Sometimes when downloading PDBs from AlphaFold, we run into this error:
Waiting at most 5 seconds for missing files.
MissingOutputException in rule download_pdbs in file /Users/dennis/Code/ProteinCartography/Snakefile, line 256:
Job 1185 completed successfully, but some output files are missing. Missing files after 5 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
It's unclear what the source of the error is here - usually starting the pipeline up again resolves the issue, and changing the duration of --latency-wait doesn't seem to have an impact on the frequency with which this happens. This could be a result of some kind of rate limiting from making many download requests, or some other reason. Would be great to resolve.
Sometimes when downloading PDBs from AlphaFold, we run into this error:
It's unclear what the source of the error is here - usually starting the pipeline up again resolves the issue, and changing the duration of
--latency-waitdoesn't seem to have an impact on the frequency with which this happens. This could be a result of some kind of rate limiting from making many download requests, or some other reason. Would be great to resolve.