-
Notifications
You must be signed in to change notification settings - Fork 678
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
com.upplication.s3fs.S3Path error when running with ignite #77
Comments
Hi @PhilPalmer, Thanks for the detailed bug report. I guess this is due to this change - we no longer specify Also note that you're a teeny bit out of date with nextflow, but I doubt that this will have any effect. Phil |
Also, another thing to try is to use three slashes with the s3 URL - no idea why, but I came across that suggestion from @pditommaso when delving into the nextflow gitter history with google: https://gitter.im/nextflow-io/nextflow?at=580fca4bba810c1d5fd00d6d |
This sounds like a NF bug, however my suggestion is to force the execution of @ewels The problem with K8s you are referring is related to process like get_software_versions. |
Yes, you're exactly right @pditommaso - I was a little over zealous in removing the local statements, but figured that it didn't really hurt (until now!). I've added it back in PR #78. |
For the records nextflow-io/nextflow#843 |
@PhilPalmer - the pull request is now merged. If you could give it a try that would be great! It should work fine if you use |
@ewels it worked with |
Great stuff, thanks for reporting and testing the fix! This will go out as part of the next stable pipeline release when it's ready. |
Hey,
I've tried to run the test profile without changing any of the parameters. The only thing I did change was the working directory to an aws S3 path. The command I ran was:
This gave the following error
com.upplication.s3fs.S3Path
as shown below:Nextflow.log file can be found here: nextflow.log
However I have noticed that i do not get the error with an older version of the repo:
2cf2f0f779d39463b09d874449cbb9fdb9f58d2f
So I think some change between that version of the repo and present has caused an error when running rnaseq from an S3 working directory
Any help to fix this error would be much appreciated, thanks in advance
The text was updated successfully, but these errors were encountered: