subshell gunzip not functional, no error

[ilight1542]

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:
`