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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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Info: Regarding symlinks #67

Closed susheelbhanu closed 1 year ago

susheelbhanu commented 1 year ago

Hi,

I just tried to run VIBRANT on a set of metagenome assemblies that were symlinked from a different folder location.

The log file showed that it could not find the fasta sequences. Re-running with a direct copy of the same file.

Maybe this information could be added to Notes somewhere or simply left here for future reference.

Thank you, Susheel

KrisKieft commented 1 year ago

Hi,

I've used symlinks before I haven't had any issues. Did you try head -n 1 $file or something from the current directory to verify that the link was set up properly for VIBRANT to find it? Let me know if the issue persists.

susheelbhanu commented 1 year ago

Hey Kris,

I was just about to close the issue. It so happened that the job ran out of memory. Sorry for the confusion!

I only realized this later 'cos vibrant kept running and snakemake was touching the files 🤷🏽‍♂️.

I can confirm now that the symlinks were not the issue.

Thanks for the prompt response!