sequenceserver 2.0.0.rc8 → 2.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 449efaa2619fd2c83a4116480c78ae6b892804f2f9bc23c3d074b8b0493985c5
-  data.tar.gz: 393f9da8bd3df53bff3ed3a137a5d9484ad5ec9cfa1de3c7b15c3f1a6833f092
+  metadata.gz: 25c2424857780517682276d21694f8ab0c3594772b82f08dcdca1934dcf23fd9
+  data.tar.gz: 3e27329d829825b7a3a73f14ebdecad514648381dbba914cfca6ee63564c795a
 SHA512:
-  metadata.gz: de2fdcef61a8fcdbe8907935a1f0b545219698fe9d37fcad6cd40aaa50e779010b7e91a9158eb76590baed78ce3743cdc173b664ff5d0969dfaca42eb6bd621c
-  data.tar.gz: a65c243d19435021b00a360ddfa8f617fa58e5944dd55117a8865f11dec4554a86e577cdfee3013a82638dc45de697a33156da1ba0a2fedd8e2936a7d760d5d9
+  metadata.gz: 5137bf6118ee0044a0b8d5b1979f525686d7dd1698d6c795682d39a6c9d8247410104441fb642a585e6df9a18ad827336c8f61215f9e3c8c68fb387e0b6e2f41
+  data.tar.gz: e7ec5cebd2595b3a5f90cb750ce583161821e1be22dfcf14b1ba1fbe11dda440105795ac04b06caeb456c0f78e55db50d730704db8972667ca8d7acae5170692

data/bin/sequenceserver

@@ -308,34 +308,6 @@ begin
             exit! unless set?
           end
         end
-      rescue SequenceServer::INCOMPATIBLE_BLAST_DATABASES => e
-        unless list_databases? || make_blast_databases?
-          # Print error raised.
-          puts
-          puts e
-
-          # Offer user to format the FASTA files.
-          database_dir = SequenceServer.config[:database_dir]
-          puts
-          puts <<~MSG
-            Incompatible databases can cause BLAST searches and other features of
-            SequenceServer to fail unexpectedly.
-            You can view incompatible databases and choose to reformat them below.
-            Alternatively, please remove them from databases directory.
-
-            View incompatible databases? [y/n] (Default: y).
-          MSG
-          puts
-          print '>> '
-          response = STDIN.gets.to_s.strip
-          unless response =~ /^[n]$/i
-            reformatted = SequenceServer.makeblastdb.reformat
-            exit! if reformatted.empty? && !set?
-            redo unless set?
-          else
-            exit! unless set?
-          end
-        end
       rescue SequenceServer::ENOENT,
         SequenceServer::CONFIG_FILE_ERROR,
         SequenceServer::BLAST_DATABASE_ERROR,
@@ -382,8 +354,28 @@ begin
 
       if make_blast_databases?
         if SequenceServer.makeblastdb.scan
-          SequenceServer.makeblastdb.run
-        else
+          puts
+          puts <<~MSG
+          SequenceServer has scanned your databases directory and will now offer
+          to convert FASTA files into BLAST databases. It will also offer to
+          reformat any old-format BLAST databases and those created without
+          the -parse_seqids option of makeblastdb (-parse_seqids option is
+          required for sequence retrieval to correctly work).
+
+          Note that reformatting process can be slow large BLAST databases and
+          fail if sequence identifiers are longer than 50 characters. While we
+          exepect the reformatting process to work in most other cases, things
+          can inevitably go wrong. Thus, please back up your databases before
+          reformatting and post any issues to our Google Group/GitHub so that
+          we can all learn from it.
+
+          Proceed? [y/n] (Default: y).
+          MSG
+          puts
+          print '>> '
+          response = STDIN.gets.to_s.strip
+          SequenceServer.makeblastdb.run unless response =~ /^[n]$/i
+          else
           puts "All FASTA files in #{SequenceServer.config[:database_dir]} " \
                'are formatted.'
         end

data/lib/sequenceserver/api_errors.rb

@@ -41,7 +41,11 @@ module SequenceServer
     def message
       <<~MSG
         Looks like there's a problem with one of the query sequences, selected
-        databases, or advanced parameters.
+        databases, or advanced parameters. Details of the error are included
+        below. Please ask on our
+        <a href="https://github.com/wurmlab/sequenceserver/issues" target="_blank">issue tracker</a>
+        or on our <a href="https://groups.google.com/g/sequenceserver">forum</a> if you are
+        not sure what the error message means, or if the error message is just a number.
       MSG
     end
 

data/lib/sequenceserver/blast/constants.rb

@@ -2,7 +2,7 @@
 module SequenceServer
   # Define constanst used by BLAST module.
   module BLAST
-    ERROR_LINE = /Error:\s(.*)/
+    ERROR_LINE = /Error:\s(.*)/i
 
     ALGORITHMS = %w[blastn blastp blastx tblastn tblastx].freeze
 

data/lib/sequenceserver/blast/hit.rb

@@ -21,8 +21,8 @@ module SequenceServer
       # representation.
       def to_json(*args)
         # List all attributes that we want to send to the browser.
-        properties = %i[number id accession title length score identity
-                        qcovs sciname evalue hsps links]
+        properties = %i[number id accession title length total_score
+                        qcovs sciname hsps links]
         properties.inject({}) { |h, k| h[k] = send(k); h }.to_json(*args)
       end
 
@@ -71,23 +71,12 @@ module SequenceServer
       # client.
       ###
 
-      # Returns the sum of scores of all HSPs.
-      def score
+      # Returns the sum of scores of all HSPs. Displayed in the tabular summary
+      # of hits in the HTML report. Should probably be calculated in browser?
+      def total_score
         hsps.map(&:score).reduce(:+)
       end
 
-      # Returns the sum of identity of all HSPs divided by sum of length of all
-      # HSPs (expressed as percentage).
-      def identity
-        hsps.map(&:identity).reduce(:+) * 100 / hsps.map(&:length).reduce(:+)
-      end
-
-      # Returns the minimum evalue of all HSPs of the Hit. This is shown in the
-      # tabular overview of hits in the HTML report.
-      def evalue
-        hsps.first.evalue
-      end
-
       private
 
       # Returns the report object that this hit is a part of. This is used to

data/lib/sequenceserver/blast/job.rb

@@ -60,28 +60,19 @@ module SequenceServer
 
         # Handle error. See [1].
         case exitstatus
-        when 1
-          # Error in query sequence or options.
+        when 1..2
+          # 1: Error in query sequences or options.
+          # 2: Error in BLAST databases.
           error = IO.foreach(stderr).grep(ERROR_LINE).join
           error = File.read(stderr) if error.empty?
-          fail InputError, error
-        when 2
-          fail InputError, <<~MSG
-            BLAST signalled a problem with the databases that you searched.
-
-            Most likely one or more of your databases were created using an
-            older version of BLAST. Please consider recreating the databases
-            using BLAST #{BLAST_VERSION}.
-
-            As a temporary solution, you can try searching one database at a time.
-          MSG
+          fail InputError, "(#{exitstatus}) #{error}"
         when 4
           # Out of memory. User can retry with a shorter search, so raising
           # InputError here instead of SystemError.
           fail InputError, <<~MSG
-            Ran out of memory. Please try a smaller query, or searching fewer and smaller
+            Ran out of memory. Please try a smaller query, fewer and smaller
             databases, or limiting the output by using advanced options.
-            MSG
+          MSG
         when 6
           # Error creating output files. It can't be a permission issue as that
           # would have been caught while creating job directory. But we can run
@@ -98,7 +89,7 @@ module SequenceServer
           fail SystemError, <<~MSG
             BLAST failed abruptly (exit status: #{exitstatus}). Most likely there is a
             problem with the BLAST+ binaries.
-            MSG
+          MSG
         end
       end
       # rubocop:enable Metrics/CyclomaticComplexity
@@ -155,7 +146,7 @@ module SequenceServer
       end
 
       def allowed_chars
-        /\A[a-z0-9\-_\. ']*\Z/i
+        /\A[a-z0-9\-_\. ',]*\Z/i
       end
 
       def disallowed_options
@@ -167,4 +158,4 @@ end
 
 # References
 # ----------
-# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/
+# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/ (Appendices)

data/lib/sequenceserver/blast/report.rb

@@ -25,6 +25,7 @@ module SequenceServer
       def initialize(job)
         super do
           @queries = []
+          @querydb = job.databases
         end
       end
 
@@ -42,7 +43,8 @@ module SequenceServer
         }.update(search_id: job.id,
                  submitted_at: job.submitted_at.utc,
                  imported_xml: !!job.imported_xml_file,
-                 seqserv_version: SequenceServer::VERSION).to_json
+                 seqserv_version: SequenceServer::VERSION,
+                 non_parse_seqids: !!job.databases&.any?(&:non_parse_seqids?)).to_json
       end
 
       private
@@ -80,13 +82,12 @@ module SequenceServer
       # Get database information (title and type) from job yaml or from XML.
       # Sets `querydb` and `dbtype` attributes.
       def extract_db_info(ir)
-        if job.databases.empty?
+        if @querydb.empty?
           @querydb = ir[3].split.map do |path|
             { title: File.basename(path) }
           end
           @dbtype = dbtype_from_program
         else
-          @querydb = job.databases
           @dbtype = @querydb.first.type
         end
       end
@@ -176,6 +177,7 @@ module SequenceServer
       def parse_xml(xml)
         node_to_array Ox.parse(xml).root
       rescue Ox::ParseError
+        fail 'Error parsing XML file' if job.imported_xml_file
         fail InputError, <<~MSG
           BLAST generated incorrect XML output. This can happen if sequence ids in your
           databases are not unique across all files. As a temporary workaround, you can

data/lib/sequenceserver/config.rb

@@ -99,6 +99,7 @@ module SequenceServer
       {
         host: '0.0.0.0',
         port: 4567,
+        databases_widget: 'classic',
         options: {
           blastn:  ['-task blastn', '-evalue 1e-5'],
           blastp:  ['-evalue 1e-5'],
@@ -106,7 +107,9 @@ module SequenceServer
           tblastx: ['-evalue 1e-5'],
           tblastn: ['-evalue 1e-5']
         },
-        num_threads: 1
+        num_threads: 1,
+        num_jobs: 1,
+        job_lifetime: 43200
       }
     end
   end

data/lib/sequenceserver/database.rb

@@ -19,14 +19,14 @@ module SequenceServer
   # SequenceServer will always place BLAST database files alongside input FASTA,
   # and use `parse_seqids` option of `makeblastdb` to format databases.
   Database = Struct.new(:name, :title, :type, :nsequences, :ncharacters,
-                        :updated_on) do
+                        :updated_on, :format, :categories) do
 
     extend Forwardable
 
     def_delegators SequenceServer, :config, :sys
 
     def initialize(*args)
-      args[2].downcase! # database type
+      args[2].downcase!   # type
       args.each(&:freeze)
       super
 
@@ -34,6 +34,7 @@ module SequenceServer
     end
 
     attr_reader :id
+    alias path name
 
     def retrieve(accession, coords = nil)
       cmd = "blastdbcmd -db #{name} -entry '#{accession}'"
@@ -48,10 +49,36 @@ module SequenceServer
       nil
     end
 
-    def include?(accession)
-      cmd = "blastdbcmd -entry '#{accession}' -db #{name}"
-      out, = sys(cmd, path: config[:bin])
-      !out.empty?
+    # Returns true if the database contains the given sequence id.
+    # Returns false otherwise.
+    def include?(id)
+      cmd = "blastdbcmd -entry '#{id}' -db #{name}"
+      sys(cmd, path: config[:bin]) rescue false
+    end
+
+    def v4?
+      format == '4'
+    end
+
+    def v5?
+      format == '5'
+    end
+
+    # Return true if the database was _not_ created using the -parse_seqids
+    # option of makeblastdb.
+    def non_parse_seqids?
+      return if alias?
+      case format
+      when '5'
+        (%w[nog nos pog pos] & extensions).length != 2
+      when '4'
+        (%w[nog nsd nsi pod psd psi] & extensions).length != 3
+      end
+    end
+
+    # Returns true if the database was created using blastdb_aliastool.
+    def alias?
+      (%w[nal pal] & extensions).length == 1 && extensions.count == 1
     end
 
     def ==(other)
@@ -65,6 +92,16 @@ module SequenceServer
     def to_json(*args)
       to_h.update(id: id).to_json(*args)
     end
+
+    private
+
+    def extensions
+      # The glob pattern used here is quite relaxed. This is to capture
+      # multipart databases as well. It is possible that non-blast-database
+      # extensions may also be picked. However, that shouldn't be a problem
+      # as we only check whether certain required extensions are present or not.
+      @extensions ||= Dir["#{path}*{n,p}*"].map { |p| p.split('.').last }.sort.uniq
+    end
   end
 
   # Model Database's eigenclass as a collection of Database objects.
@@ -80,9 +117,8 @@ module SequenceServer
         @collection ||= {}
       end
 
-      def collection=(databases_attrs)
-        databases_attrs.each do |db_attrs|
-          db = Database.new(*db_attrs)
+      def collection=(databases)
+        databases.each do |db|
           collection[db.id] = db
         end
       end
@@ -102,6 +138,30 @@ module SequenceServer
         collection.values
       end
 
+      def tree
+        all.each_with_object({}) do |db, data|
+          data[db.type] ||= []
+          use_parent = '#'
+          db.categories.each_with_index do |entry, index|
+            parent = index.zero? ? '#' : db.categories[0..(index - 1)].join('-')
+            use_id = db.categories[0..index].join('-')
+            element = { id: use_id, parent: parent, text: entry }
+            data[db.type] << element unless data[db.type].include?(element)
+            use_parent = use_id
+          end
+
+          data[db.type] <<
+            {
+              id: db.id,
+              parent: use_parent,
+              text: db.title,
+              icon: 'glyphicon glyphicon-file'
+            }
+
+          yield(db, data[db.type].last) if block_given?
+        end
+      end
+
       def each(&block)
         all.each(&block)
       end

data/lib/sequenceserver/job.rb

@@ -51,7 +51,7 @@ module SequenceServer
 
       # Thread pool used for running BLAST searches.
       def pool
-        @pool ||= Pool.new(SequenceServer.config[:num_threads])
+        @pool ||= Pool.new(SequenceServer.config[:num_jobs] || 1)
       end
     end
 

data/lib/sequenceserver/makeblastdb.rb

@@ -11,17 +11,6 @@ module SequenceServer
   #   makeblastdb.scan && makeblastdb.run
   #
   class MAKEBLASTDB
-    # We want V5 databases created using -parse_seqids for proper function of
-    # SequenceServer. This means each database should be comprised of at least 9
-    # files with the following extensions. Databases created by us will have two
-    # additional files with the extensions nhd and nhi, or phd and phi, due to
-    # the use of -hash_index option. Finally, multipart databases will have one
-    # additional file with the extension nal or pal.
-    REQUIRED_EXTENSIONS = {
-      'nucleotide' => %w{ndb nhr nin nog nos not nsq ntf nto}.freeze,
-      'protein' => %w{pdb phr pin pog pos pot psq ptf pto}.freeze
-    }
-
     extend Forwardable
 
     def_delegators SequenceServer, :config, :sys
@@ -70,18 +59,12 @@ module SequenceServer
     # Returns true if the databases directory contains one or more incompatible
     # databases.
     #
-    # Note that it is okay to only use V4 databases or only V5 databases. It is
+    # Note that it is okay to only use V4 databases or only V5 databases.
     # Incompatibility arises when they are mixed.
     def any_incompatible?
-      return false if @fastas_to_reformat.empty?
-      # We need to compare @fastas_to_reformat to @formatted_fastas, but the
-      # latter contains extra attributes. However, the first attribute, i.e,
-      # path is common to both and sufficient for our needs.
-      to_reformat = @fastas_to_reformat.map(&:first)
-      formatted = @formatted_fastas.map(&:first)
-      # Check that they are not equal. Using intersection operator ensures
-      # comparison even if their order differs.
-      formatted & to_reformat != formatted
+      return false if @formatted_fastas.all? { |ff| ff.v4? || ff.alias? }
+      return false if @formatted_fastas.all? { |ff| ff.v5? || ff.alias? }
+      true
     end
 
     # Runs makeblastdb on each file in `@fastas_to_format` and
@@ -109,8 +92,8 @@ module SequenceServer
       # Make the intent clear as well as ensure the program won't crash if
       # we accidentally call reformat before calling scan.
       return unless @fastas_to_reformat
-      @fastas_to_reformat.select do |path, title, type|
-        make_blast_database('reformat', path, title, type)
+      @fastas_to_reformat.select do |path, title, type, non_parse_seqids|
+        make_blast_database('reformat', path, title, type, non_parse_seqids)
       end
     end
 
@@ -120,34 +103,36 @@ module SequenceServer
     # formatted. Adds to @formatted_fastas.
     def determine_formatted_fastas
       blastdbcmd.each_line do |line|
-        path, title, type, *rest = line.split('	')
+        path, *rest = line.chomp.split("\t")
         next if multipart_database_name?(path)
-        @formatted_fastas << [path, title, type.strip.downcase, *rest]
+        rest << get_categories(path)
+        @formatted_fastas << Database.new(path, *rest)
       end
     end
 
     # Determines which FASTA files in the database directory require
     # reformatting. Adds to @fastas_to_format.
     def determine_fastas_to_reformat
-      @formatted_fastas.each do |path, title, type|
-        required_extensions = REQUIRED_EXTENSIONS[type]
-        exts = Dir["#{path}.*"].map { |p| p.split('.').last }.sort
-        next if (exts & required_extensions) == required_extensions
-
-        @fastas_to_reformat << [path, title, type]
+      @formatted_fastas.each do |ff|
+        if ff.v4? || ff.non_parse_seqids?
+          @fastas_to_reformat << [ff.path, ff.title, ff.type, ff.non_parse_seqids?]
+        end
       end
     end
 
     # Determines which FASTA files in the database directory are
     # unformatted. Adds to @fastas_to_format.
     def determine_unformatted_fastas
-      Find.find(database_dir) do |path|
+      # Add a trailing slash to database_dir - Find.find doesn't work as
+      # expected without the trailing slash if database_dir is a symlink
+      # inside a docker container.
+      Find.find(database_dir + '/') do |path|
         next if File.directory?(path)
         next unless probably_fasta?(path)
         next if @formatted_fastas.any? { |f| f[0] == path }
 
         @fastas_to_format << [path,
-          make_db_title(File.basename(path)),
+          make_db_title(path),
           guess_sequence_type_in_fasta(path)]
       end
     end
@@ -157,7 +142,7 @@ module SequenceServer
     # by `determine_formatted_fastas`.
     def blastdbcmd
       cmd = "blastdbcmd -recursive -list #{config[:database_dir]}" \
-            ' -list_outfmt "%f	%t	%p	%n	%l	%d"'
+            ' -list_outfmt "%f	%t	%p	%n	%l	%d	%v"'
       out, err = sys(cmd, path: config[:bin])
       errpat = /BLAST Database error/
       fail BLAST_DATABASE_ERROR.new(cmd, err) if err.match(errpat)
@@ -167,10 +152,11 @@ module SequenceServer
     end
 
     # Create BLAST database, given FASTA file and sequence type in FASTA file.
-    def make_blast_database(action, file, title, type)
+    def make_blast_database(action, file, title, type, non_parse_seqids = false)
       return unless make_blast_database?(action, file, type)
       title = confirm_database_title(title)
-      taxonomy = taxid_map(file) || taxid
+      extract_fasta(file) unless File.exist?(file)
+      taxonomy = taxid_map(file, non_parse_seqids) || taxid
       _make_blast_database(file, type, title, taxonomy)
     end
 
@@ -200,11 +186,10 @@ module SequenceServer
 
     # Check if a '.taxid_map.txt' file exists. If not, try getting it
     # using blastdbcmd.
-    def taxid_map(db)
+    def taxid_map(db, non_parse_seqids)
+      return if non_parse_seqids
       taxid_map = db.sub(/#{File.extname(db)}$/, '.taxid_map.txt')
-      if !File.exist?(taxid_map) || File.zero?(taxid_map)
-        extract_taxid_map(db, taxid_map)
-      end
+      extract_taxid_map(db, taxid_map) if !File.exist?(taxid_map)
       "-taxid_map #{taxid_map}" if !File.zero?(taxid_map)
     end
 
@@ -213,22 +198,23 @@ module SequenceServer
     # Using 0 as taxid is equivalent to not setting taxid for the database
     # that will be created.
     def taxid
+      default = 0
       print 'Enter taxid (optional): '
       user_response = STDIN.gets.strip
-      "-taxid #{user_response ? Integer(user_response) : 0}"
+      "-taxid #{user_response.empty? && default || Integer(user_response)}"
     rescue ArgumentError # presumably from call to Interger()
       puts 'taxid should be a number'
       retry
     end
 
     def _make_blast_database(file, type, title, taxonomy)
-      extract_fasta(file) unless File.exist?(file)
-      cmd = "makeblastdb -parse_seqids -hash_index -in #{file} " \
-            "-dbtype #{type.to_s.slice(0, 4)} -title '#{title}'" \
+      cmd = "makeblastdb -parse_seqids -hash_index -in '#{file}'" \
+            " -dbtype #{type.to_s.slice(0, 4)} -title '#{title}'" \
             " #{taxonomy}"
       out, err = sys(cmd, path: config[:bin])
       puts out.strip
       puts err.strip
+      return true
     rescue CommandFailed => e
       puts <<~MSG
         Could not create BLAST database for: #{file}
@@ -278,8 +264,16 @@ module SequenceServer
       !(db_name.match(%r{.+/\S+\.\d{2,3}$}).nil?)
     end
 
+    def get_categories(path)
+      path
+        .gsub(config[:database_dir], '') # remove database_dir from path
+        .split('/')
+        .reject(&:empty?)[0..-2] # the first entry might be '' if database_dir does not end with /
+    end
+
     # Returns true if first character of the file is '>'.
     def probably_fasta?(file)
+      return false unless file.match(/((cds)|(fasta)|(fna)|(pep)|(cdna)|(fa)|(prot)|(fas)|(genome)|(nuc)|(dna)|(nt))$/i)
       File.read(file, 1) == '>'
     end
 
@@ -288,7 +282,8 @@ module SequenceServer
     # For example:
     # Cobs1.4.proteins.fasta -> Cobs 1.4 proteins
     # S_invicta.xx.2.5.small.nucl.fa -> S invicta xx 2.5 small nucl
-    def make_db_title(db_name)
+    def make_db_title(path)
+      db_name = File.basename(path)
       db_name.tr!('"', "'")
       # removes .fasta like extension names
       db_name.gsub!(File.extname(db_name), '')

data/lib/sequenceserver/routes.rb

@@ -79,6 +79,10 @@ module SequenceServer
         options: SequenceServer.config[:options]
       }
 
+      if SequenceServer.config[:databases_widget] == 'tree'
+        searchdata.update(tree: Database.tree)
+      end
+
       # If a job_id is specified, update searchdata from job meta data (i.e.,
       # query, pre-selected databases, advanced options used). Query is only
       # updated if params[:query] is not specified.

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '2.0.0.rc8'.freeze
+  VERSION = '2.0.0'.freeze
 end

data/lib/sequenceserver.rb

@@ -5,11 +5,7 @@ require 'resolv'
 # Top level module / namespace.
 module SequenceServer
   # The default version of BLAST that will be downloaded and configured for use.
-  BLAST_VERSION = '2.10.0+'.freeze
-  # The minimum version of BLAST that SequenceServer is happy to run with. This
-  # is for compatiblity with older database formats. Users will download BLAST
-  # themselves.
-  MIN_BLAST_VERSION = '2.9.0+'.freeze
+  BLAST_VERSION = '2.12.0+'.freeze
 
   # Default location of configuration file.
   DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze
@@ -78,9 +74,9 @@ module SequenceServer
       Thread.abort_on_exception = true if development?
 
       # Now locate binaries, scan databases directory, require any plugin files.
+      load_extension
       init_binaries
       init_database
-      load_extension
 
       # The above methods validate bin dir, database dir, and path to plugin
       # files. Port and host settings don't need to be validated: if running
@@ -141,7 +137,8 @@ module SequenceServer
         puts "     -  http://#{ip_address}:#{config[:port]}"
         puts "     -  http://#{hostname}:#{config[:port]}" if hostname
         puts '   To share your setup with anyone in the world, ask your IT team'
-        puts '   for a public IP address.'
+        puts '   for a public IP address or consider the SequenceServer cloud'
+        puts '   hosting service: https://sequenceserver.com/cloud'
         puts '   To disable sharing, set :host: key in config file to 127.0.0.1'
         puts '   and restart server.'
       end
@@ -205,12 +202,19 @@ module SequenceServer
 
       makeblastdb.scan
       fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if !makeblastdb.any_formatted?
-      fail INCOMPATIBLE_BLAST_DATABASES, config[:database_dir] if makeblastdb.any_incompatible?
 
       Database.collection = makeblastdb.formatted_fastas
       Database.each do |database|
-        logger.debug("Found #{database.type} database '#{database.title}'" \
-                     " at '#{database.name}'")
+        logger.debug "Found #{database.type} database '#{database.title}' at '#{database.path}'"
+        if database.non_parse_seqids?
+          logger.warn "Database '#{database.title}' was created without using the" \
+                      ' -parse_seqids option of makeblastdb. FASTA download will' \
+                      " not work correctly (path: '#{database.path}')."
+        elsif database.v4?
+          logger.warn "Database '#{database.title}' is of older format. Mixing" \
+                      ' old and new format databases can be problematic' \
+                      "(path: '#{database.path}')."
+        end
       end
     end
 
@@ -245,7 +249,7 @@ module SequenceServer
       end
       version = out.split[1]
       fail BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE if version.empty?
-      fail BLAST_NOT_COMPATIBLE, version unless is_compatible(version, MIN_BLAST_VERSION)
+      fail BLAST_NOT_COMPATIBLE, version unless is_compatible(version, BLAST_VERSION)
     end
 
     def server_url