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_1_length_55421_cov_26.1146_ID_4744408 (54221bp)
Best alignment score: 36102.0 (LEN: 36102, 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: 53970.5, number of alignments: 2, unaligned bases: 0
		This contig is misassembled.
			Excluding internal overlap of size 1 between Alignment 1 and 2: 41879 59998 | 18120 1 | 18120 18120 --> 41880 59998 | 18119 1 | 18119 18119
			Real Alignment 1: 41880 59998 | 18119 1 | 18119 18119 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_1_length_55421_cov_26.1146_ID_4744408
			  Extensive misassembly (relocation, inconsistency = 1200) between these two alignments
			Real Alignment 2: 4578 40679 | 54221 18120 | 36102 36102 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_1_length_55421_cov_26.1146_ID_4744408

CONTIG: NODE_7_length_3447_cov_44.4894_ID_2480336 (3447bp)
Best alignment score: 3431.8 (LEN: 3447, IDY: 99.56), Total number of alignments: 1
		One align captures most of this contig: 3 3449 | 3447 1 | 3447 3447 | 99.56 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_7_length_3447_cov_44.4894_ID_2480336

CONTIG: NODE_29_length_219_cov_25.5122_ID_8985538 (763bp)
Best alignment score: 219.0 (LEN: 219, IDY: 100.00), Total number of alignments: 3
			Looking for the best set of alignments (out of 3 total alignments)
			The best set is below. Score: 432.0, number of alignments: 3, unaligned bases: 211
		This contig is misassembled.
			Real Alignment 1: 4394 4612 | 1 219 | 219 219 | 100.0 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_29_length_219_cov_25.5122_ID_8985538
			  Extensive misassembly (relocation, inconsistency = -1426) between these two alignments
			Real Alignment 2: 3395 3573 | 428 605 | 179 178 | 91.62 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.fa NODE_29_length_219_cov_25.5122_ID_8985538
			  Extensive misassembly (relocation, inconsistency = -1860) between these two alignments
			Real Alignment 3: 1717 1871 | 609 763 | 155 155 | 96.77 | meta_ref_2_Lactobacillus_delbrueckii_bulgaricus_ATCC_BAA-365_32_60k.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_2/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_2/contigs_reports/minimap_output/meta_contigs_2.used_snps

Results:
	Local Misassemblies: 0
	Misassemblies: 3
		Relocations: 3
		Translocations: 0
		Inversions: 0
	Scaffold gap extensive misassemblies: 0
	Scaffold gap local misassemblies: 0
	Misassembled Contigs: 2
	Misassembled Contig Bases: 54984
	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: 57976
	Raw Aligned Bases in Assembly: 58220
	Total Aligned Bases in Assembly (with "Extras"): 58220

	SNPs: 34
	Insertions: 0
	Deletions: 1