You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
cannot send zipped vcfs into be parsed via a subshell at runtime, creates unexpected behavior
eg multivcfanalyzer NA ref.fasta NA results_dir/ T 30 5 0.9 0.1 NA $(gunzip test1.vcf.gz test2.vcf.gz)
The command executes and creates all outputs but does not actually analyze the files. no error message is returned.
outstream
MultiVCFAnalyzer - 0.85.2
by Alexander Herbig
No positions to exclude provided! All positions will be used!
Excluding positions...
0 SNP positions excluded.
Writing SNP table:
.//snpTable.tsv
Writing SNP table with uncertainty calls:
.//snpTableWithUncertaintyCalls.tsv
Writing SNP alignment (fasta):
.//snpAlignment.fasta
Writing SNP alignment including reference genome (fasta):
.//snpAlignmentIncludingRefGenome.fasta
Writing full alignment including reference genome (fasta):
.//fullAlignment.fasta
Writing genotypes for structure analysis:
.//structureGenotypes.tsv
Writing genotypes for structure analysis (no missing data columns):
.//structureGenotypes_noMissingData-Columns.tsv
No outgroup has been defined. All samples will be treated equally.
All done! (0 minutes)
info.txt
MultiVCFAnalyzer - 0.85.2
by Alexander Herbig
Input files:
Reference genome fasta file: Mammoth_MT_Krause.fasta
Reference genome gene annotation (gff): NA
List of positions to exclude (gff): NA
SNP effect analysis result file (from SnpEff): NA
Output files:
Output directory: ./
SNP alignment (fasta): .//snpAlignment.fasta
SNP alignment including entry for reference genome (fasta): .//snpAlignmentIncludingRefGenome.fasta
SNP table: .//snpTable.tsv
SNP table with uncertainty calls: .//snpTableWithUncertaintyCalls.tsv
SNP table to be used as input for SnpEff: .//snpTableForSnpEff.tsv
SNP table to be used as input for STRUCTURE: .//structureGenotypes.tsv
SNP table to be used as input for STRUCTURE (no columns with missing data): .//structureGenotypes_noMissingData-Columns.tsv
SNP calling statistics: .//snpStatistics.tsv
Parameters:
Minimal genotyping quality (GATK): 30.0
Minimal coverage for base call: 5
Minimal allele frequency for homozygous call: 0.9
Minimal allele frequency for heterozygous call: 0.1
Write allele frequencies: true
Additional notes:
Reference genome name: NC_007596.2 Mammuthus primigenius mitochondrion, complete genome
Number of genomes (vcf files): 0
Run started: 29 Oct 2021 14:55:59 GMT
Run finished: 29 Oct 2021 14:55:59 GMT
List of VCF files:
`
The text was updated successfully, but these errors were encountered:
cannot send zipped vcfs into be parsed via a subshell at runtime, creates unexpected behavior
eg
multivcfanalyzer NA ref.fasta NA results_dir/ T 30 5 0.9 0.1 NA $(gunzip test1.vcf.gz test2.vcf.gz)
The command executes and creates all outputs but does not actually analyze the files. no error message is returned.
outstream
MultiVCFAnalyzer - 0.85.2
by Alexander Herbig
No positions to exclude provided! All positions will be used!
Excluding positions...
0 SNP positions excluded.
Writing SNP table:
.//snpTable.tsv
Writing SNP table with uncertainty calls:
.//snpTableWithUncertaintyCalls.tsv
Writing SNP alignment (fasta):
.//snpAlignment.fasta
Writing SNP alignment including reference genome (fasta):
.//snpAlignmentIncludingRefGenome.fasta
Writing full alignment including reference genome (fasta):
.//fullAlignment.fasta
Writing genotypes for structure analysis:
.//structureGenotypes.tsv
Writing genotypes for structure analysis (no missing data columns):
.//structureGenotypes_noMissingData-Columns.tsv
No outgroup has been defined. All samples will be treated equally.
All done! (0 minutes)
info.txt
MultiVCFAnalyzer - 0.85.2
by Alexander Herbig
Input files:
Reference genome fasta file: Mammoth_MT_Krause.fasta
Reference genome gene annotation (gff): NA
List of positions to exclude (gff): NA
SNP effect analysis result file (from SnpEff): NA
Output files:
Output directory: ./
SNP alignment (fasta): .//snpAlignment.fasta
SNP alignment including entry for reference genome (fasta): .//snpAlignmentIncludingRefGenome.fasta
SNP table: .//snpTable.tsv
SNP table with uncertainty calls: .//snpTableWithUncertaintyCalls.tsv
SNP table to be used as input for SnpEff: .//snpTableForSnpEff.tsv
SNP table to be used as input for STRUCTURE: .//structureGenotypes.tsv
SNP table to be used as input for STRUCTURE (no columns with missing data): .//structureGenotypes_noMissingData-Columns.tsv
SNP calling statistics: .//snpStatistics.tsv
Parameters:
Minimal genotyping quality (GATK): 30.0
Minimal coverage for base call: 5
Minimal allele frequency for homozygous call: 0.9
Minimal allele frequency for heterozygous call: 0.1
Write allele frequencies: true
Additional notes:
Reference genome name: NC_007596.2 Mammuthus primigenius mitochondrion, complete genome
Number of genomes (vcf files): 0
Run started: 29 Oct 2021 14:55:59 GMT
Run finished: 29 Oct 2021 14:55:59 GMT
List of VCF files:
`
The text was updated successfully, but these errors were encountered: