soedinglab/MMseqs2: MMseqs2 Release 13-45111

New Taxonomy Workflow (new feature and breaking change)

We introduce a new taxonomy workflow for assigning taxonomic labels to nucleotide sequences by searching against protein reference databases. For details see:

Mirdita M, Steinegger M, Breitwieser F, Söding J, Levy Karin E: Fast and sensitive taxonomic assignment to metagenomic contigs. bioRxiv, doi: 10.1101/2020.11.27.401018 (2020)

The nucleotide-to-protein taxonomic assignment is now much faster and is optimized towards annotation of contigs. If you use MMseqs2 taxonomy to assign taxonomic labels to short reads, consider using the --orf-filter 0 parameter to disable the new filter stage as it can reject too many short query sequences. MMseqs2 is still considerably faster with this parameter set.

As our nucleotide-to-nucleotide taxonomic assignment does not support the 2bLCA assignment mode for stable lowest-common-ancestor computation, we previously set MMseqs2 to perform LCA assignment by top-hit (--lca-mode 4) as default. Approximate (see manuscript) 2bLCA is now again the default and we automatically switch to top-hit if given nucleotide-to-nucleotide input.

• --slice-search in now called --exhaustive-search
• Unify --compress --summarize --omit-consensus (in result2msa) to --msa-format-mode

• Add GTDB and CDD to databases downloader #410
• Add nrtotaxmapping to create taxonomy mapping from NR
• Add unpackdb to split a database into separate files #406
• Add majoritylca module for majority voting based taxonomy from alignment results
• Add cpdb and lndb
• Taxonomy information is stored in binary format (a single db_taxonomy file, instead of db_{named,nodes,merged}.dmp,db_mapping) to speed up read-in. Old format is still supported.
• --exhaustive-search is usable with ungapped alignments (--alignment-mode 4)
• Allow sequence/result database input in taxonomyreport #401/#408
• msa2profile/result can skip the first sequence with --skip-query
• createtaxdb can create a taxdb by mapping through .source in addition to .lookup (--tax-mapping-mode 1)
• splitsequence can create a sequence database with original headers
• align can return short cluster format if only identifiers are required --alignment-output-mode
• tar2db can be used multi-threaded if input allows (e.g. .tar containing .gz files)
• Encode species names in taxonomy blocklist to make sure we don't block random nodes in * e.g. GTDB)
• Split non-index parts over additional files in split index case to reduce peak memory use
• proteinaln2nucl can now compute scores and e-values
• createdb can create a sequence database from a database containing fasta files (e.g. created by tar2db)
• Add MMSEQS_FORCE_MERGE environment variable to force generating fully merged databases
• Improved many descriptions, warnings and error messages

• Fix filterresult off by one issue removing wrong sequences
• Fix addtaxonomy always crashing due to invalid check #355
• Reduce numbers of calls to posix_memalign to fix lock contention on macOS
• extractorfs doesn't flood warnings due to short sequences anymore
• expand2profile --pca is correctly set to 0
• msa2profile always copies .lookup/source files instead of symlinking
• Clustering of clustering input would not work with set-cover or connected-component
• Short circuit --cluster-reassign if nothing can be reassigned
• Fix temporary files not getting removed in linclust/cluster with --remove-tmp--files
• Fix kmermatcher setting user k-mer pattern in auto k-mer selection and breaking
• Krona taxonomyreport was not working if no sequence was unclassified
• Make Matcher::resultToBuffer buffer sizes consistent (could crash with very long backtraces, needs further refactoring)
• Fix multiple locations where Util::checkAllocation could never be called as it would have crashed before
• Whitespace containing parameters do not break workflows anymore (e.g. passing whitespaces to --sub-mat)
• taxonomyreport and addtaxonomy parameter were not adjustable in easy-taxonomy
• E-value parameters are now correctly parsed as doubles instead of floats #379
• Add symlinks to splitdb #376
• Increase maximum number of open files in DBReader
• Include file size and modified date of inputs in temporary file hash calculation #372
• --cov-mode 5 was not working #371
• Database downloader deals correctly with redirects now
• result2profile could crash if target database contained much longer sequences than query database
• Stop symlinking header database (and other ancillary files) in filterresult

• Add vector of predefined substitution matrices to add additional matrices in subprojects
• Don't create false _has_{builtin,attribute} macros (see https://github.com/simd-everywhere/simde/issues/691#issuecomment-753686859)
• Add USE_SYSTEM_ZSTD cmake flag to use system provided zstd #411
• Replace texlive with tectonic for faster/prettier userguide
• Add more instructions to simd.h
• Add initial fixes to get MMseqs2 working on s390x (work in progress)
• Prebuilt macOS binary is now a Universal Mac Binary supporting SSE, AVX and Apple Silicon NEON
• Build ARM64/PPC64LE binaries by cross-compiling
• Add missing licenses and READMEs for vendored libraries #403
• Update ALP to 1.98
• Update xxhash to v0.8.0