update

Author: sinamajidian

FastOMA.nf

@@ -62,6 +62,7 @@ process omamer_run{
 
 
 process infer_roothogs{
+    cpus  10      // useful for linclust
     time {15.h}    // including linclust
     memory {200.GB}
     publishDir = [

FastOMA/_utils_roothog.py

@@ -495,8 +495,8 @@ def collect_unmapped_singleton(rhogs_prots, unmapped,prot_recs_all,unmapped_sing
 
 
 def run_linclust(fasta_to_cluster="singleton_unmapped.fa"):
-    num_threads = 5 # /work/FAC/FBM/DBC/cdessim2/default/smajidi1/software/miniconda/envs/fastoma/bin/
-    command_clust = "mmseqs easy-linclust --threads " + str(
+    num_threads = 10 # todo how to assign more cpu for this step
+    command_clust = _config.mmseqs_executable_path +" easy-linclust --threads " + str(
         num_threads) + " " + fasta_to_cluster + " singleton_unmapped tmp_linclust"
 
     logger_hog.debug("linclust rooting started" + command_clust)

FastOMA/check_fastoma_input.py

@@ -146,7 +146,7 @@ def add_internal_node_prune(species_tree,species_names):
                     node.name=node_name_new
 
                 node_names.add(node.name)
-                logger_hog.debug("The internal node name has special chars " + node_name + " which is changed to " + node.name)
+                logger_hog.debug("The internal node name has special chars or repeated " + node_name + " which is changed to " + node.name)
             else:
                 node_names.add(node_name)