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This is low priority, since it does not prevent the pipeline for functioning correctly.
If a taxon is supplied for which there is no data, the following output is produced by datasets summary genome taxon --as-json-lines pseudeurotiaceae > Pseudeurotiaceae.json:
Error: The taxonomy name 'pseudeurotiaceae' (taxid: '34379') is valid, but no genome data is currently available for this taxon.
Use datasets summary genome taxon <command> --help for detailed help about a command.
The exitcode returned is 1, which makes nextflow think the process failed and it retries. In this case, it actually worked, there is just no data, so ideally it would return an exit code of 0 and an empty JSON file. A check should be added to modules/local/find_assemblies.nf for the phrase "is valid, but no genome data is currently available for this taxon" and make an empty JSON file and return exit code 0.
The text was updated successfully, but these errors were encountered:
This is low priority, since it does not prevent the pipeline for functioning correctly.
If a taxon is supplied for which there is no data, the following output is produced by
datasets summary genome taxon --as-json-lines pseudeurotiaceae > Pseudeurotiaceae.json
:The exitcode returned is 1, which makes nextflow think the process failed and it retries. In this case, it actually worked, there is just no data, so ideally it would return an exit code of 0 and an empty JSON file. A check should be added to
modules/local/find_assemblies.nf
for the phrase "is valid, but no genome data is currently available for this taxon" and make an empty JSON file and return exit code 0.The text was updated successfully, but these errors were encountered: