Closed susheelbhanu closed 1 year ago
Hi,
Thank you for your interest in PHIST. All temporary files generated by PHIST are stored in the same directory as the results (predictions.csv
and common_kmers.csv
). It looks like the directory where you are trying to save results does not exist. Could you please check if the directory exists (/work/projects/nomis/assemblies/virome_results/phist/
)?
In the next PHIST update, we will simplify running the tool by providing the out_dir
argument (and the output directory will be created if it does not exist)/
python3 phist.py [options] <virus_dir> <host_dir> <out_dir>
Hey @aziele Thanks for your reply. The directory was also likely removed by snakemake so I'm trying to create it before the file is run. Will keep you posted.
Hi @susheelbhanu, we have simplified the command line that invokes PHIST.
python3 phist.py [options] <virus_dir> <host_dir> <out_dir>
Instead of specifying the path to the output files (common_kmers.csv
and predictions.csv
), you can just provide the output directory for the results (<out_dir>
). PHIST will create the directory if it does not exist.
Thanks @aziele. This will help streamline things a lot. I worked around it by creating the directory upfront, so this is helpful.
I'm assuming that i simply need to pull the updated repo?
Hope it helps. Yes, you just need to pull the update repo.
Awesome, thank you!
Hi,
I'm trying to run PHIST in a
snakemake
workflow. However, i'm getting the below error:My run command looks like this:
is this an issue with creating a
tmp folder
?