Error in STITCH - Execution halted

[vigneshravi]

I have installed STITCH using the recommended workflow. I am trying to execute the test script on the test bams but encounter the following error. Any help to understand this error and solve is much appreciated!

bash-4.2$ ./STITCH.R --chr=chr19 --bamlist=bamlist.txt --posfile=pos.txt --genfile=gen.txt --outputdir=./ --K=4 --nGen=100 --nCores=1
Error in STITCH(chr = opt$chr, posfile = opt$posfile, K = opt$K, nGen = opt$nGen,  :
  unused arguments (reference_shuffleHaplotypeIterations = eval(parse(text = opt$reference_shuffleHaplotypeIterations)), useTempdirWhileWriting = opt$useTempdirWhileWriting, output_haplotype_dosages = opt$output_haplotype_dosages)
Execution halted

[rwdavies]

Argh, my bad. Simple answer is to git checkout to the last release commit i.e. git checkout 46d68218ed3e16fa60f635d3366621cff430ed59 then it should make the CLI file match the last release (this just worked for me and corrected your error). Longer answer is that the CLI function isn't included in the release and tracks the master branch, and I've pushed some stuff to master that I should clearly bundle into a release

[rwdavies]

Hey, did this fix the issue for you?

[zihhuafang]

Hi, I ran into the same issue and it was fixed after git checkout. Thank you again!

[rwdavies]

This should now be fixed with the new version. I'll close this once the new version is up on bioconda.

[rwdavies]

OK, I had to release another version to fix bioconda problems, but this should be sorted now. I'll try harder to avoid making changes to the API on master between releases next time

[vigneshravi]

Version 1.5.6 helped fix the error I posted. Thank you!