Aligning contigs to reference...
	Aligning contigs to the reference
Filtering alignments...
Parsing coords...
Loading reference...
	Loaded [meta_ref_1_Lactobacillus_plantarum_22_55k.fa]
	Total Regions: 1
	Total Region Length: 54999
Analyzing contigs...
CONTIG: NODE_2_length_49658_cov_2.58581_ID_2497514 (49658bp)
Best alignment score: 49648.1 (LEN: 49658, IDY: 99.98), Total number of alignments: 1
		One align captures most of this contig: 5305 54962 | 1 49658 | 49658 49658 | 99.98 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_2_length_49658_cov_2.58581_ID_2497514

CONTIG: NODE_10_length_714_cov_2.71927_ID_9333852 (714bp)
Best alignment score: 713.0 (LEN: 714, IDY: 99.86), Total number of alignments: 1
		One align captures most of this contig: 78 791 | 714 1 | 714 714 | 99.86 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_10_length_714_cov_2.71927_ID_9333852

CONTIG: NODE_29_length_219_cov_25.5122_ID_8985538 (763bp)
Best alignment score: 197.4 (LEN: 219, IDY: 90.13), Total number of alignments: 2
			Looking for the best set of alignments (out of 2 total alignments)
			The best set is below. Score: 330.4, number of alignments: 2, unaligned bases: 361
		This contig is misassembled.
			Real Alignment 1: 4643 4861 | 1 219 | 219 219 | 90.13 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_29_length_219_cov_25.5122_ID_8985538
			  Extensive misassembly (relocation, inconsistency = -1425) between these two alignments
			Real Alignment 2: 3645 3827 | 428 610 | 183 183 | 100.0 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_29_length_219_cov_25.5122_ID_8985538

Analyzing coverage...
Writing SNPs into /home/psgendb/BIRCHDEV/install/quast-5.2.0/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/minimap_output/meta_contigs_2.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_1/contigs_reports/minimap_output/meta_contigs_2.used_snps

Results:
	Local Misassemblies: 0
	Misassemblies: 1
		Relocations: 1
		Translocations: 0
		Inversions: 0
	Scaffold gap extensive misassemblies: 0
	Scaffold gap local misassemblies: 0
	Misassembled Contigs: 1
	Misassembled Contig Bases: 763
	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: 50774
	Raw Aligned Bases in Assembly: 50774
	Total Aligned Bases in Assembly (with "Extras"): 50774

	SNPs: 27
	Insertions: 4
	Deletions: 4