Logging to stdout

[mbhall88]

I used the --stdout option but noticed there is some logging that is also send to stdout. For example

^M    Finished processing 1 of 1 (100.00%) bins.
^M    Finished processing 1 of 1 (100.00%) bin metadata.
             Name  Completeness  Contamination         Completeness_Model_Used  Translation_Table_Used  Coding_Density  Contig_N50  Average_Gene_Length  Genome_Size  GC_Content  Total_Coding_Sequences  Total_Contigs  Max_Contig_Length Additional_Notes
07_final_assembly        100.00           2.07 Neural Network (Specific Model)                      11            0.85     2865049               291.18      3260218        0.38                    3174              6            2865049             None

The code does seem to specifically write to stdout for this logging

CheckM2/checkm2/predictQuality.py

Lines 367 to 371 in f0a9eb2

	if logging.root.level == logging.INFO or logging.root.level == logging.DEBUG:
	statusStr = ' Finished processing %d of %d (%.2f%%) bins.' % (
	processed, total_bins, float(processed) * 100 / total_bins)
	sys.stdout.write('\r{}'.format(statusStr))
	sys.stdout.flush()