miga-base 1.3.8.2 → 1.3.9.0

data/lib/miga/remote_dataset/download.rb

@@ -6,28 +6,40 @@ class MiGA::RemoteDataset
   # Class-level
   class << self
     ##
-    # Download data from the +universe+ in the database +db+ with IDs +ids+ and
-    # in +format+. If passed, it saves the result in +file+. Additional
-    # parameters specific to the download method can be passed using +extra+.
-    # Returns String. The +obj+ can also be passed as MiGA::RemoteDataset or
-    # MiGA::Dataset.
-    def download(universe, db, ids, format, file = nil, extra = [], obj = nil)
-      ids = [ids] unless ids.is_a? Array
-      getter = @@UNIVERSE[universe][:dbs][db][:getter] || :download
-      method = @@UNIVERSE[universe][:method]
-      opts = {
-        universe: universe,
-        db: db,
-        ids: ids,
-        format: format,
-        file: file,
-        extra: extra,
-        obj: obj
+    # Return hash of options used internally for the getter methods, including
+    # by +download+. The prepared request is for data from the +universe+ in the
+    # database +db+ with IDs +ids+ and in +format+. If passed, it saves the
+    # result in +file+. Additional parameters specific to the download method
+    # can be passed using +extra+. The +obj+ can also be passed as
+    # MiGA::RemoteDataset or MiGA::Dataset
+    def download_opts(
+          universe, db, ids, format, file = nil, extra = {}, obj = nil)
+      universe_hash = @@UNIVERSE[universe]
+      database_hash = universe_hash.dig(:dbs, db)
+      getter = database_hash[:getter] || :download
+      action = database_hash[:method] || universe_hash[:method]
+
+      {
+        universe: universe,  db:   db,    ids: ids.is_a?(Array) ? ids : [ids],
+        format:   format,    file: file,  obj: obj,
+        extra:    (database_hash[:extra] || {}).merge(extra),
+        _fun:     :"#{getter}_#{action}"
       }
-      doc = send("#{getter}_#{method}", opts)
+    end
+
+    ##
+    # Returns String. The prequired parameters (+params+) are identical to those
+    # of +download_opts+ (see for details)
+    def download(*params)
+      opts = download_opts(*params)
+      doc = send(opts[:_fun], opts)
+
       unless opts[:file].nil?
         ofh = File.open(opts[:file], 'w')
-        ofh.print doc.force_encoding('UTF-8')
+        unless opts[:file] =~ /\.([gb]?z|tar|zip|rar)$/i
+          doc = normalize_encoding(doc)
+        end
+        ofh.print doc
         ofh.close
       end
       doc
@@ -39,9 +51,9 @@ class MiGA::RemoteDataset
     # +obj+ (mandatory): MiGA::RemoteDataset
     # +ids+ (mandatory): String or Array of String
     # +file+: String, passed to download
-    # +extra+: Array, passed to download
+    # +extra+: Hash, passed to download
     # +format+: String, passed to download
-    def ncbi_asm_rest(opts)
+    def ncbi_asm_get(opts)
       url_dir = opts[:obj].ncbi_asm_json_doc&.dig('ftppath_genbank')
       if url_dir.nil? || url_dir.empty?
         raise MiGA::RemoteDataMissingError.new(
@@ -58,8 +70,8 @@ class MiGA::RemoteDataset
 
     ##
     # Download data from NCBI GenBank (nuccore) database using the REST method.
-    # Supported +opts+ (Hash) are the same as #download_rest and #ncbi_asm_rest.
-    def ncbi_gb_rest(opts)
+    # Supported +opts+ (Hash) are the same as #download_rest and #ncbi_asm_get.
+    def ncbi_gb_get(opts)
       # Simply use defaults, but ensure that the URL can be properly formed
       o = download_rest(opts.merge(universe: :ncbi, db: :nuccore))
       return o unless o.strip.empty?
@@ -70,54 +82,83 @@ class MiGA::RemoteDataset
         File.unlink(opts[:file]) if File.exist? opts[:file]
         opts[:file] = "#{opts[:file]}.gz"
       end
-      ncbi_asm_rest(opts)
+      ncbi_asm_get(opts)
     end
 
     ##
-    # Download data using the REST method. Supported +opts+ (Hash) include:
+    # Download data using the GET method. Supported +opts+ (Hash) include:
     # +universe+ (mandatory): Symbol
-    # +db+ (mandatory): Symbol
-    # +ids+ (mandatory): Array of String
+    # +db+: Symbol
+    # +ids+: Array of String
     # +format+: String
-    # +extra+: Array
-    def download_rest(opts)
+    # +extra+: Hash
+    def download_get(opts)
       u = @@UNIVERSE[opts[:universe]]
-      url = sprintf(
-        u[:url], opts[:db], opts[:ids].join(','), opts[:format], *opts[:extra]
-      )
-      url = u[:api_key][url] unless u[:api_key].nil?
-      download_url url
+      download_uri(u[:uri][opts], u[:headers] ? u[:headers][opts] : {})
+    end
+
+    ##
+    # Download data using the POST method. Supported +opts+ (Hash) include:
+    # +universe+ (mandatory): Symbol
+    # +db+: Symbol
+    # +ids+: Array of String
+    # +format+: String
+    # +extra+: Hash
+    def download_post(opts)
+      u = @@UNIVERSE[opts[:universe]]
+      uri = u[:uri][opts]
+      payload = u[:payload] ? u[:payload][opts] : ''
+      headers = u[:headers] ? u[:headers][opts] : {}
+      net_method(:post, uri, payload, headers)
+    end
+
+    ##
+    # Download data using the FTP protocol. Supported +opts+ (Hash) include:
+    # +universe+ (mandatory): Symbol
+    # +db+: Symbol
+    # +ids+: Array of String
+    # +format+: String
+    # +extra+: Hash
+    def download_ftp(opts)
+      u = @@UNIVERSE[opts[:universe]]
+      net_method(:ftp, u[:uri][opts])
+    end
+
+    ##
+    # Redirects to +download_get+ or +download_ftp+, depending on the URI's
+    # protocol
+    def download_net(opts)
+      u = @@UNIVERSE[opts[:universe]]
+      if u[:scheme][opts] == 'ftp'
+        download_ftp(opts)
+      else
+        download_get(opts)
+      end
     end
 
     ##
     # Alias of download_rest
-    alias download_net download_rest
+    alias download_rest download_get
+
+    ##
+    # Download the given +URI+ and return the result regardless of response
+    # code. Attempts download up to three times before raising Net::ReadTimeout.
+    def download_uri(uri, headers = {})
+      net_method(:get, uri, headers)
+    end
 
     ##
     # Download the given +url+ and return the result regardless of response
     # code. Attempts download up to three times before raising Net::ReadTimeout.
-    def download_url(url)
-      doc = ''
-      @timeout_try = 0
-      begin
-        DEBUG 'GET: ' + url
-        URI.parse(url).open(read_timeout: 600) { |f| doc = f.read }
-      rescue => e
-        @timeout_try += 1
-        raise e if @timeout_try >= 3
-
-        sleep 5 # <- For: 429 Too Many Requests
-        DEBUG "RETRYING after: #{e}"
-        retry
-      end
-      doc
+    def download_url(url, headers = {})
+      download_uri(URI.parse(url), headers)
     end
 
     ##
     # Looks for the entry +id+ in +dbfrom+, and returns the linked
     # identifier in +db+ (or nil).
     def ncbi_map(id, dbfrom, db)
-      doc = download(:ncbi_map, dbfrom, id, :json, nil, [db])
+      doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
       return if doc.empty?
 
       tree = MiGA::Json.parse(doc, contents: true)
@@ -134,8 +175,34 @@ module MiGA::RemoteDataset::Download
   ##
   # Download data into +file+
   def download(file)
-    format = self.class.UNIVERSE[universe][:dbs][db][:format]
-    # MiGA::MiGA.DEBUG "download: #{universe}, #{db}, #{ids}, #{format}"
-    self.class.download(universe, db, ids, format, file, [], self)
+    self.class.download(*download_params(file))
+  end
+
+  def universe_hash
+    self.class.UNIVERSE[universe]
+  end
+
+  def database_hash
+    universe_hash.dig(:dbs, db)
+  end
+
+  def download_params(file = nil)
+    [universe, db, ids, database_hash[:format], file, {}, self]
+  end
+
+  def download_opts(file = nil)
+    self.class.download_opts(*download_params(file))
+  end
+
+  def download_uri
+    universe_hash[:uri][download_opts]
+  end
+
+  def download_headers
+    universe_hash[:headers][download_opts]
+  end
+
+  def download_payload
+    universe_hash[:payload][download_opts]
   end
 end

data/lib/miga/remote_dataset.rb

@@ -193,7 +193,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
 
     doc = MiGA::Json.parse(
       MiGA::RemoteDataset.download(
-        :gtdb, :genome, gtdb_genome, 'taxon-history', nil, ['']
+        :gtdb, :genome, gtdb_genome, 'taxon-history'
       ),
       contents: true
     )
@@ -237,15 +237,24 @@ class MiGA::RemoteDataset < MiGA::MiGA
   private
 
   def get_ncbi_taxid_from_web
-    return nil if ncbi_asm_json_doc.nil?
+    # Check first if metadata was pulled from NCBI already
+    taxid = metadata.dig(:ncbi_dataset, :organism, :tax_id)
+    return taxid if taxid
 
-    ncbi_asm_json_doc['taxid']
+    # Otherwise, try to get the Assembly JSON document
+    ncbi_asm_json_doc&.dig('taxid')
   end
 
   def get_ncbi_taxid_from_ncbi
+    # Try first from Assembly data
     return get_ncbi_taxid_from_web if db == :assembly
 
-    doc = self.class.download(:ncbi, db, ids, :gb, nil, [], self).split(/\n/)
+    # Try from previously pulled NCBI data
+    taxid = metadata.dig(:ncbi_dataset, :organism, :tax_id)
+    return taxid if taxid
+
+    # Try from GenBank document (obtain it)
+    doc = self.class.download(:ncbi, db, ids, :gb, nil, {}, self).split(/\n/)
     ln = doc.grep(%r{^\s+/db_xref="taxon:}).first
     return nil if ln.nil?
 
@@ -283,14 +292,25 @@ class MiGA::RemoteDataset < MiGA::MiGA
   end
 
   def get_type_status_ncbi_asm(metadata)
-    return metadata if ncbi_asm_json_doc.nil?
+    from_type = nil
+
+    # Try first from previously pulled NCBI metadata
+    if metadata[:ncbi_dataset]
+      from_type = metadata.dig(
+        :ncbi_dataset, :type_material, :type_display_text
+      )
+    else
+      # Otherwise, check Assembly JSON document
+      return metadata if ncbi_asm_json_doc.nil?
+
+      metadata[:suspect] = (ncbi_asm_json_doc['exclfromrefseq'] || [])
+      metadata[:suspect] = nil if metadata[:suspect].empty?
+      return metadata if metadata[:is_type] # If predefined, as in SeqCode
 
-    metadata[:suspect] = (ncbi_asm_json_doc['exclfromrefseq'] || [])
-    metadata[:suspect] = nil if metadata[:suspect].empty?
-    return metadata if metadata[:is_type] # If predefined, as in SeqCode
+      from_type = ncbi_asm_json_doc['from_type']
+      from_type = ncbi_asm_json_doc['fromtype'] if from_type.nil?
+    end
 
-    from_type = ncbi_asm_json_doc['from_type']
-    from_type = ncbi_asm_json_doc['fromtype'] if from_type.nil?
     case from_type
     when nil
       # Do nothing
@@ -316,10 +336,11 @@ class MiGA::RemoteDataset < MiGA::MiGA
     a_ctg = "#{base}.AllContigs.fna"
     File.open("#{base}.start", 'w') { |ofh| ofh.puts Time.now.to_s }
     if udb[:format] == :fasta_gz
-      download "#{l_ctg}.gz"
-      system "gzip -fd '#{l_ctg}.gz'"
+      l_ctg_gz = "#{l_ctg}.gz"
+      download(l_ctg_gz)
+      self.class.run_cmd(['gzip', '-f', '-d', l_ctg_gz])
     else
-      download l_ctg
+      download(l_ctg)
     end
     File.unlink(a_ctg) if File.exist? a_ctg
     File.open("#{base}.done", 'w') { |ofh| ofh.puts Time.now.to_s }

data/lib/miga/result/stats.rb

@@ -219,6 +219,8 @@ module MiGA::Result::Stats
 
   def compute_stats_taxonomy
     stats = {}
+    return stats unless file_path(:intax_test)
+
     File.open(file_path(:intax_test), 'r') do |fh|
       fh.gets.chomp =~ /Closest relative: (\S+) with AAI: (\S+)\.?/
       stats[:closest_relative] = $1

data/lib/miga/result/versions.rb

@@ -0,0 +1,23 @@
+require 'miga/result/base'
+
+##
+# Helper module including functions for results to handle software versions
+module MiGA::Result::Versions
+  ##
+  # Return the versions hash
+  def versions
+    self[:versions]
+  end
+
+  ##
+  # Add version information for the Software used by this result
+  def add_versions(versions)
+    versions.each { |k, v| self[:versions][k.to_sym] = v }
+  end
+
+  ##
+  # Get list of software and their versions as raw text (Markdown)
+  def versions_md
+    versions.map { |k, v| "- #{k}: #{v}" }.join("\n")
+  end
+end

data/lib/miga/result.rb

@@ -3,6 +3,7 @@
 require 'miga/result/dates'
 require 'miga/result/source'
 require 'miga/result/stats'
+require 'miga/result/versions'
 
 ##
 # The result from a task run. It can be project-wide or dataset-specific.
@@ -10,6 +11,7 @@ class MiGA::Result < MiGA::MiGA
   include MiGA::Result::Dates
   include MiGA::Result::Source
   include MiGA::Result::Stats
+  include MiGA::Result::Versions
 
   # Class-level
   class << self
@@ -151,7 +153,11 @@ class MiGA::Result < MiGA::MiGA
   ##
   # Initialize and #save empty result
   def create
-    @data = { created: Time.now.to_s, stats: {}, files: {} }
+    @data = {
+      created: Time.now.to_s,
+      stats: {}, files: {},
+      versions: { 'MiGA' => MiGA::VERSION.join('.') }
+    }
     save
   end
 

data/lib/miga/taxonomy/base.rb

@@ -6,14 +6,15 @@ class MiGA::Taxonomy < MiGA::MiGA
     ##
     # Returns cannonical rank (Symbol) for the +rank+ String
     def normalize_rank(rank)
+      return unless rank
       return rank.to_sym if @@_KNOWN_RANKS_H[rank.to_sym]
 
       rank = rank.to_s.downcase
-      return nil if rank == 'no rank'
+      return if rank == 'no rank'
 
       rank = @@RANK_SYNONYMS[rank] unless @@RANK_SYNONYMS[rank].nil?
       rank = rank.to_sym
-      return nil unless @@_KNOWN_RANKS_H[rank]
+      return unless @@_KNOWN_RANKS_H[rank]
 
       rank
     end

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 8, 2].freeze
+  VERSION = [1.3, 9, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 8, 8)
+  VERSION_DATE = Date.new(2024, 1, 22)
 
   ##
   # References of MiGA

data/scripts/assembly.bash

@@ -10,6 +10,7 @@ cd "$PROJECT/data/05.assembly"
 miga date > "$DATASET.start"
 
 # Interpose (if needed)
+interpose=no
 TF="../04.trimmed_fasta"
 b=$DATASET
 if [[ -s "$TF/${b}.2.fasta" || -s "$TF/${b}.2.fasta.gz" ]] ; then
@@ -22,6 +23,7 @@ if [[ -s "$TF/${b}.2.fasta" || -s "$TF/${b}.2.fasta.gz" ]] ; then
         gzip -cd "$TF/${b}.${s}.fasta.gz" > "${b}.${s}.tmp"
       fi
     done
+    interpose=yes
     FastA.interpose.pl "$cr" "$b".[12].tmp
     rm "$b".[12].tmp
     miga add_result -P "$PROJECT" -D "$DATASET" -r trimmed_fasta -f
@@ -62,5 +64,17 @@ FastA.length.pl "$DATASET.AllContigs.fna" | awk '$2>=1000{print $1}' \
 
 # Finalize
 miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$interpose" == "yes" ]] ; then
+    echo "=> Enveomics Collection: FastA.interpose.pl"
+    echo "version unknown"
+  fi
+)
+=> IDBA-UD
+version unknown
+VERSIONS
 

data/scripts/cds.bash

@@ -19,7 +19,7 @@ fi
 # Run Prodigal
 TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
 case "$TYPE" in
-  metagenome|virome)
+  metagenome|virome|plasmid)
     prodigal -a "${DATASET}.faa" -d "${DATASET}.fna" -o "${DATASET}.gff3" \
       -f gff -q -i "../05.assembly/${DATASET}.LargeContigs.fna" -p meta
     ;;
@@ -68,6 +68,12 @@ for ext in gff3 faa fna ; do
 done
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+=> Prodigal
+$(prodigal -v 2>&1 | grep . | perl -pe 's/^Prodigal //')
+VERSIONS
 

data/scripts/distances.bash

@@ -10,13 +10,111 @@ cd "$PROJECT/data/09.distances"
 miga date > "$DATASET.start"
 
 # Check quality
-miga stats -P "$PROJECT" -D "$DATASET" -r essential_genes --compute-and-save
-inactive=$(miga ls -P "$PROJECT" -D "$DATASET" -m inactive | cut -f 2)
-[[ "$inactive" == "true" ]] && exit
+MARKERS=$(miga ls -P "$PROJECT" -D "$DATASET" --markers \
+  | wc -l | awk '{print $1}')
+if [[ "$MARKERS" -eq "1" ]] ; then
+  miga stats -P "$PROJECT" -D "$DATASET" -r essential_genes --compute-and-save
+  inactive=$(miga ls -P "$PROJECT" -D "$DATASET" -m inactive | cut -f 2)
+  [[ "$inactive" == "true" ]] && exit
+fi
 
 # Run distances
 ruby -I "$MIGA/lib" "$MIGA/utils/distances.rb" "$PROJECT" "$DATASET"
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+fastaai=no
+aai=no
+ani=no
+blast=no
+blat=no
+diamond=no
+fastani=no
+case $(miga option -P "$PROJECT" -k haai_p) in
+  fastaai)
+    fastaai=yes
+    ;;
+  diamond)
+    diamond=yes
+    aai=yes
+    ;;
+  blast)
+    blast=yes
+    aai=yes
+    ;;
+esac
+
+case $(miga option -P "$PROJECT" -k aai_p) in
+  diamond)
+    diamond=yes
+    aai=yes
+    ;;
+  blast)
+    blast=yes
+    aai=yes
+    ;;
+esac
+
+case $(miga option -P "$PROJECT" -k ani_p) in
+  blast)
+    blast=yes
+    ani=yes
+    ;;
+  blat)
+    blat=yes
+    ani=yes
+    ;;
+  fastani)
+    fastani=yes
+    ;;
+esac
+
+
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$fastaai" == "yes" ]] ; then
+    echo "=> FastAAI"
+    fastaai version 2>&1 | perl -pe 's/.*=//'
+  fi
+)
+$(
+  if [[ "$fastani" == "yes" ]] ; then
+    echo "=> FastANI"
+    fastANI --version 2>&1 | grep . | perl -pe 's/^version //'
+  fi
+)
+$(
+  if [[ "$aai" == "yes" ]] ; then
+    echo "=> Enveomics Collection: aai.rb"
+    aai.rb --version 2>&1 | perl -pe 's/.*: //'
+  fi
+)
+$(
+  if [[ "$ani" == "yes" ]] ; then
+    echo "=> Enveomics Collection: ani.rb"
+    ani.rb --version 2>&1 | perl -pe 's/.*: //'
+  fi
+)
+$(
+  if [[ "$blast" == "yes" ]] ; then
+    echo "=> NCBI BLAST+"
+    blastp -version 2>&1 | tail -n 1 | perl -pe 's/.*: blast //'
+  fi
+)
+$(
+  if [[ "$blat" == "yes" ]] ; then
+    echo "=> BLAT"
+    blat 2>&1 | head -n 1 | perl -pe 's/.* v\. //' | perl -pe 's/ fast .*//'
+  fi
+)
+$(
+  if [[ "$diamond" == "yes" ]] ; then
+    echo "=> Diamond"
+    diamond --version 2>&1 | perl -pe 's/^diamond version //'
+  fi
+)
+VERSIONS
+

data/scripts/essential_genes.bash

@@ -70,4 +70,17 @@ fi
 
 # Finalize
 miga date > "${DATASET}.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+=> Enveomics Collection: HMM.essential.rb
+$(HMM.essential.rb --version 2>&1 | perl -pe 's/.*: //')
+$(
+  if [[ "$NOMULTI" -eq "1" ]] ; then
+    echo "=> FastAAI"
+    fastaai version 2>&1 | perl -pe 's/.*=//'
+  fi
+)
+VERSIONS
+

data/scripts/mytaxa.bash

@@ -15,7 +15,7 @@ if [[ "$MIGA_MYTAXA" == "no" ]] ; then
     > "$DATASET.nomytaxa.txt"
 else
   # Check type of dataset
-  MULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --multi \
+  MULTI=$(miga ls -P "$PROJECT" -D "$DATASET" --multi \
     | wc -l | awk '{print $1}')
   if [[ "$MULTI" -eq "1" ]] ; then
     # Check requirements
@@ -98,5 +98,20 @@ else
 fi
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$MIGA_MYTAXA" != "no" && "$MULTI" -eq "1" ]] ; then
+    echo "=> MyTaxa"
+    MyTaxa | grep Version: | perl -pe 's/.*: //'
+    echo "=> Diamond"
+    diamond --version 2>&1 | perl -pe 's/^diamond version //'
+    echo "=> Krona"
+    ktImportText | head -n 2 | tail -n 1 | awk '{ print $3 }'
+  fi
+)
+VERSIONS
+

data/scripts/mytaxa_scan.bash

@@ -14,7 +14,7 @@ if [[ "$MIGA_MYTAXA" == "no" ]] ; then
     > "$DATASET.nomytaxa.txt"
 else
   # Check type of dataset
-  NOMULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --no-multi \
+  NOMULTI=$(miga ls -P "$PROJECT" -D "$DATASET" --no-multi \
     | wc -l | awk '{print $1}')
   if [[ "$NOMULTI" -eq "1" ]] ; then
     # Check requirements
@@ -97,5 +97,18 @@ else
 fi
 
 # Finalize
-miga date > "$DATASET.done"
-miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f
+miga date > "${DATASET}.done"
+cat <<VERSIONS \
+  | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
+=> MiGA
+$(miga --version)
+$(
+  if [[ "$MIGA_MYTAXA" != "no" && "$NOMULTI" -eq "1" ]] ; then
+    echo "=> MyTaxa"
+    MyTaxa | grep Version: | perl -pe 's/.*: //'
+    echo "=> Diamond"
+    diamond --version 2>&1 | perl -pe 's/^diamond version //'
+  fi
+)
+VERSIONS
+