diff --git a/rules/phlanprof.smk b/rules/phlanprof.smk index 150b1365797d5b4a047c2b2395dede62cce9281a..d25dac313be53b6b2d88510317600ce87a1a2784 100644 --- a/rules/phlanprof.smk +++ b/rules/phlanprof.smk @@ -305,7 +305,8 @@ rule strphlan_clade_profiling: {input.samples_metadata} \ {output.clade_result_dir}/{wildcards.clade}.fasta \ {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_1.png \ - {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_2.png; fi') &>{log} + {output.clade_result_dir}/RAxML_bestTree.{wildcards.clade}.tree_2.png || \ + echo "strainphlan_ggtree.R halted with non-zero exit status!"; fi') &>{log} ''' def aggregate_clade_profiles(wildcards):