I recently have been running into an error in “main_workflow.smk” with latency wait. The error message is attached in the image below. The error only occurs when I run our complete local genomes (~4,500 genomes). However I do not see this error when I run genomes for from the last 4 epi weeks although they both use identical build.yaml files. Subsampling schemes for both runs are identical except the volume (~4,500 local genomes, ~1,500 north america, ~500 global contextual sequences → for the complete build, and ~500 + 500 + 250 genomes respectively for the last 4 epi weeks).
Not sure why this is happening. Yes, I have installed/updated the latest ncov repos in my Ubuntu environment, and have installed/updated the nextstrain conda environment.
My command looks like this: snakemake --cores 6 --configfile my_profiles/nebraskabuild/builds.yaml --latency-wait 30 --use-conda
MissingOutputException in line 665 of /mnt/c/Users/ncov/workflow/snakemake_rules/main_workflow.smk: Job Missing files after 30 seconds: results/LocationName/tree_raw.nwk This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Job id: 6 completed successfully, but some output files are missing. 6
Yes, I have increased the latency wait time to 60 seconds and get the same error message.
I have glanced through the page to see if others have reported a similar error message. This was pretty close… (Error in "main_workflow.smk" file in --latency-wait - #4 by james)
- Yes, I have both reference genomes’ names in metadata updated in the metadata
Will appreciate any troubleshooting help
Team, Thanks for all your work advancing genomic surveillance efforts globally! Couldn’t appreciate you all enough!!