knausb
commented
1 year ago 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).
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