
VALIDATION REPORT
eva-sub-cli vcligeneratedversion
❌ You requested to run the shallow validation, please run full validation before submitting the data
	---
	VCF File: input_fail.vcf
	Variant lines validated in VCF: 10000
	Entries used in Fasta: 24
	---
	VCF File: input_passed.vcf
	Variant lines validated in VCF: 10000
	Entries used in Fasta: 24
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PROJECT SUMMARY
General details about the project
	Project Title: My cool project
	Validation Date: 2023-08-31 12:34:56
	Submission Directory: /test/submission/dir
	Files mapping:
		---
		VCF File: input_fail.vcf
		Fasta File: input_fail.fa
		Analysis: A
		---
		VCF File: input_pass.vcf
		Fasta File: input_pass.fa
		Analysis: B
		---
		VCF File: input_test.vcf
		Fasta File: input_test.fa
		Analysis: could not be linked
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METADATA VALIDATION RESULTS
Ensures that required fields are present and values are formatted correctly.
For requirements, please refer to the EVA website (https://www.ebi.ac.uk/eva/?Submit-Data).
    ❌ Metadata validation check
	Full report: /path/to/metadata/metadata_spreadsheet_validation.txt
		Sheet: Files | Row:  | Column:
		Error: Sheet "Files" is missing
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		Sheet: Project | Row: 2 | Column: Project Title
		Error: Column "Project Title" is not populated
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		Sheet: Project | Row: 2 | Column: Description
		Error: Column "Description" is not populated
		---
		Sheet: Project | Row: 2 | Column: Tax ID
		Error: Column "Tax ID" is not populated
		---
		Sheet: Project | Row: 2 | Column: Center
		Error: Column "Center" is not populated
		---
		Sheet: Analysis | Row: 2 | Column: Analysis Title
		Error: Column "Analysis Title" is not populated
		---
		Sheet: Analysis | Row: 2 | Column: Description
		Error: Column "Description" is not populated
		---
		Sheet: Analysis | Row: 2 | Column: Experiment Type
		Error: Column "Experiment Type" is not populated
		---
		Sheet: Analysis | Row: 2 | Column: Reference
		Error: Column "Reference" is not populated
		---
		Sheet: Sample | Row: 3 | Column: Sample Accession
		Error: Column "Sample Accession" is not populated
		---
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VCF VALIDATION RESULTS
Checks whether each file is compliant with the VCF specification (http://samtools.github.io/hts-specs/VCFv4.4.pdf).
Also checks whether the variants' reference alleles match against the reference assembly.
	input_fail.vcf
		❌ Assembly check: 26/36 (72.22%)
		First 10 errors per category are below. Full report: /path/to/assembly_failed/report
			Parsing error: The assembly checking could not be completed: Contig 'chr23' not found in assembly report
			Mismatch error: Chromosome 1, position 35549, reference allele 'G' does not match the reference sequence, expected 'c'
			Mismatch error: Chromosome 1, position 35595, reference allele 'G' does not match the reference sequence, expected 'a'
			Mismatch error: Chromosome 1, position 35618, reference allele 'G' does not match the reference sequence, expected 'c'
			Mismatch error: Chromosome 1, position 35626, reference allele 'A' does not match the reference sequence, expected 'g'
			Mismatch error: Chromosome 1, position 35639, reference allele 'T' does not match the reference sequence, expected 'c'
			Mismatch error: Chromosome 1, position 35643, reference allele 'T' does not match the reference sequence, expected 'g'
			Mismatch error: Chromosome 1, position 35717, reference allele 'T' does not match the reference sequence, expected 'g'
			Mismatch error: Chromosome 1, position 35819, reference allele 'T' does not match the reference sequence, expected 'a'
			Mismatch error: Chromosome 1, position 35822, reference allele 'T' does not match the reference sequence, expected 'c'
		❌ VCF check: 1 critical errors, 1 non-critical errors
		First 10 errors per category are below. Full report: /path/to/vcf_failed/report
			Critical error: Line 4: Error in meta-data section.
			Non-critical error: Sample #11, field AD does not match the meta specification Number=R (expected 2 value(s)). AD=..
	input_passed.vcf
		✔ Assembly check: 247/247 (100.0%)
		✔ VCF check: 0 critical errors, 0 non-critical errors
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SAMPLE NAME CONCORDANCE CHECK
Checks whether information in the metadata is concordant with that contained in the VCF files, in particular sample names.
	❌ Analysis A: Sample names in metadata do not match with those in VCF files
		First 10 errors per category are below. Full report: /path/to/sample/report
			Samples described in the metadata but not in the VCF files:  SampleA1, SampleA2 , SampleA3, SampleA4, SampleA5, SampleA6, SampleA7, SampleA8, SampleA9, SampleA10
			Samples in the VCF files but not described in the metadata: A1Sample ,  A2Sample, A3Sample, A4Sample, A5Sample, A6Sample, A7Sample, A8Sample, A9Sample, A10Sample
	✔ Analysis B: Sample names in metadata match with those in VCF files
	❌ Analysis C: Sample names in metadata do not match with those in VCF files
		First 10 errors per category are below. Full report: /path/to/sample/report
			Samples described in the metadata but not in the VCF files: SampleC1 ,  SampleC2, SampleC3, SampleC4
			Samples in the VCF files but not described in the metadata: C1Sample ,  C2Sample, C3Sample, C4Sample
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REFERENCE GENOME INSDC CHECK
Checks that the reference sequences in the FASTA file used to call the variants are accessioned in INSDC.
Also checks if the reference assembly accession in the metadata matches the one determined from the FASTA file.
	metadata_asm_match.fa
		✔ All sequences are INSDC accessioned.
		✔ Analysis A: Assembly accession in metadata is compatible
	metadata_asm_not_found.fa
		✔ All sequences are INSDC accessioned.
		❌ No assembly accession found in metadata
			Full report: /path/to/metadata_asm_not_found.yml
			Assembly accession found in metadata: Not found
			Assembly accession(s) compatible with FASTA: GCA_1
	metadata_asm_not_match.fa
		✔ All sequences are INSDC accessioned.
		❌ Analysis B: Assembly accession in metadata is not compatible
			Full report: /path/to/metadata_asm_not_match.yml
			Assembly accession found in metadata: GCA_2
			Assembly accession(s) compatible with FASTA: GCA_1
	metadata_error.fa
		Warning: The following results may be incomplete due to problems with external services.
		Please try again later for complete results.
		Error message: 500 Server Error: Internal Server Error for url: https://www.ebi.ac.uk/eva/webservices/contig-alias/v1/chromosomes/md5checksum/hjfdoijsfc47hfg0gh9qwjrve
		✔ All sequences are INSDC accessioned.
		✔ Analysis C: Assembly accession in metadata is compatible
	not_all_insdc.fa
		❌ Some sequences are not INSDC accessioned
			First 10 sequences not in INSDC. Full report: /path/to/not_all_insdc_check.yml
				Sequence name: 2
				Refget md5: hjfdoijsfc47hfg0gh9qwjrve
				---
		✔ Analysis A: Assembly accession in metadata is compatible
