Aligning contigs to reference...
	Aligning contigs to the reference
Filtering alignments...
Parsing coords...
Loading reference...
	Loaded [meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa]
	Total Regions: 1
	Total Region Length: 59999
Analyzing contigs...
CONTIG: NODE_8_length_182_cov_2.81102 (1152bp)
Best alignment score: 638.0 (LEN: 638, IDY: 100.00), Total number of alignments: 2
			Looking for the best set of alignments (out of 2 total alignments)
			The best set is below. Score: 796.1, number of alignments: 2, unaligned bases: 336
		This contig is misassembled.
			Real Alignment 1: 3395 3573 | 182 5 | 179 178 | 91.62 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_8_length_182_cov_2.81102
			  Scaffold gap between these two alignments, gap lengths difference (reference vs assembly) = 1020 (extensive)
			Real Alignment 2: 1717 2354 | 840 203 | 638 638 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_8_length_182_cov_2.81102

CONTIG: NODE_15_length_55106_cov_26.0999 (55106bp)
Best alignment score: 55106.0 (LEN: 55106, IDY: 100.00), Total number of alignments: 1
		One align captures most of this contig: 4893 59998 | 1 55106 | 55106 55106 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_15_length_55106_cov_26.0999

CONTIG: NODE_33_length_929_cov_25.7529 (929bp)
Best alignment score: 929.0 (LEN: 929, IDY: 100.00), Total number of alignments: 1
		One align captures most of this contig: 844 1772 | 1 929 | 929 929 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_33_length_929_cov_25.7529

CONTIG: NODE_35_length_850_cov_25.8629 (850bp)
Best alignment score: 836.0 (LEN: 850, IDY: 98.35), Total number of alignments: 1
		One align captures most of this contig: 3 852 | 1 850 | 850 850 | 98.35 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_35_length_850_cov_25.8629

CONTIG: NODE_39_length_1141_cov_25.1602 (1141bp)
Best alignment score: 1141.0 (LEN: 1141, IDY: 100.00), Total number of alignments: 1
		One align captures most of this contig: 2300 3440 | 1 1141 | 1141 1141 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_39_length_1141_cov_25.1602

Analyzing coverage...
Writing SNPs into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/minimap_output/meta_contigs_1.used_snps

Analysis is finished!
Founded SNPs were written into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/minimap_output/meta_contigs_1.used_snps

Results:
	Local Misassemblies: 0
	Misassemblies: 0
		Relocations: 0
		Translocations: 0
		Inversions: 0
	Scaffold gap extensive misassemblies: 1
	Scaffold gap local misassemblies: 0
	Misassembled Contigs: 0
	Misassembled Contig Bases: 0
	Misassemblies Inter-Contig Overlap ("Extra" Aligned Bases): 0
Unaligned Contigs: 0 + 0 part
Half Unaligned Contigs with Misassemblies: 0
Unaligned Bases in Fully and Partially Unaligned Contigs: 0

Ambiguously Mapped Contigs: 0
Total Bases in Ambiguously Mapped Contigs: 0
"Extra" Aligned Bases in Ambiguously Mapped Contigs: 0
Note that --allow-ambiguity option was set to "one" and only first alignment per each of these contigs was used (there is no "extra" aligned bases).

	Covered Bases in Reference: 58677
	Raw Aligned Bases in Assembly: 58842
	Total Aligned Bases in Assembly (with "Extras"): 58842

	SNPs: 28
	Insertions: 0
	Deletions: 1