--- a/gene_family_aligner.xml	Mon Oct 30 09:52:00 2017 -0400
+++ b/gene_family_aligner.xml	Thu Dec 21 09:14:22 2017 -0500
@@ -47,7 +47,11 @@
         #end if
     #end if
 #end if
-&>proc.log
+&>gene_family_aligner_log.txt;
+if [[ $? -ne 0 ]]; then
+    find geneFamilyAlignments_dir -type d -maxdepth 1 -exec cp gene_family_aligner_log.txt {} \;
+    exit 1;
+fi
     ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
@@ -129,7 +133,6 @@
             <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
             <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
         </collection>
-
     </outputs>
     <tests>
         <test>