diff --git a/SemiBin/main.py b/SemiBin/main.py index 963dfa3..40f7428 100644 --- a/SemiBin/main.py +++ b/SemiBin/main.py @@ -841,7 +841,7 @@ def generate_sequence_features_single(logger, contig_fasta, sys.stderr.write( f"Error: abundances from strobealign-aemb can only be used when samples used above or equal to 5.\n") sys.exit(1) - + logger.info('Reading abundance information from abundance files.') abun, abun_split = generate_cov_from_abundances(abundances, output, contig_fasta, binned_length) data = kmer_whole @@ -913,9 +913,6 @@ def fasta_sample_iter(fn): sys.exit(1) must_link_threshold = get_must_link_threshold(contig_length_list) if args.ml_threshold is None else args.ml_threshold - - logger.info('Calculating coverage for every sample.') - binning_threshold = {} for sample in sample_list: binning_threshold[sample] = utils.compute_min_length( @@ -924,6 +921,7 @@ def fasta_sample_iter(fn): args.ratio) if args.bams: + logger.info('Calculating coverage for every sample.') with Pool(min(args.num_process, len(args.bams))) as pool: results = [ pool.apply_async( @@ -1008,6 +1006,7 @@ def fasta_sample_iter(fn): data_split.to_csv(ofile) if args.abundances: + logger.info('Reading abundance information from abundance files.') abun_split = generate_cov_from_abundances(args.abundances, os.path.join(args.output, 'samples'), args.contig_fasta, sep=args.separator, contig_threshold_dict=binning_threshold) abun_split = abun_split.reset_index() columns_list = list(abun_split.columns)