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gbouras13 / hybracter

Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.
MIT License
95 stars 7 forks source link

Can this program be run on an external hard drive? #83

Open JavierFFavieres opened 2 months ago

JavierFFavieres commented 2 months ago

My computer is running low on storage, so I was trying to run it on an external server comprised of hard drives. However, each time I get the error 'Snakemake failed'.

In the computer itself it runs smoothly (with only a few genomes at a time), so I guess the program and its dependencies are properly installed, meaning the only difference is the location of the files.

Is there any way to circumvent this and run it on my server?

Thank you in advance, Javier

gbouras13 commented 2 months ago

Hi @JavierFFavieres

This is very strange - I can't think of any reason it wouldn't work on external drives.

Can you give some more detail on the error e.g. what dependency specifically errors out?

George

JavierFFavieres commented 2 months ago

Yes, of course. Sorry for not elaborating earlier. These are the error messages:

Outputting passed long reads

WorkflowError: Error recording metadata for finished job ([Errno 1] Operation not permitted: '/media/ARU/Javi_temp/Hybracter_test/.snakemake/metadata/tmplabuwj.aHlicmFj'). Please ensure write permissions for the directory /media/ARU/Javi_temp/Hybracter_test/.snakemake Removing output files of failed job filtlong since they might be corrupted: hybracter_results/processing/qc/39CS_filt.fastq.gz, hybracter_results/versions/39CS/filtlong.version Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-07-22T101436.643248.snakemake.log WorkflowError: At least one job did not complete successfully. [2024:07:22 10:30:14] ERROR: Snakemake failed

Javier

gbouras13 commented 2 months ago

Hi @JavierFFavieres ,

The error stems from permissions on your harddrive, not Hybracter (I think!)

Error recording metadata for finished job ([Errno 1] Operation not permitted: '/media/ARU/Javi_temp/Hybracter_test/.snakemake/metadata/tmpl_abuwj_.aHlicmFj'). Please ensure write permissions for the directory /media/ARU/Javi_temp/Hybracter_test/.snake-make

You may need to allow write access on your disk - see e.g. https://askubuntu.com/questions/90339/how-do-i-set-read-write-permissions-my-hard-drives

George

JavierFFavieres commented 1 month ago

Thank you so much for clarifying. I will look into it.

Thanks a lot Javier