AMRFinderPlus v3.11.8

NOTE: This version uses the blastx option -mt_mode 1 which was released in BLAST+ version 2.12.0, but there was a bug in the Mac OSX implementation. The current latest BLAST+ version (2.13.0) does not have that bug, so this release is only compatible with BLAST+ 2.13.0 on the Mac.

The Bioconda package for BLAST+ 2.13.0 was not compiled for the Mac for some reason (bioconda/bioconda-recipes#35897), so the latest BLAST+ version available in bioconda for Mac OSX is 2.12.0. For that reason this version will not be released in bioconda.

We are working on a fix and hope to have a new compatible with bioconda release soon.

• Performance improvements by optimizing blast parameters
  • Faster by 70% on single-threaded on nucleotide-only run
  • Faster by 64% on single-threaded protein-only run
  • Faster by 58% on single-threaded combined run
• Improved handling of special characters
  • To simplify issues I would avoid '#' ',' '%' '=' '&' and ':' in sequence identifiers, though they should now be correctly handled with escape sequences in GFF files. See the documentation of --gff for more information.
  • Fixed handling for FASTA identifiers with leading underscore "_" (#115)
  • Added --annotation_format standard

AMRFinderPlus v3.11.4

This includes a new amrfinder_index program to re-index the AMRFinderPlus database.

It also includes some mostly cosmetic code and error message cleanup and minor updates to github actions.

There were no changes in the way AMRFinderPlus is run or how it works.

AMRFinderPlus v3.11.2

Changes:

• New --print_node option will append the hierarchy node ID for each hit. This allows the user to differentiate hits with the same gene symbol, but different nodes on the hierarchy
• Switch to gnu++17
• Improvements to detect known frame shifting point mutations. These changes are not used by database versions 2022-10-11.2 or before

This release is database format backward compatible with the 3.10 series. However, we hope to release a new database that requires the improvements to frame-shift mutation detection included with this release soon.

AMRFinderPlus v3.10.45

AMRFinder Plus version 3.10.45 just switches from absolute paths in the link to the latest database directory to relative links (Issue #101).

It also adds a warning for unknown organism option with the --gpipe_org handling in effect (those options should probably only be used by the NCBI Pathogen Detection pipeline).

If neither of those are something you care about (which is probably the case) feel free to skip this release.

AMRFinderPlus v3.10.42

This is a bug-fix release for GitHub Issue #99.

The issue was that a protein had a decent blast match to a database point-mutation reference as well as being an HMM hit. This was introduced by a combination of recent code and database changes. This release also includes some code reorganization and cleanup, but there should be no other functional differences.

AMRFinderPlus v3.10.40

New experimental feature --annotation_format option automatically parses the output of some data sources and annotation pipelines. This was inspired by @axbazin in issue #91. See the documentation for the --annotation_format option for details.

Because we don't have a lot of experience with some of the data sources it is possible the parsing will not work on some inputs that differ from our test data. If you experience problems with the --annotation_format feature please let us know and send input files that don't work to [email protected] so we can improve the parsing.

We also made some additional optimization code changes which should cause a modest speed increase on some input.

AMRFinderPlus v3.10.36

Bug fix release

When multiple identical BLASTX hits occurred in the same query contig, only one hit was optimal and the other hits were less optimal. This bug was apparently introduced in some of the speed optimizations we made in the last year or so.

The problem case appears to be fairly rare in our data. In hundreds of thousands of assemblies in the Pathogen Detection system we see evidence of this issue in less than 0.04% of AMRFinderPlus runs, however it may be more frequent in other data.

A big thank you to fengyuchengdu who reported this bug in issue #94.

AMRFinderPlus v3.10.30

This release fixes a couple of rare bugs we discovered in our own testing and adds a --database_version option.

• New --database_version option to report versions of database and software as requested in issue #86
• Bug that could cause multiple rows with different "Method"s to be returned for a single query sequence. We only saw this occasionally, but it did happen. The multiple rows could include a less-preferred hit and had the same or almost the same coordinates.
• Bug that could cause AMRFinderPlus to crash for a given query sequence to a multi-domain protein depending on the order of rows returned by blast (which is apparently indeterminate in some cases). We had trouble replicating this one and hadn't seen it before so we believe it's very rare.

AMRFinderPlus v3.10.24

AMRFinderPlus v3.10.24 is a bug fix release for a bug that isn't exercised by any of our databases at the time of this release.

For previous versions of AMRFinderPlus a deletion mutation that overlapped a substitution mutation in the database meant that the substitution mutation would not be detected. We do not not have that situation in current databases so we did not notice the issue earlier. When preparing for our next database release we found that the including the planned Escherichia pmrB_RPISLR6del mutation means that the already released pmrB_L10P mutation would not be detected. This release fixes this bug in advance of our next database release.

AMRFinderPlus v3.10.23

This is yet another release whose only effect is on database updates. This time changing back to HTTPS for database updates.

As with the previous two releases ( 3.10.20 and 3.10.21 ) most people will see no difference in behavior. Unfortunately moving to the FTP protocol for database updates caused issues for some of our users because of firewall rules (e.g., #78), so to minimize those issues we are moving back to HTTPS.