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_6_length_49658_cov_2.58581 (48458bp)
Best alignment score: 37170.6 (LEN: 37178, IDY: 99.98), Total number of alignments: 2
			Looking for the best set of alignments (out of 2 total alignments)
			The best set is below. Score: 48197.2, number of alignments: 2, unaligned bases: 0
		This contig is misassembled.
			Real Alignment 1: 43683 54962 | 11280 1 | 11280 11280 | 99.97 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_6_length_49658_cov_2.58581
			  Extensive misassembly (relocation, inconsistency = 1200) between these two alignments
			Real Alignment 2: 5305 42482 | 48458 11281 | 37178 37178 | 99.98 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_6_length_49658_cov_2.58581

CONTIG: NODE_8_length_182_cov_2.81102 (1152bp)
Best alignment score: 284.0 (LEN: 285, IDY: 99.65), Total number of alignments: 2
			Looking for the best set of alignments (out of 2 total alignments)
			The best set is below. Score: 409.0, number of alignments: 2, unaligned bases: 685
		This contig is misassembled.
		This contig is partially unaligned. (Aligned 467 out of 1132 non-N bases (41.25%))
			Warning! This contig is more unaligned than misassembled. Contig length is 1152 (number of Ns: 20) and total length of all aligns is 467
		Alignment: 3645 3826 | 182 1 | 182 182 | 100.0 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_8_length_182_cov_2.81102
		Alignment: 3112 3396 | 868 1152 | 285 285 | 99.65 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_8_length_182_cov_2.81102
		Unaligned bases: 685

CONTIG: NODE_18_length_714_cov_2.71927 (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 | 1 714 | 714 714 | 99.86 | meta_ref_1_Lactobacillus_plantarum_22_55k.fa NODE_18_length_714_cov_2.71927

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_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_1/contigs_reports/minimap_output/meta_contigs_1.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: 48458
	Misassemblies Inter-Contig Overlap ("Extra" Aligned Bases): 0
Unaligned Contigs: 0 + 1 part
Half Unaligned Contigs with Misassemblies: 1
Unaligned Bases in Fully and Partially Unaligned Contigs: 665

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: 49639
	Raw Aligned Bases in Assembly: 49639
	Total Aligned Bases in Assembly (with "Extras"): 49639

	SNPs: 13
	Insertions: 0
	Deletions: 0