Write tree commands to details log

PanACoTA/tree_module/fasttree_func.py

@@ -113,7 +113,7 @@ def run_fasttree(alignfile, boot, outdir, model, quiet):
     logfile = os.path.join(outdir, align_name + ".fasttree.log")
     treefile = os.path.join(outdir, align_name + ".fasttree_tree.nwk")
     cmd = f"FastTreeMP -nt {model} -noml -nocat {bootinfo} -log {logfile} {alignfile}"
-    logger.info("Fasttree command: " + cmd)
+    logger.details("Fasttree command: " + cmd)
     if quiet:
         fnull = open(os.devnull, 'w')
     else:
@@ -121,5 +121,4 @@ def run_fasttree(alignfile, boot, outdir, model, quiet):
     stdout = open(treefile, "w")
     error = ("Problem while running Fasttree. See log file ({}) for "
              "more information.").format(logfile)
-    logger.details(cmd)
     utils.run_cmd(cmd, error, stdout=stdout, eof=True, logger=logger, stderr=fnull)

PanACoTA/tree_module/iqtree_func.py

@@ -126,12 +126,11 @@ def run_tree(alignfile, boot, outdir, quiet, threads, **kwargs):
         prefix = f"--prefix {treefile}"
     cmd = (f"{soft} -s {alignfile} {threadinfo} -m {model} {mem_info} {bootinfo} {wb_info} "
     	   f"{seqtype} {prefix} -quiet {fast}")
-    logger.info("IQtree command: " + cmd)
+    logger.details("IQtree command: " + cmd)
     if quiet:
         fnull = open(os.devnull, 'w')
     else:
         fnull = None
     error = (f"Problem while running IQtree. See log file ({logfile}) for "
              "more information.")
-    logger.details(cmd)
     utils.run_cmd(cmd, error, eof=True, logger=logger, stderr=fnull)