AMRFinderPlus v3.10.21

AMRFinderPlus 3.10.21 changes from using the HTTPS to FTP protocol for
database updates. We're making this change because of a failure of amrfinder -u
to work because of a change in the HTTPS server for ftp.ncbi.nlm.nih.gov
that caused database updates to fail for a day and also led to the emergency
release of version 3.10.20 as well as server-based mitigation measures taken on
18-Jan-2021.

AMRFinderPlus relied on the server generated list of files, and when a footer
was added to the server-generated file list page, updates started to fail. Ironically
the easiest way to future-proof automatic AMRFinderPlus database updates was
to move back to the FTP protocol for updates because the file list is built into the
FTP protocol.

If this causes issues for your application please let us know at pd-help@ncbi.nlm.nih.gov.
Version 3.10.20 is functionally equivalent and will continue to work for the
foreseeable future with identical results to version 3.10.21 (but using HTTP for
database updates).

AMRFinderPlus v3.10.20

The database update feature amrfinder -u or amrfinder -U was not working for a short time. This is because the format of the dynamically generated HTTP listing of files on ftp.ncbi.nlm.nih.gov was changed by admins, something we didn't know was in the works.

For a day or so (some time on 13-Jan-2022 to 10:41am EST on 14-Jan-2022) versions prior to 3.10.20 would crash if a database update was attempted. We quickly developed and released released a patched version of the software that can handle the changes (3.10.20). In the meantime we realized there was a way to mitigate the issue on the server, so we implemented that as well. As of 10:41am EST on 14-Jan-2022 versions of AMRFinderPlus newer than 3.2 should all work again.

Apologies for the alarmist earlier version of this message. All should be well now, and we are discussing ways to make the system more robust in the future. (Some discussion on issue #70). At this time there is no functional reason to prefer this version over 3.10.18 (other than just wanting to be the cool kid with the latest).

AMRFinderPlus v3.10.18

This is purely a bug fix release, it should be transparent to the end user

This is a fix for a rare bug we've only seen when a specific partial tccP was used as a query. The query sequence caused AMRFinderPlus to crash because two equal-scoring alignments were made from a single query sequence to two locations in the same tccP gene. We don't think it's very common and aren't aware of anyone seeing this in production.

AMRFinderPlus v3.10.16

Changes AMRFinderPlus v3.10.16 should be minimal to the end user.

This release requires at least database version 2021-09-30.1

• New functionality was added to enable a BLAST-based cutoff to suppress reporting by an HMM. We added this in preparation for the next database release.
• We refactored the tests included with the distribution and the GitHub actions.

AMRFinderPlus v3.10.14

This is a minor bug fix release to work around a relatively obscure bug in the mac version of blast caused by the combination of short input sequences and the new -mt_mode 1 parameter to blast. To our knowledge the bug only affected AMRFinderPlus running on short sequences on MacOSX.

AMRFinderPlus v3.10.11

Changes in this version:

• Bug fix: Previous versions of AMRFinderPlus missed some point mutations in Klebsiella parC and gyrA when the query gene was more similar to the E. coli reference.
• Several improvements that increase speed and improve parallelization. Speedups range from a few percent to more than 70% depending on number of threads and the characteristics of the input sequence.
• Fix for database --update bug when parent directories did not exist (#57)
• Improved error message on missing blast database (issue #53)
• Bug fix: AMRFinderPlus will remove '-' from files passed to HMMER / BLAST because some versions of HMMER choke on protein files with '-' characters

AMRFinderPlus v3.10.5

AMRFinderPlus v3.10.5 includes two new features and a couple of bug fixes.

Changes in this version:

• New options to output a nucleotide FASTA with 5' flanks
• Option to report all equal scoring hits on multiple lines
• Fix to report both point mutations when two known point mutations occur right next to each other
• Added error checking for writability of /tmp or $TMPDIR

AMRFinderPlus v3.10.1

This release adds new handling for pbp alleles in Streptococcus pneumoniae in conjunction with
AMRFinderPlus database release 2021-03-01.1

This new handling enables AMRFinderPlus to identify genes by BLAST for a specific --organism that diverge more than a curated cutoff from the reference.

AMRFinderPlus v3.9.8

This release contains a potential fix for issue #45 by reading the environment variable TMPDIR.
It also contains the unrelated substitution of system calls for some shell commands which should not affect the AMRFinderPlus output or behavior.

AMRFinderPlus v3.9.3

AMRFinderPlus v3.9.3 is a new version that includes new features that required a format change to the database.

Changes in this version:

• Alleles may now have different classes and subclasses from their parent node
• The blaEC family was moved to "plus", while specific alleles remain in the "core" set
• Fusion genes are now reported on only one line with gene symbols and product names separated by '/'

In order to use the latest version of the AMRFinderPlus database (2020-11-09.1 at the time of release) you must upgrade to this version of the software.

Because this version is incompatible with AMRFinderPlus databases from previous versions, amrfinder -u must be run once this update is installed to get the latest version of the database.