Releases | Open Source Science

amr - AMRFinderPlus v4.0.23

At some point the PGAP GFF file output will be standardized to match other GFF files produced at NCBI; this release is to handle the small change in PGAP output. This release has no other differences from version 4.0.22, so if you're not using the --pgap or --annotation_format pgap options there is no need to update.

With the--pgap or --annotation_format pgap options AMRFinderPlus previously relied on the older non-standard format for the Name= section of the attributes field of the GFF to identify the associated protein sequence. With this update the --pgap option will parse either version of the GFF output of PGAP.

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Published by evolarjun about 1 year ago

amr - AMRFinderPlus v4.0.22

This release includes: - A bug fix for Issue [https://github.com/ncbi/amr/issues/164] where AMRFinderPlus crashed on the combination of GZipped input files and --nucleotide_output or --protein_output. - StxTyper version 1.0.42 which has some fixes for incomplete operons.

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Published by evolarjun about 1 year ago

amr - AMRFinderPlus v4.0.19

This version of AMRFinderPlus updates to StxTyper 1.0.40 and makes use of the --threads option to StxTyper that is new to that version. In addition we made some improvements to the tests, both at GitHub and in the included install tests.

No changes to results other than stx_operon results from StxTyper, and those changes should be minor. See the StxTyper release notes for details.

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Published by evolarjun over 1 year ago

amr - AMRFinderPlus v4.0.15

This release incorporates changes to standardize and improve the reporting format for StxTyper results in AMRFinderPlus. StxTyper is only run when the -organism Escherichia and -plus options are used and a nucleotide file is used as input. See the StxTyper release 1.0.31 for the details of these fairly minor changes in output format. There are no biologically significant differences in results with this release.

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Published by evolarjun over 1 year ago

amr - AMRFinderPlus v4.0.3

NOTE: This is a new major revision of AMRFinderPlus that has a changed database format. You will need to run amrfinder -U to get database release 2024-10-22.1 or later to use this version. This AMRFinderPlus includes StxTyper version 1.0.27 for E. coli Stx operon typing.

Software and database format changes - See https://github.com/evolarjun/amr/wiki/New-in-AMRFinderPlus/ for more details. - StxTyper (https://github.com/ncbi/stxtyper) which accurately types full-length stx operons now included with AMRFinderPlus. - Database filename changes to standardize filenames and make writing scripts easier (See https://github.com/ncbi/amr/wiki/New-in-AMRFinderPlus for more information). - Column names in output have been changed to more closely other NCBI Pathogen Detection resources such as MicroBIGG-E. - Point mutations can now be reported with symbols different from the standard format. - The optional hierarchy_node field will now contain two node IDs for fusion proteins and stx operons separated by '::'. - The ability to have different curated blast cutoffs at multiple levels of the hierarchy with the same reference protein has been added. - The same protein can be used both as a reference gene to be reported and as the reference for point mutations.

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Published by evolarjun over 1 year ago

amr - AMRFinderPlus v3.12.8

AMRFinderPlus v3.12.8 includes a new database format version. Because this version is incompatible with AMRFinderPlus databases from previous versions, amrfinder -u must be run once the software update is installed to get the latest version of the database.

This update includes the changes: - Reference proteins now have stop codons. Input proteins that are not terminated with a ‘’ character are assumed to have a ‘’ at the end. - Extended proteins are no longer “EXACT” hits, so the protein names will be that of the parent node for alleles. - If a protein is hit by blast and the Blast Rule is violated, the Blast Rule of the parent family is checked, etc.

This means that Previously extended hits that were 100% identical to, but longer than proteins in the database were called with the method "EXACTP" and now they are called "BLASTP". Blast results will still indicate that 100% of the database reference was covered at 100% identity, and you should still see that the "Target length" is longer than the "Reference sequence length".

Extended hits to allele sequences that were previously called EXACTP already had the element symbol was one node up the hierarchy (i.e. the gene symbol, not the allele symbol) the "Sequence name" was that of the ALLELE reference, and thus inconsistent with the element symbol assigned. This has been changed. Again, this does not affect previous "Element symbol" calls.
In combined protein + nucleotide runs of AMRFinderPlus extended protein sequences with exact matches in the database were ignored and the nucleotide match was taken resulting in an EXACTX match with no protein accession provided. Now the protein match with method BLASTP will be reported.

To reiterate, gene symbols should not change. Sequence names will only change if the query is an extended version of a protein 100% identical and completely covering an allele in the database.

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Published by evolarjun over 2 years ago

amr - AMRFinderPlus v3.11.26

Fix for rare crash and change in behavior of hierarchy_node. This release will likely have no effect for most AMRFinderPlus users.

Fixes an unusual crash when using the --ident_min option with very low identity cutoffs (we generally don't recommend using this option).
A change in the behavior of the --print_node option. It will now print the node associated with the element reported, rather than the most specific node hit. This changes the node reported for non-exact blast hits to reference sequences of named alleles to report the parent node. It should have no effect on all other hits and does not affect the behavior of AMRFinderPlus in any field other than hierarchy_node.

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Published by evolarjun over 2 years ago

amr - AMRFinderPlus v3.11.20

This is a minor bug-fix release with two fixes:

Fix for a protein sequence that could cause AMRFinderPlus to crash. This was very rare, we saw one failure in running on over a million assemblies and all RefSeq proteins.
Found and fixed another case where AMRFinderPlus would produce two lines for what should really be a single partial hit reported.

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Published by evolarjun almost 3 years ago

amr - AMRFinderPlus v3.11.18

AMRFinderPlus version 3.11.17 is another minor bug fix release

It fixes a bug where some point mutation results could be duplicated in AMRFinderPlus output. There will no longer be two rows in the AMRFinderPlus output for these circumstances.

This bug only affected a few point mutations that occur at/near the end of proteins where we had to add mutated reference sequences to a BLAST database to get BLAST to align through them. We have only seen this bug in our data for the following point mutations: ftsII336IKYRI, ftsIN337NYRIN, mgrBW47R, and ramRA19V. See the point mutations in the Reference Gene Catalog for more information about those specific mutations.

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Published by evolarjun almost 3 years ago

amr - AMRFinderPlus v3.11.17

This is a minor software release update with two changes. A bug fix for a very rare bug with mild consequences, and a minor improvement in the functionality of the --update option.

The release fixes a bug when AMRFinderPlus is run in combined nucleotide and protein mode where only a partial gene was assembled for proteins with long amino-acid repeats (e.g., espF, CAI43856.1). In the right circumstances AMRFinderPlus could report multiple combined hits to the same gene with the same start and stop coordinates. We've only seen the exact triggering circumstances a few times in more than a million assemblies, so it should be very rare. This release fixes that bug.

The release also contains a minor improvement to amrfinder_update to also create the parent database directory if it doesn't exist when amrfinder_update is run.

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Published by evolarjun almost 3 years ago

amr - AMRFinderPlus v3.11.14

This release addresses a few issues brought up on GitHub.

Changes: - On failure no -o output file is created - https://github.com/ncbi/amr/issues/115 - AMRFinderPlus will now automatically decompress files ending in .gz with gunzip (this relies on gunzip being in PATH) - https://github.com/ncbi/amr/issues/61 - AMRFinderPlus does not support unicode, but it will not check GFF files to prohibit extended ASCII or UTF-8 characters specifically (still prohibits GFF files with ASCII control characters between 0x00 and 0x1F) - https://github.com/ncbi/amr/issues/119 - Add reporting of curl error messages - https://github.com/ncbi/amr/issues/120

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Published by evolarjun about 3 years ago

amr - AMRFinderPlus v3.11.11

This release has two primary changes

Version checking for blast on Mac to avoid the bug in BLAST 2.12.0 with the -mt_mode parameter
Updated handling of special characters in the sequence identifiers in GFF and FASTA files.

Special character handling

Implemented special character handling in GFF files according to https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md. The following need to be escaped in the sequence identifiers using URL-style codes in .gff files:

# (comment start)
tab (%09)
newline (%0A)
carriage return (%0D)
% percent (%25)
control characters (%00 through %1F, %7F)
; semicolon (%3B)
= equals (%3D)
& ampersand (%26)
, comma (%2C)

Added input checking for nucleotide sequences because 'makeblastdb' truncates and/or alters sequence identifiers with the following characteristics. Now nucleotide FASTA identifiers (characters after '>' and before the first whitespace) with any of the following will cause amrfinder to exit with an error message.

FASTA identifier starts with '?'
FASTA identifier contains the two character sequence ',,' or '\t' (the character '\' followed by the character 't')
FASTA identifier ends with ';' '~' ',' or '.'

Bug fix for Bioconda compatibility

On Mac the BLAST parameter -mt_mode requires BLAST version 2.13.0 to run on short query sequences.

This release includes a bug-fix to allow AMRFinderPlus to be compatible with Bioconda which doesn't have BLAST+ version 2.13.0 for the Mac. The previous release 3.11.8 could not be added to Bioconda because at the time of release Bioconda did not have BLAST+ version 2.13.0 for Mac.

See also release notes for version 3.10.8: https://github.com/ncbi/amr/releases/tag/amrfinder_v3.11.8

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Published by evolarjun about 3 years ago

amr - 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 (https://github.com/bioconda/bioconda-recipes/pull/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 "_" (https://github.com/ncbi/amr/issues/115)
- Added --annotation_format standard

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Published by evolarjun about 3 years ago

amr - 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.

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Published by evolarjun over 3 years ago

amr - 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.

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Published by evolarjun over 3 years ago

amr - 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 https://github.com/ncbi/amr/issues/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.

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Published by evolarjun over 3 years ago

amr - AMRFinderPlus v3.10.42

This is a bug-fix release for GitHub Issue https://github.com/ncbi/amr/issues/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.

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Published by evolarjun over 3 years ago

amr - 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 https://github.com/ncbi/amr/issues/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 pd-help@ncbi.nlm.nih.gov so we can improve the parsing.

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

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Published by evolarjun almost 4 years ago

amr - 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 https://github.com/ncbi/amr/issues/94.

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Published by evolarjun almost 4 years ago

amr - 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 https://github.com/ncbi/amr/issues/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.

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Published by evolarjun about 4 years ago

amr - 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 pmrBRPISLR6del mutation means that the already released pmrBL10P mutation would not be detected. This release fixes this bug in advance of our next database release.

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Published by evolarjun about 4 years ago

amr - 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., https://github.com/ncbi/amr/issues/78), so to minimize those issues we are moving back to HTTPS.

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Published by evolarjun over 4 years ago

amr - 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).

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Published by evolarjun over 4 years ago

amr - 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 https://github.com/ncbi/amr/issues/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).

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Published by evolarjun over 4 years ago

amr - 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.

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Published by evolarjun over 4 years ago

amr - 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.

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Published by evolarjun almost 5 years ago

amr - 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.

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Published by evolarjun almost 5 years ago

amr - 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 (https://github.com/ncbi/amr/issues/57)
Improved error message on missing blast database (issue https://github.com/ncbi/amr/issues/53)
Bug fix: AMRFinderPlus will remove '-' from files passed to HMMER / BLAST because some versions of HMMER choke on protein files with '-' characters

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Published by evolarjun almost 5 years ago

amr - 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

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Published by evolarjun about 5 years ago

amr - 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.

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Published by evolarjun over 5 years ago

amr - 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.

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Published by evolarjun over 5 years ago

amr - 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.

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Published by evolarjun over 5 years ago

amr - AMRFinderPlus v3.8.28

AMRFinderPlus v3.8.28 has several changes, new features requested by users, and some optimization of the handling of certain edge cases.

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. (https://github.com/ncbi/amr/issues/16)
New --proteinoutput and --nucleotideoutput 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 (https://github.com/ncbi/amr/issues/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 "INTERNALSTOP" is detected at a locus that also has a protein, the protein result will be reported with Method of INTERNALSTOP (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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Published by evolarjun over 5 years ago

amr - AMRFinderPlus v3.8.4

AMRFinderPlus v3.8.4 includes changes related to an NCBI initiative to change from using GI's to Accessions as the primary sequence identifier, which has necessitated a change in the database format.

This includes fixes for a few bugs including fixing the path issues using bioconda on the Mac to install AMRFinderPlus and improved error messages for issue https://github.com/ncbi/amr/issues/28.

In order to use the latest version of the AMRFinderPlus database (2020-05-04.1 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.

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Published by evolarjun about 6 years ago

amr - AMRFinderPlus v3.6.15

The primary update in this release is the way HMM accessions are handled for hits that are both based on BLAST and HMM hits. It also includes a minor bug fix.

HMM id and HMM description columns no longer use data from matching node in the hierarchy
Fix for space in database path issue https://github.com/ncbi/amr/issues/23
Fixed bug where missing DNA sites were not output using --mutation_all

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Published by shumwaym about 6 years ago