Assign_Indiv_by_Geno.R function of Demuxafy.sif problems with the vcf

[ElenaSLuis]

Hey! I'm trying to use Assign_Indiv_by_Geno.R function of Demuxafy.sif from data of demuxlet code. It seems the problem is with the FORMAT, but I don't undestand very well...

apptainer exec Demuxafy.sif Assign_Indiv_by_Geno.R -r /home/elenasl/scRNAseq/freemuxlet/vcf_chr/GRCh38_1000G_MAF0.01_GeneFiltered_ChrEncoding_Sorted_polyIC.vcf \

-c /home/elenasl/scRNAseq/freemuxlet/output_polyIC.clust1.vcf.gz -o /home/elenasl/scRNAseq/freemuxlet/
System has not been booted with systemd as init system (PID 1). Can't operate.
Failed to connect to bus: Host is down
Scanning file to determine attributes.
File attributes:
meta lines: 242
header_line: 243
variant count: 7139809
column count: 8
Meta line 242 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 7139809
Character matrix gt cols: 8
skip: 0
nrows: 7139809
row_num: 0
Processed variant: 7139809
All variants processed
Scanning file to determine attributes.
File attributes:
meta lines: 32
header_line: 33
variant count: 2204998
column count: 11
Meta line 32 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 2204998
Character matrix gt cols: 11
skip: 0
nrows: 2204998
row_num: 0
Processed variant: 2204998
All variants processed
Found GT genotype format in cluster vcf. Will use that metric for cluster correlation.
Detected / separator for GT genotype format in cluster vcf

Error in if (colnames(x@gt)[1] != "FORMAT") { :
argument is of length zero
Calls: as_tibble -> extract.gt
Execution halted

thank you in advance,

Elena

[knausb]

Hi @ElenaSLuis , I do not know what 'Demuxafy.sif' is. It appears to use vcfR, but I have no knowledge of how it attempts to use vcfR. Perhaps this questions would be more appropriate to direct at the authors of Demuxafy? If you would like to pursue this I suggest you review suggestions I've posted here (https://knausb.github.io/vcfR_documentation/reporting_issue.html).