nf-core / nf-core/modules

fmh-funprofiler silent errors

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#12,416 0 comments 0 reactions 1 assignee View on GitHub

@nickp60 is already working on this.

Since Jul 24, 2026.

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Description

Have you checked the docs?
Description of the bug

Both the test database I created in nf-core/test-datasets and the test data used here for fmh-funprofiler are formatted incorrectly but the tool doesn't raise a proper error. One of the two issues is fixed here, and will be working on figuring out whats wrong with the db in test-datasets asap. Just wanted to raise the warning here in case anyone else notices the issue.

Command used and terminal output
nf-core test modules/fmh-funprofiler
Relevant files

The relevant section of the log is as follows:

selecting specified query k=11
loaded query: test_1.fastq.gz... (k=11, protein)
query sketch has scaled=1000; will be dynamically downsampled as needed.
...no compatible signatures in 'test.sig'; skipping
--
loaded 3 total signatures from 1 locations.
after selecting signatures compatible with search, 0 remain.
ERROR in prefetch: after picklists and patterns, no signatures to search!?
Creating metagenome sketch...
Sketch of the metagenome has been saved to test_1.fastq.gz_sketch_1784839912.sig.zip
Running sourmash prefetch...
sourmash prefetch test_1.fastq.gz_sketch_1784839912.sig.zip test.sig -o test_1.fastq.gz_gather_1784839914.tmp -k 11 --scaled 1000 --protein --threshold-bp 1000
sourmash prefetch results have been stored to test_1.fastq.gz_gather_1784839914.tmp
Prefetch output file is empty. No matches in KEGG KOs found. Creating an empty KO profile CSV
System information

No response

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