Error After Updating Nextflow and Phoenix Versions

[Ashita2619]

Hello Everyone,

After updating both Nextflow and Phoenix to the latest versions, I am encountering an error while running the pipeline. The error occurs during the CDC_PHOENIX:PHOENIX_EXQC:ASSET_CHECK (1) process.

The pipeline fails with the error message mentioned below.

1. I have verified the paths to the input files and dependencies.
2. I have checked the Nextflow and Phoenix logs, but I am unable to identify the root cause of the issue.

Question:

1. Are there any known issues with the updated versions of Nextflow and Phoenix?
2. Could the error be related to changes in file paths or input/output configurations introduced in the new versions?

Thanks,
Ashita Jawali

[jvhagey]

Hi Ashita, what version of nextflow are you using? I don't know of an issue with particular versions of Nextflow and PHoeNIx except for some issues with Docker. I think the issue is that the output file name was changed from Phoenix_Output_Report.tsv to Phoenix_Summary.tsv in v2.0.2. I think if you just change that name reference in the wrapper you will be good. Let me know if that resolves the issue. We changed the name of the file in response to feedback from our compliance program. Any files with "report" in the name were replaced by "summary" in file names to avoid confusion regarding the difference between public health results (i.e. summary) and diagnostic results (i.e. report).

[Ashita2619]

The Nextflow version I am using currently is 24.10.3 and the Phoenix version is 2.1.1. I tried changing the Phoenix_Output_Report.tsv to Phoenix_Summary.tsv as per your suggestion in my helper function but still I am getting the same error.

[jvhagey]

Hey, so I ran a set of samples with the same version of nextflow and phoenix and didn't get any error so I think there is some other hiccup coming from the wrapper script. Is the author of the script, Adrian I assume (?), still around to look into it? If not I can try to pull the script and see what the issue is.

[Ashita2619]

No, Adrian is not around to look into it he left the organization. It would be of great help if you could look into the script.

Thanks,
Ashita

[jvhagey]

ok, after pulling the script and running it with singularity it finished fine. So that got me thinking this was a docker issue and looks like it was brought up in another issue already #175 . Can you implement the change suggested there and try again?

[Ashita2619]

I implemented the changes as mentioned and it was working fine until i got this error which is attached below:

[jvhagey]

So this is related to the kraken2 database. Check the path you are giving it, it should have the file ktaxonomy.tsv in the krakendb folder you give it. You should be using a kraken2db from here, I suggest the standard-8 version. you want to click on the .tar.gz link to download it. As of March 2023, each index includes the required ktaxonomy.tsv file.