VDJ_call_MIXCR not working because "Require tsv file type, got tempmixcrlc.out.vdjca" in "system(paste0(custom.cmd.call, " ", mixcr.directory,"/mixcr.jar exportAlignments --preset full -descrsR1 -vAlignment -dAlignment -jAlignment -aaMutations VRegion -aaMutations JRegion -nMutations VRegion -nMutations JRegion tempmixcrlc.out.vdjca tempmixcrlc.out.tsv",sep=""))"

jianwu1 commented 1 year ago

Dear Platypus team,

Thank you for developing this amazing package and the analyses available for TCR data are fabulous!

Can I ask a question about VDJ_call_MIXCR?

I got this error when running the code:

VDJ_mixcr_out <- VDJ_call_MIXCR(
  VDJ = vgm$VDJ, 
  mixcr.directory = "/Users/jianwu/miniforge3/envs/py_arm64/share/mixcr-4.4.1-0",
  custom.cmd.call <- "java -jar",
  species = "mmu", 
  platypus.version = "v3", 
  operating.system = "Darwin",
  simplify = TRUE)

I went into the source code and the changed all the output .txt file names from .txt. to .tsv. However I'm still encountering this error of not being able to produce .tsv file. I imported the edited source code file locally before importing Platypus so it's not because the code was not updated. I don't know if it's a positional argument misalignment error but I can't find any problems after checking the command for exportAlignments in MIXCR.

Do you mind giving me some help please?

Best wishes,

Jian

seibikobara commented 1 year ago

This is not a complete solution, but MiXCR.4.0.0 version works for me. I am eagerly waiting for Platypus to be updated to incorporate the latest version of MiXCR

jianwu1 commented 1 year ago

@seibikobara Hi Seibi, Thank you very much! I'll try MiXCR.4.0.0! Same. I'm looking forward to their updates too. It's a great package for analysing TCR data but they haven't got time to reply to any of the issues I had.

alexyermanos commented 1 year ago

sorry for the delay in answering and bringing this to our attention. we are currently reworking the package to avoid calling mixcr at all for full length VDJ and VJ sequences (and also for the germlines) --> the function at the following link https://github.com/alexyermanos/Platypus/blob/master/R/VDJ_extract_germline_consensus_ref.R is what we currently use to retrieve this information directly from the 10x VDJ output. We will try to update the mixcr pipeline in the near future (and accompanying vignettes)

alexyermanos / Platypus