Should database overwrites be requested by the user? or disabled by user? #16
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Hi @rpetit3, Thanks for the compliment! Keep 'em coming :-) We have it automatically overwriting to simplify things for users (and our support) if/when the database gets moved or corrupted, but we're open to reconsidering and/or adding an option. What is your concern about the way it currently overwrites the database? |
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I think this is a fringe case, but I'm using amrfinder within a conda environment create by Nextflow (https://www.nextflow.io/docs/latest/conda.html). When the workflow is run, if a conda environment doesn't exist, Nextflow will create it. After creation, amrfinder requires the database to be updated. So, in Nextflow I check to make sure the database exists, and if it doesn't go ahead and update. Occasionally I get instances where multiple jobs try to update at the same time each overwriting one another. I fixed this by updating earlier (a single time) in the workflow. Probably wasn't the best idea to have multiple jobs trying to update at once, but it got me to wondering: Why update (and overwrite) to the same version of a database? This led to the |
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Thanks @rpetit3, That's not something we had thought about since we update so infrequently. I'll talk it over with the rest of the team and see what we can do. I'm glad you've been able to fix the issue short-term and we'll discuss how we can fix it with AMRFinderPlus in the future. |
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I suggest having 2 workflows:
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Release 3.8.28
- amrfinder -u option no longer overwrites databases if they already exist.
New --force_update option will still overwrite the database as the old -u
option did. ([#16])
- New --protein_output and --nucleotide_output options will produce FASTA files
containing the sequence of AMRFinderPlus hits
- --mutation_all output has been streamlined and some bugs have been fixed
- New --name option will prepend a "Name" field to every row of the
AMRFinderPlus report ([#25])
- Fusion genes are now reported with both element symbols separated by a '/' on
both lines of the report. E.g., aac(6')-Ie/aph(2'')-If2
- For HMM-only hits (have HMM in the method column which means they do not have
BLAST results that meet cutoff) BLAST statistics will now be reported
if any alignment at that location was made.
- When in COMBINED (nucleotide + protein) mode and when an "INTERNAL_STOP" is detected
at a locus that also has a protein, the protein result will be reported with
Method of INTERNAL_STOP (Previously the nucleotide result was reported. This
would affect the identity, length, and coverage statistics AMRFinderPlus reports.
- Improved handling of partial alignments for point-mutation detection, including
prioritization of translated matches (POINTX) when the protein match identifies fewer
known SNPs.
- Incorrect amino acids inferred by protein annotations extended in the 5' (N-terminal)
direction because correct annotations start with alternative start codons will
no longer count as mismatches.
- Small improvements in performance.
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It only took us a year :-), but we finally implemented your suggestion @rpetit3 in release 3.8.28. The Thanks for your suggestion! |
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Thank you very much! This will work great! |
Really great tool @evolarjun! I'm curious to get your thoughts on handling existing databases.
Currently if a database already exists it is overwritten then downloaded again.
I wonder if it would be better to raise an error and require the user to explicitly tell amrfinder (ex
--force) to overwrite the existing database.An alternative, would be allow user to disable the overwrite (ex.
--skip_existing).The text was updated successfully, but these errors were encountered: