error in unused argument when running pileup_and_phase.R

[MigleMi]

Dear creators, I have a problem when running pileup_and_phase.R. The pileup part was successful but I run to this error at the last phasing step, the error message is here:

[I::pileup_positions_with_fetch][Thread-36] 94.00% SNPs processed. [I::pileup_positions_with_fetch][Thread-36] 96.00% SNPs processed. [I::pileup_positions_with_fetch][Thread-36] 98.00% SNPs processed. [I::main] All Done! [I::main] end time: 2023-04-19 20:41:46 [I::main] time spent: 11800 seconds. Error in numbat:::preprocess_allele(sample = label, vcf_pu = vcf_pu, vcf_phased = vcf_phased, : unused argument (gtf_transcript = gtf_transcript) Calls: %>% -> filter Execution halted

I have checked the arguments while in R, it looks like the argument should be gtf
> numbat:::preprocess_allele( sample= vcf_pu= vcf_phased= AD= DP= barcodes= gtf= gmap=
what could be an issue here?
Thank you!

[teng-gao]

Hello, most likely you're using the pileup_and_phase script from an old version of Numbat. The argument name changed some time ago.