Find assemblies faild with test run

[alarawms]

Description of the bug

When running the pipeline with the demo (test) flag, I get the error:
[a8/89c123] NOTE: Process NFCORE_PATHOGENSURVEILLANCE:PREPARE_INPUT:FIND_ASSEMBLIES (33958) terminated with an error exit status (1) -- Execution is retried (1)
During the step of finding assemblies the pipeline fails.

however the first parts of the pipeline runs smoothly
[8f/3b3b3f] NFCORE_PATHOGENSURVEILLANCE:PREPARE_INPUT:SAMPLESHEET_CHECK (test.csv) [100%] 1 of 1 ✔
[12/559483] NFC…PATHOGENSURVEILLANCE:PREPARE_INPUT:SRATOOLS_FASTERQDUMP (SRR18850314) [100%] 1 of 1 ✔ [8f/4be284] NFCORE_PATHOGENSURVEILLANCE:PREPARE_INPUT:BBMAP_SENDSKETCH (LF1) [100%] 1 of 1 ✔
[b2/684a8c] NFCORE_PATHOGENSURVEILLANCE:PREPARE_INPUT:INITIAL_CLASSIFICATION (LF1) [100%] 1 of 1 ✔

Command used and terminal output

Relevant files

No response

System information

No response

[zachary-foster]

Thanks for the report! Can you send the .nextflow.log? I have noticed some issues with steps that communicate with NCBI lately. It has been getting worse over time. I will try to replicate the error. In the mean time, you could add an NCBI API key as described in the usage documentation if you have not already and that might help.

[zachary-foster]

I think I have fixed the issue on the development fork. It seems the NCBI API updated and we had to update the software used to deal with this. You can try the development version like so until we push a release:

nextflow run grunwaldlab/pathogensurveillance -r 1.1.0dev  -profile test,docker -resume --outdir test_profiles_out/test

[alarawms]

Resolved.