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VADR 1.x release notes

VADR 1.6.4 release (June 2024): Bug fix release

  • no code changes (results should be identical to 1.6.3)
  • removes unnecessary file testfiles/github-issues/iss70-cdsstopn3p/.#1.ntlist that was accidentally included in versions 1.6 to 1.6.3, and which causes a problem for the bioconda recipe (github issue #78)
  • adds use Mozilla::CA to v-build.pl to help with issue on Mac OS/X (github issue #80) and adds note about requirement of this module to documentation on installation

VADR 1.6.3 release (December 2023): (very) Minor update

  • adds --forcegene and --forcequal options to v-annotate.pl for controlling feature table output of qualifiers
  • adds function and gene_syn qualifiers to feature table output

VADR 1.6.2 release (December 2023): Bug fix release

  • fixes a problem with installing VADR on silicon Macs with M1/M2 chips
  • removes separate installation of the HMMER package, scripts use copies of HMMER executables installed with Infernal instead

VADR 1.6.1 release (November 2023): (very) Minor update

  • changes extrant{5,3} alerts (EXTRA_SEQUENCE_{START,END}) from fatal to non-fatal by default, and default minimum length threshold to trigger alerts from 5 down to 1.
  • adds support for extrant5_exc and extrant3_exc exceptions in model info files.

VADR 1.6 release (November 2023): Major update

  • adds new extrant{5,3} alerts (EXTRA_SEQUENCE{_START,_END}) for extra sequence 5' or expected start or 3' of expected stop
  • adds new mutspst{5,3} alerts (MUTATION_AT_SPLICE_SITE) for unexpected non-canonical donor splice site (not GT) at 5' end of intron or acceptor splice site (not AG) at 3' end of intron.
  • protein validation using blastx now selects either longest or best-scoring alignment based on which yields fewer alerts. The v-annotate.pl --xlongest option has been removed as it is now unnecessary.
  • makes alert exception support more consistent and adds exceptions for low similarity alerts (lowsim*). See documentation/annotate.md#exceptions for details.
  • improves CM-based alignment of extra sequence at 5' and 3' ends using cmalign from infernal 1.1.5
  • improves detailed error message for cdsstopn alert when CDS is 3' truncated
  • overhauls miniscripts/build-add-to-blast-db.pl for adding new proteins to model's blastx protein library
  • adds support for sig_peptides in v-build.pl
  • adds detailed tutorial on advanced model building using RSV as an example in documentation/advbuild.md
  • adds count-ambigs.pl, longest-N-stretch.pl and esl-alipid-per-seq-stats.pl perl scripts to miniscripts/. These are used in the advanced model building tutorial.

bug fixes:

  • fixes bug with reporting codon_start and truncation status of multi-segment CDS if at least one segment is completely missing due to truncation (github issue #72)
  • fixes bug in reporting of early stops in multi-segment CDS (github issue #71)
  • fixes bug preventing reporting of in-frame early stop codon (cdsstpon) if they are the final 3 nt of the sequence (github issue #70)

other changes:

  • updates dependencies installed with VADR:
    • blast+ version 2.15.0
    • infernal version 1.1.5
    • hmmer version 3.4
    • sequip version 0.10
    • minimap2 version 2.26
    • fasta version 36.3.8h (unchanged)

VADR 1.5.1 release (February 2023): Bug fix release

  • fixes bug that caused a failure during blastx parsing in rare cases, found during RSV testing. Logged as github issue #68.
  • fixes bug that caused incorrect frameshift alert details in rare cases. Logged as github issue #69.

VADR 1.5 release (September 2022): Major update

  • adds support for minimap2-based determination of seeds as an alternative to blastn-based seeds with the v-annotate.pl --minimap2 option
  • installation now installs minimap2 v2.24
  • adds two columns to .sda suffixed output files with information relevant if --minimap2 used
  • fixes a bug related to processing of blastn output when top scoring hit is on the reverse strand
  • fixes a bug that caused incorrect sequence coordinates to be reported for insertnn alerts on the reverse strand

VADR 1.4.2 release (July 2022): Minor update

  • adds new lowsim{5,3,i}l alerts (LOW_FEATURE_SIMILARITY{_START,_END}) for long (>=30 nt by default) regions of low similarity, and modifies lowsim{5,3,i}n alerts to be non-fatal for misc_featurizable features (misc_not_failure:"1" in modelinfo file)
  • modifies installation of FASTA to allow alignment of sequences up to 250Kb with glsearch (previously 40Kb limit) and increases maximum allowed filename length
  • adds --r_lowsim{ok,xf,xl,xd} options to v-annotate.pl to allow not reporting lowsim* alerts within identified N-rich regions and controlling related thresholds
  • fixes a bug with -r in that causes a cdsstopp alert to be erroneously reported in rare situations (github issue #58)
  • fixes a bug with -s or -r that can cause parse_blast.pl to fail if the blastn alignment is plus/minus for query/subject and the final alignment line length is exactly 1 nt (github issue #61)

VADR 1.4.1 release (January 2022): Bug fix release

  • fixes bug that prevented reporting of some dupregin alerts (DUPLICATE_REGIONS) previously reported in vadr 1.3 and earlier versions; only relevant when -s is used.
  • nmiscftr alert (TOO_MANY_MISC_FEATURES) now only reported if a sequence has >= 4 misc_features due to 'misc_not_failure' attributes in model info file. Previously a sequence with >= 3 misc_features caused a nmiscftr alert. (Default value of --nmiscftrthr changed from 3 to 4.)

VADR 1.4 release (December 2021): Major update

v-annotate.pl changes summary:

  • frameshift detection and alerts have changed
  • how blastn is used with the -s and -r options has changed
  • alerts related to ambiguous nucleotides at beginning/end of sequences and features have changed
  • with -r option, N-rich sequence regions of unexpected lengths may now be replaced with expected nucleotides from reference in some situations
  • alerts related to early stop codons (cdsstopn, mutend*) are now detected and reported in some situations for truncated CDS
  • is_deletable field for features now supported in model info file for to allow a feature to be completely deleted without triggering a fatal deletins alert (triggers non-fatal deletina alert instead)
  • adds support for 'alternative features' with alternative_ftr_set and alternative_ftr_set_subn fields for features in model info files
  • adds support for excluded regions from frameshift and indefinite strand (indfstrn) and duplicate region (dupregin) alerts with frameshift_exc, indfstrn_exc and dupregin_exc fields for features in model info files

bug fixes:

  • fixes bug related to parantheses in feature product strings (github issue #47)

other changes:

  • updates version of BLAST+ dependency installed with vadr to 2.12.0+

more detail on some v-annotate.pl changes:

  • frameshift detection and alerts have changed:

    • 'expected' frame now defined as frame of first nucleotide in a CDS, and 'shifted' regions are any regions (above length thresholds) that differ from expected. Old (v1.3) definition of 'dominant' frame as frame that most nucleotides in a CDS exist in is abandoned.
    • fst{hi,lo,uk}cf5 and fst{hi,lo,uk}cf3 alerts for frameshifts at 5' and 3' end no longer exist, partly because shifted regions at the 5' end of CDS are no longer possible. These alerts are replaced by fst{hi,lo,uk}cft alerts for frameshifts that are not restored before the end of a CDS. fst{hi,lo,uk}cfi alerts still exist for frameshifts that are restored before the end of a CDS.
    • frameshift 'alert detail' in .alt and .alt.list files has been changed to include information on the mutation that causes the frameshift, the mutation that restores frame (if any), and a summary string showing the frame and length of all regions in the CDS that are in a different frame.

  • how blastn is used with the -s and -r options has changed:

    • with -s, entire top-scoring blastn HSP (with indels) is now used as a seed (with some caveats to avoid large gaps and gaps in start/stop codons) and fixed for the downstream global alignment of each sequence. Previously, only longest ungapped region in the top-scoring HSP was used as the seed. This leads to faster processing of some sequences.
  • default blastn parameters changed to: -word_size 7 -gapopen 2 -gapextend 1 -reward 1 -penalty -2 -xdrop_gap_final 110 Previously (vadr 1.1 to 1.3) only -word_size 7 was used, so blastn parameters used were implicitly (mostly defaults): -word_size 7 -gapopen 0 -gapextend 2.5 -reward 1 -penalty -2 -xdrop_gap_final 100 This leads to more desired gap placement for some sequences and more replacement of stretches of Ns with -r for some sequences.

  • alerts related to ambiguous nucleotides at beginning/end of sequences and features have changed:

    • all ambiguous nucleotides are now treated as Ns were previously treated. This impacts alerts ambgnt{5,3}s, ambgnt{5,3}f, and ambgnt{5,3}c. The short description/error for these alerts was modified to have 'AMBIGUITY' instead of 'N' (e.g. 'AMBIGUITY_AT_START' replaces 'N_AT_START').
    • new ambgcd5c (AMBIGUITY_IN_START_CODON) added and reported when 5' complete CDS has a start codon that begins with a canonical nucleotide but that includes an ambiguous nt. This alert makes it so that no other start codon alert (e.g. mutstart) will be reported.
    • new ambgcd3c (AMBIGUITY_IN_STOP_CODON) added and reported when 3' complete CDS has a stop codon that ends with a canonical nucleotide but that includes an ambiguous nt. This alert makes it so that no other stop codon alert (e.g. mutendcd) will be reported.
    • ambgcd5c and ambgcd3c impact CDS coordinate trimming in feature table output in that all 3 nt of a start or stop codon are considered ambiguities (feature coordinates will not include the start and/or stop codon)

  • with -r option, N-rich sequence regions of unexpected lengths may now be replaced with expected nucleotides from reference in some situations

    • if difference between expected and actual length is <= 10 nt, the region is 'aligned' by flushing sequence region left or right with respect to reference and counting matches with expected reference. If >= 1 non-N exists and >= 0.75 fraction of non-Ns match the expected nt in the reference by flushing either left or right the region is replaced. Relevant information in .rpn output file has been expanded.

VADR 1.3 release (July 2021): Major update

v-annotate.pl changes:

  • adds new alerts and new options for controlling alert thresholds. In many cases this is by splitting existing alerts and/or options into multiple options for greater user control. adds separate options for controlling length thresholds for lowsim{5,3,i}s vs lowsim{5,3,i}f alerts (--lowsim5term split into --lowsim5seq and --lowsim5ftr; --lowsim3term split into --lowsim3seq and --lowsim3ftr; --lowsimint split into --lowsimiseq and --lowsimiftr;)
    • splits alerts indf{5,3}loc alerts related to indefinite annotation into indf{5,3}lcc (coding) and indf{5,3}lcn (non-coding) for more control over these alerts (INDEFINITE_ANNOTATION_START,END) for coding versus non-coding features. Adds options to control each alert threshold separately.

  • splits frameshift alerts into separate 5', 3' and internal instances depending on where they occur in CDS. Specifically fst{hi,lo,uk}cnf split into fst{hi,lo,uk}{5,3,i}cf. Different length thresholds can be set for each 5', 3' and internal with options: --fstmminnt5, --fstminnt3 and --fstminnti.

  • list of new alerts in v1.3 and related alerts from v1.2 that no longer exist:

    new 1.3 alert | related 1.2 alert (no longer exists) | alert description
------------- | ------------------------------------ | -----------------
*fsthicf3*    | *fsthicnf* | POSSIBLE_FRAMESHIFT_HIGH_CONF
*fsthicf5*    | "          | "
*fsthicfi*    | "          | " 
*fstlocf3*    | *fstlocnf* | POSSIBLE_FRAMESHIFT_LOW_CONF
*fstlocf5*    | "          | "
*fstlocfi*    | "          | "
*fstukcf3*    | *fstukcnf* | POSSIBLE_FRAMESHIFT
*fstukcf5*    | "          | "
*fstukcfi*    | "          | "
*indf3lcc*    | *indf3loc* | INDEFINITE_ANNOTATION_END
*indf3lcn*    | "          | "
*indf5lcc*    | *indf5loc* | INDEFINITE_ANNOTATION_START
*indf5lcn*    | "          | "
*lowsim3c*    | *lowsim3f* | LOW_FEATURE_SIMILARITY_END
*lowsim3n*    | "          | "
*lowsim5c*    | *lowsim5f* | LOW_FEATURE_SIMILARITY_START
*lowsim5n*    | "          | "
*lowsimic*    | *lowsimif* | LOW_FEATURE_SIMILARITY
*lowsimin*    | "          | "

    • adds information, including sequence and model coordinates, to output files related to alerts:

      • modifies .alt file format by adding four fields: seq coords, seq len, mdl coords and mdl len
      • modifies .alt.list file format by adding four fields: model, feature type, seq coords and mdl coords
      • adds feature type, sequence coords and model coords to error lines of .fail.tbl files
      • various changes to detailed alert messages, mainly to avoid redundancy with information in the new sequence and model coordinate fields

    • adds markdown documentation file for "Explanations and examples of v-annotate.pl detailed alert and error messages" in documentation/alerts.md.

    • with --keep or --out_stk, output stockholm alignment files now include per-column reference model position annotation

    • fixes bug that sometimes caused the incorrect model strand to be output in model coordinates in .ftr files

    • slightly modifies how N-replacment works with -r:

      • sets different minimum fraction of Ns in a region for replacement for internal regions (0.5) and regions at the end of a sequence (0.25). Previously both values were 0.25. The options --rminfracti and --rminfract5 and --rminfract3 allow user to change this.
      • allows some overlap in blastn hits when identifying candidate regions for N replacment with -r (github issue #37)

    • with --split, makes splitting of small sequence files more efficient by placing a minimum of one sequence into each chunk

    v-build.pl changes:

    • fixes bug that allows use of blastn .fa database in model directory created by v-build.pl

VADR 1.2.1 release (June 2021): Bug fix update

  • The vadr-install.sh script was updated in two ways:
    • to download and build the FASTA package from github instead of downloading pre-built executables from https://faculty.virginia.edu/wrpearson/fasta/executables/ which has been decommissioned since the v1.2 release.
    • to enable two step installation: download necessary files in step 1 and build programs in step 2 (github issue #36).
  • NO changes at all were made to the code between versions v1.2 and v1.2.1 so results from v1.2 and v1.2.1 should be identical. There is no need to upgrade to v1.2.1 from v1.2 if you already have v1.2 installed.

VADR 1.2 release (April 2021): Major update

v-annotate.pl changes:

  • adds support for an alternative alignment program, glsearch from the FASTA software package; FASTA is now installed by the vadr-install.sh script. glsearch drastically reduces the maximum amount of memory needed for alignment, especially for viruses > 20Kb, e.g. SARS-CoV-2. glsearch is used instead of the default cmalign program when the --glsearch option is used.
  • adds support for splitting up the input fasta file into chunks and processing each chunk independently and then combining results before exiting to reduce maximum memory usage by invoking the --split option.
  • adds support for parallelization using multiple threads ( threads) with the --cpu <n> option. Currently only works in combination with --split or --glsearch.
  • the default set of models, which previously was caliciviruses and flaviviruses, has been split into two separate model sets and the default set is now only caliciviruses. Both sets still installed by default and flaviviruses models can be used with the --mkey flavi --mdir $VADRMODELDIR/vadr-models-flavi options.
  • some rare errors related to start and stop codons that can be corrected by doctoring (i.e. slightly changing) the alignment computed by cmalign or glsearch are now corrected which removes the errors.
  • slightly improved detailed error messages for MUTATION_AT_END errors to indicate positions of full codon
  • expensive validation of CM file is no longer performed by default, but can still be with the --val_only option
  • updates .ftr format by adding par idx field for parent index of feature

v-build.pl changes:

  • nucleotide blastn database is now built from DNA sequence file, not cmemit -c consensus sequence as it was previously

Other changes:

  • updates versions of Bio-Easel dependency installed with vadr to Bio-Easel 0.14

VADR 1.1.3 release (February 2021): Minor update

v-annotate.pl changes:

  • adds support for allowing sequences to pass with some feature-specific fatal alerts for features with misc_not_failure:"1" listed in input modelinfo file. Originally implemented to allow SARS-CoV-2 sequences with certain ORF8 errors to still pass. More information in documentation/annotate.md.
  • indf5loc and indf3loc alerts no longer reported for CDS or features with identical coordinates to a CDS (e.g. gene) because these are subject to more stringent tests involving start/stop codons
  • improved detailed error messages for CDS_HAS_STOP_CODON errors when predicted CDS have lengths that are not a multiple of 3
  • outputs separate fasta files of all passing seqs and all failing seqs, can be turned off with --out_nofasta
  • fixes bug with -r when number of leading 5' Ns exceeds expected number as determined by alignment to best-matching model (github issue #30)
  • with -p, qsub commands now execute a shell script with relevant command instead of including command in qsub call, allowing arbitrarily long commands and removing need for --longdir option.

Other changes:

  • updates versions of dependencies installed with vadr to:
    • infernal 1.1.4 (allowing v-build.pl to build large >25Kb models, e.g. coronaviridae)
    • hmmer 3.3.2
    • ncbi-blast 2.11.0+
    • Bio-Easel 0.13
    • sequip 0.08

VADR 1.1.2 release (November 2020): Minor update

  • adds v-annotate.pl option --mlist to specify only a subset of models in the model info file be used
  • adds v-annotate.pl option --msub to substitute models after the classification stage
  • adds v-annotate.pl option --xsub to substitute blast dbs for the blastx protein validation stage
  • adds v-annotate.pl options to separately modify minimum length for lowsim5s/lowsim5f and lowsim3s/lowsim3f alerts
  • adds 'benchmark mode' for v-test.pl with -m that produces output detailing differences between expected and observed output files
  • enforces that model names not include '(' or ')' (github issue #22)
  • fixes bug in install script that prevented building on some Ubuntu OS versions (github issue #24)

VADR 1.1.1 release (July 2020): Minor update

  • in feature table output (only) features that start and/or end with one or more ambiguous 'N' nucleotides now have their start and stop positions 'trimmed' to the first or final non-N to be consisent with how GenBank annotates such features, and adds related --noftrtrim and --notrim options to turn this off for some or all types of features
  • in .ftr output file, adds two new columns that list number of consecutive Ns at beginning and end of each feature (often 0)
  • adds ambgnt5c, ambgnt3c alerts for CDS features that start/end with one or more Ns, non-fatal by default
  • adds ambgnt5f, ambgnt3f alerts for non-CDS features that start/end with one or more Ns, non-fatal by default
  • adds ftskipfl alert for rare case that >= 1 per-feature fatal alerts exist, but none of those features are included in the output feature table
  • adds deletinf alert for a sequence that has a feature with a complete segment deleted, fatal by default
  • adds deletins alert for a sequence that has a complete feature deleted, fatal by default
  • sequence names must now be 50 characters or less to be consistent with GenBank submission rules, adds --noseqnamemax option to relax this restriction (github issue #12)
  • fixes bug with deleted features causing v-annotate.pl to fail (github issue #21)
  • fixes bug with -s and duplicate blastn hits in models with repetitive regions (github issue #13)

VADR 1.1 release (May 2020): Major update

  • adds -s option for accelerating v-annotate.pl, using fixed alignment regions derived from blastn, mainly useful for SARS-CoV-2 annotation
  • adds -r option for v-annotate.pl for replacing Ns with expected nucleotides where possible, motivated by the high fraction of Ns in many SARS-CoV-2 sequences
  • adds --hmmer option for profile HMM based protein validation
  • makes fsthicnf alert fatal by default
  • adds ambgnt5s and ambgnt3s alerts, non-fatal by default
  • several bug fixes and other less significant new options
  • additional tests

VADR 1.0.6 release (April 2020): Bug fix release

  • protein_id qualifiers now accession-only unless --forceid used.
  • --execname option added to v-{annotate,build,test}.pl

VADR 1.0.5 release (March 2020): Minor update

  • adds protein_id qualifiers to CDS and mat_peptide features in output feature tables.

VADR 1.0.4 release (March 2020): Bug fix release

  • fixes installation test (do-install-tests-{local,parallel}.sh), which failed in 1.0.3.

VADR 1.0.3 release (March 2020): Minor update

  • Adds frameshift detection capability with associated fsthicnf and fstlowcnf alerts, as non-fatal alerts.
  • Several bug fixes to previously untested code related to negative strand and multisegment features.
  • More tests (entoy100a model).

VADR 1.0.2 release (January 2020): Bug fix release

  • Minor update: CDS features that are 5' truncated but not 3' truncated are now inspected for a valid stop codon (mutendcd alert reported if stop is invalid). Also, adds more informative error message for mutstart alerts.

VADR 1.0.1 release (December 2019): Minor update

  • Minor update: adds --nomisc option to v-annotate.pl for preventing conversion of some types of features to misc_feature if they have fatal alerts.

VADR 1.0 release (November 2019): First major release

For more information, see the git log for the develop branch.