error log file: Could not create symlink of /media/clinomics/Expansion/BUSCO_v5_Metaeuk/RmCVSA/run_arthropoda_odb10/metaeuk_output/tmp/1758328062591366650!

I'm using BUSCO 5.6.0 and metaeuk Version: 6bd769fff83c04c6b9a6ad958b257f6ddc4656a3 I'm running BUSCO in genome mode using the arthropoda_odb10 lineage.

I would really appreciate any help! metaeuk_run1_out.log bbtools_out.log busco.log metaeuk_run1_err.log