checking for <4 taxa to stop raxml from crashing

scripts/set_processPooledVcf.pl

@@ -56,28 +56,36 @@ sub main{
   system("pairwiseDistances.pl --numcpus $$settings{numcpus} < $filteredAlignment | sort -k3,3n | tee $pairwise | pairwiseTo2d.pl > $pairwiseMatrix");
   die if $?;
 
-        # Process a resulting VCF: make an MSA; remove uninformative sites; find pairwise distances;
-        # find Fst; make a tree; calculate the eigenvector
+  my $numSamples=`grep -c ">" $filteredAlignment` + 0;
+  die "ERROR: could not count the number of samples in $filteredAlignment" if $?;
+
+  # Process a resulting VCF: make an MSA; remove uninformative sites; find pairwise distances;
+  # find Fst; make a tree; calculate the eigenvector
   my $indexCase="$$settings{prefix}.eigen.tsv";
   system("set_indexCase.pl $pairwise | sort -k2,2n > $indexCase");
   die "ERROR with set_indexCase.pl" if $?;
 
   # TODO Fst
 
-  # RAxML puts everything into the CWD and so we have to work around that.
-  system("cp $filteredAlignment $$settings{tempdir}/; cd $$settings{tempdir}; launch_raxml.sh -n $$settings{numcpus} $filteredAlignment suffix");
-  die "ERROR with launch_raxml.sh" if $?;
-  for (qw(RAxML_bestTree RAxML_bipartitionsBranchLabels RAxML_bipartitions RAxML_bootstrap RAxML_info)){
-    system("mv -v $$settings{tempdir}/$_.suffix $$settings{prefix}.$_");
-    die "ERROR: could not move $$settings{tempdir}/$_.suffix: $!" if $?;
-  }
+  # Can work with trees if there are enough samples
+  if($numSamples >= 4){
+    # RAxML puts everything into the CWD and so we have to work around that.
+    system("cp $filteredAlignment $$settings{tempdir}/; cd $$settings{tempdir}; launch_raxml.sh -n $$settings{numcpus} $filteredAlignment suffix");
+    die "ERROR with launch_raxml.sh" if $?;
+    for (qw(RAxML_bestTree RAxML_bipartitionsBranchLabels RAxML_bipartitions RAxML_bootstrap RAxML_info)){
+      system("mv -v $$settings{tempdir}/$_.suffix $$settings{prefix}.$_");
+      die "ERROR: could not move $$settings{tempdir}/$_.suffix: $!" if $?;
+    }
 
-  # TODO: reroot the tree
-  #rerootLongestBranch("$$settings{prefix}.RAxML_bipartitions",$settings);
+    # TODO: reroot the tree
+    #rerootLongestBranch("$$settings{prefix}.RAxML_bipartitions",$settings);
 
-  # Get combined distance statistics on the tree
-  system("cladeDistancesFromTree.pl -t $$settings{prefix}.RAxML_bipartitions -p $$settings{prefix}.pairwise.tsv --outprefix $$settings{prefix}");
-  die "ERROR with cladeDistancesFromTree.pl" if $?;
+    # Get combined distance statistics on the tree
+    system("cladeDistancesFromTree.pl -t $$settings{prefix}.RAxML_bipartitions -p $$settings{prefix}.pairwise.tsv --outprefix $$settings{prefix}");
+    die "ERROR with cladeDistancesFromTree.pl" if $?;
+  } else {
+    logmsg "WARNING: only $numSamples samples are in the alignment; skipping tree-building.";
+  }
 
   return 0;
 }