WSP files not opening properly - Can't find associated FCS files

[Sithara85]

Hi,

As you know we have been working on ~10,000 samples FCS files and generated gating set and workspace files. Now we were trying to open the wsp files in FlowJO and it is not opening properly. It shows a red 'X' on the filename in FlowJo and can't find associated fcs so we can't inspect the populations gated.

Do you have any idea what's going on?

I have used below code to create the gating set and then ran docker/ singularity to create wsp files. As you notice I have used gsub to remove the white spaces in wsp files as save_gs was throwing error. But we tried to change the names with fcs name but it is not opening properly.

template = gs_add_gating_method(
  gs_EM3,
  alias = "CD28Gate",
  pop = "+/-",
  parent = "root",
  dims = "CD28",
  gating_method = "mindensity",
  gating_args = "gate_range = c(1000,15000)")
print(gs_pop_get_count_fast(gs_EM3))
fcs_file <- basename(f)

outputRoot = paste0(opt$outputDir, fcs_file)
addedWSP = paste0(outputRoot,"_CT_EM3")
addedWSP = gsub(" ", "_", addedWSP)
print(paste0("adding and renaming nodes and writing to ", addedWSP))
save_gs(gs_EM3,addedWSP)
print (file.exists(addedWSP))

}

Thank you, Sithara

[gfinak]

@Sithara85 just following up, have you resolved this issue? Can you provide a simple reproducible example using one file?

[alexheubeck]

Hi @gfinak,

I'm getting a similar issue reconnecting files to FlowJo workspaces generated with CytoML. When you create the workspace file, it connects to the associated FCS files normally. But when a collaborator has opened the workspace on a different OS, when I go to open it again, nothing will reconnect. (I'm on Mac, and my collaborators are on Windows).

Our workaround has been to open a new .wsp file, load in the files, and then copy the gating over from the CytoML generated .wsp file.

I sent this to FlowJo to see if they could diagnose it, but they haven't gotten back to me yet.

Thanks,

Alex

[Sithara85]

Hi Greg,

Yes, we resolved the issue a long time ago. I believe the issue was with some naming issue with FCS and associated WSP files. You may see multiple fields in WSP XML files relating to the FCS files and we have to confirm all matches.