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padlocbio / padloc

Locate antiviral defence systems in prokaryotic genomes
MIT License
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Failed to query server: Connection timed out #37

Closed charlottecc closed 6 months ago

charlottecc commented 7 months ago

Hello,

I've been running version 1.1.0 and 2.0.0 using this command:

padloc --fna p10_d1_D4.fa --outdir p10_d1_D4_padloc --cpu 30

I installed both versions using conda and at least version 1.1.0 was working fine a few months ago. But now when I run my command above I get the error:

[13:24:17] >> Predicting protein-coding genes with prodigal [13:24:27] >> Scanning p10_d1_D4.fa for defence system proteins [13:27:11] >> Searching p10_d1_D4.fa for defence systems Failed to query server: Connection timed out Warning message:In system("timedatectl", intern = TRUE) : running command 'timedatectl' had status 1

I'd be grateful for any advice on how to fix this issue or what might be causing it on my end.

Thanks in advance!

leightonpayne commented 6 months ago

Hi @charlottecc,

I suspect this has something to do with a lower-level issue rather than padloc itself.

Are you able to give me more information about the environment you are using padloc in?, i.e. are you working in a WSL environment? on a MacOS machine? on an linux-based HPC cluster? Has this changed since it was last working for you?

Do you get the same error if you just run: Rscript -e "library('tidyverse')"?

You can try setting a specific timezone in your shell before running padloc, for example: TZ="Pacific/Auckland" (but use whatever timezone you're in).

charlottecc commented 6 months ago

Thanks for getting back to me @leightonpayne!

I am using a linux-based HPC cluster, I added TZ='Europe/London' to my bashrc file and this seemed to fix the problem!.