diff --git a/PanACoTA/tree_module/fasttree_func.py b/PanACoTA/tree_module/fasttree_func.py index e761204cef109f1308c0b264e07fa712958bcdc6..47665301696601e264406dd740785ebdc0d6d73a 100755 --- a/PanACoTA/tree_module/fasttree_func.py +++ b/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) diff --git a/PanACoTA/tree_module/iqtree_func.py b/PanACoTA/tree_module/iqtree_func.py index 73d4ad8511e7861f381b5de7f473598588a4639d..980f0ab68eb901fad8be86d96640951e2f9df279 100644 --- a/PanACoTA/tree_module/iqtree_func.py +++ b/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)