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issue #420 catching print out from versions and alias ordering issue
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aineniamh committed Apr 8, 2022
1 parent cd4157b commit a1c2896
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions pangolin/command.py
Original file line number Diff line number Diff line change
Expand Up @@ -142,9 +142,6 @@ def main(sysargs = sys.argv[1:]):

# Parsing analysis mode flags to return one of 'usher' or 'pangolearn'
config[KEY_ANALYSIS_MODE] = set_up_analysis_mode(args.analysis_mode, config[KEY_ANALYSIS_MODE])
print(green(f"****\nPangolin running in {config[KEY_ANALYSIS_MODE]} mode.\n****"))
if config[KEY_ANALYSIS_MODE] == "scorpio":
print(cyan(f"Warning: in `scorpio` mode only variants of concern (VOCs) defined in constellations can be assigned. `Version` column corresponds to constellation_version.\n"))

snakefile = get_snakefile(thisdir,config[KEY_ANALYSIS_MODE])

Expand All @@ -159,6 +156,9 @@ def main(sysargs = sys.argv[1:]):
# by allowing query to accept 0 to many arguments

print(green(f"****\nPangolin running in {config[KEY_ANALYSIS_MODE]} mode.\n****"))
if config[KEY_ANALYSIS_MODE] == "scorpio":
print(cyan(f"Warning: in `scorpio` mode only variants of concern (VOCs) defined in constellations can be assigned. `Version` column corresponds to constellation_version.\n"))

print_ram_warning(config[KEY_ANALYSIS_MODE])

# setup outdir and outfiles
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