ml tree is updated for new proteins

Author: Emrah Akkoyun

workflow/envs/raxml-ng.yml

@@ -1,5 +1,7 @@
-name: raxml-ng 
+name: raxml-ng
 channels:
   - bioconda
+  - conda-forge 
 dependencies:
   - raxml-ng = 1.0.2 
+  - openmpi = 4.0.5 

workflow/scripts/raxml-ng.sh

@@ -10,6 +10,12 @@ tree_num=$6
 # recommended # threads
 thread_num=`raxml-ng --parse --msa $trimmed_msa --model $raxml_model --nofile|grep "Recommended number of threads"|awk -F: {'print $2'}| xargs`
 echo "Recommended number of thread: $thread_num"
+echo "Number of CPUs on the allocated nodes: $SLURM_CPUS_ON_NODE" 
+
+if (("$thread_num" <= "$SLURM_CPUS_ON_NODE")); then
+	folder=`dirname $output_tree`
+	raxml-ng  --msa $trimmed_msa --data-type AA --model $raxml_model --prefix $folder/$raxml_out_name --seed $raxml_seed --threads $thread_num --tree rand{$tree_num} pars{$tree_num}
+else
+	echo "ERROR: Required CPU number: $thread_num. Assign more CPUs for the next submission"
+fi
 
-folder=`dirname $output_tree`
-raxml-ng  --msa $trimmed_msa --data-type AA --model $raxml_model --prefix $folder/$raxml_out_name --seed $raxml_seed --threads $thread_num --tree rand{$tree_num} pars{$tree_num}