With the --verbose flag, a call to get-all generates the user warning "No paired-read sequences available for these accession IDs." As a user, I find the warning status confusing when nothing is wrong per se. Could we downgrade this status to INFO?
Sample command and output:
$ qiime fondue get-all --i-accession-ids toy-multi-ids.qza --p-email <> --p-n-jobs 4 --output-dir work-multi --verbose
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
2022-02-11 11:17:26,567 [MainThread] [INFO] [entrezpy.esearch.esearcher.Esearcher]: {"query": "xtZfY5XUTDuY3d6sNk2pNw==", "status": "OK"}
2022-02-11 11:17:34,073 [MainThread] [INFO] [q2_fondue.sequences]: Downloading sequences for 4 accession IDs...
Downloading sequences for run SRR7871145 (attempt 1): 100%|████████████████████████████████████████████████████████████████| 4/4 [00:49<00:00, 12.43s/it, 0 failed]
2022-02-11 11:18:23,779 [MainThread] [INFO] [q2_fondue.sequences]: Download finished.
/Users/linkim/Documents/Work/Software/q2-fondue/q2_fondue/sequences.py:218: UserWarning: No paired-read sequences available for these accession IDs.
warn(warn_msg)
2022-02-11 11:18:25,344 [MainThread] [WARNING] [q2_fondue.sequences]: No paired-read sequences available for these accession IDs.
2022-02-11 11:18:25,349 [MainThread] [INFO] [q2_fondue.sequences]: Processing finished.
Saved SRAMetadata to: work-multi/metadata.qza
Saved SampleData[SequencesWithQuality] to: work-multi/single_reads.qza
Saved SampleData[PairedEndSequencesWithQuality] to: work-multi/paired_reads.qza
Saved SRAFailedIDs to: work-multi/failed_runs.qza
With the
--verboseflag, a call toget-allgenerates the user warning "No paired-read sequences available for these accession IDs." As a user, I find the warning status confusing when nothing is wrong per se. Could we downgrade this status to INFO?Sample command and output: