diff --git a/quast_libs/reads_analyzer.py b/quast_libs/reads_analyzer.py index 3f504d5ee7..5b4362ba3d 100644 --- a/quast_libs/reads_analyzer.py +++ b/quast_libs/reads_analyzer.py @@ -208,15 +208,14 @@ def run_processing_reads(main_ref_fpath, meta_ref_fpaths, ref_labels, reads_fpat if is_non_empty_file(physical_cov_fpath): logger.info(' Using existing physical coverage file: ' + physical_cov_fpath) else: - logger.info(' Will not calculate coverage (--no-icarus or --space-efficient is specified)') + logger.info(' Will not calculate coverage (--fast or --no-html, or --no-icarus, or --space-efficient is specified)') cov_fpath = None physical_cov_fpath = None if (is_non_empty_file(bed_fpath) or qconfig.no_sv) and \ - (qconfig.space_efficient or (is_non_empty_file(cov_fpath) and is_non_empty_file(physical_cov_fpath))): + (not qconfig.create_icarus_html or (is_non_empty_file(cov_fpath) and is_non_empty_file(physical_cov_fpath))): return bed_fpath, cov_fpath, physical_cov_fpath logger.info(' ' + 'Pre-processing reads...') - logger.info(' ' + 'Logging to %s...' % err_path) correct_chr_names = None if is_non_empty_file(sam_fpath): logger.info(' Using existing SAM-file: ' + sam_fpath)