Rescue systemu errors

Dockerfile

@@ -11,9 +11,9 @@ RUN mv mafft-linux64/* .
 
 RUN gem install bundler
 
-RUN \curl -sSL https://github.com/mooreryan/pasv/archive/v1.1.5.tar.gz \
+RUN \curl -sSL https://github.com/mooreryan/pasv/archive/v1.1.6.tar.gz \
     | tar -v -C /home -xz
-RUN mv /home/pasv-1.1.5 /home/pasv
+RUN mv /home/pasv-1.1.6 /home/pasv
 
 WORKDIR /home/pasv
 RUN bundle install

pasv

@@ -14,7 +14,7 @@ PasvLib.extend PasvLib::Utils
 Time.extend PasvLib::CoreExtensions::Time
 Process.extend PasvLib::CoreExtensions::Process
 
-PIPELINE_VERSION = "1.1.5"
+PIPELINE_VERSION = "1.1.6"
 VERSION_BANNER = %Q{  # Pipeline version: #{PIPELINE_VERSION}
   # Lib version: #{PasvLib::VERSION}
   # Copyright 2017 - 2018 Ryan Moore
@@ -190,6 +190,7 @@ until unfinished_queries.empty?
       cmd = "#{opts[:aligner]} #{opts[:alignment_parameters]} #{io_str}"
 
       begin
+        # This can raise either AbortIf::Exit or SystemUniversal::Error
         Process.run_it! cmd
         recs = {}
         query_rec = []
@@ -244,9 +245,9 @@ until unfinished_queries.empty?
           # map() will return this
           [:not_done, [query_head, ungapped_query_seq, query_idx]]
         end
-      rescue AbortIf::Exit
+      rescue AbortIf::Exit, SystemUniversal::Error => e
         # it failed so mark it and keep going
-        AbortIf.logger.error { "Query #{query_idx} failed.  Will try again later." }
+        AbortIf.logger.error { "Query #{query_idx} failed with error #{e.inspect}.  Will try again later." }
 
         FileUtils.rm aln_infile if File.exist? aln_infile
         FileUtils.rm aln_outfile if File.exist? aln_outfile
@@ -258,7 +259,7 @@ until unfinished_queries.empty?
   rescue Parallel::DeadWorker => e
     # In case anything goes wrong outside of the mafft alignment to
     # kill the worker.
-    AbortIf::logger.error { "There was an error in one or more of the worker threads." }
+    AbortIf::logger.error { "There was an error in one or more of the worker threads. (#{e.inspect})" }
     abort
   end