Error in the function VDJ_call_MIXCR

alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires

GNU General Public License v3.0

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Error in the function VDJ_call_MIXCR #23

Closed Andy-ChanKP closed 1 year ago

Andy-ChanKP commented 2 years ago

Hi Victor and Alex,

I encountered this error when trying to run MIXCR, and I think the error stems from some in-built codes that use "paste". I think if you guys push a change of the code to paste0, that might have solved the issue. This is just my speculations - do you know why else I am encountering this error? I can open the MIXCR menu no problem in the cluster/linux - so I got it installed correctly with a proper license.

Current code:

If using paste0:

Best, Andy

vickreiner commented 2 years ago

Hi Andy, I just pushed a new version of the function with two changes:

paste is now paste0
I made the java -jar initial call a customizable string (new parameter: custom.cmd.call) In case of any issues with calling Mixcr this may help in the future.

Please let me know if this helped! Thanks!

Andy-ChanKP commented 2 years ago

Hi Victor,

Thank you for your help!!! The customizable string is a good idea - so people can specify their java path! But the error persists...

I am thinking whether the issue might be due to my infrastructure than the codes themselves - I am running R studio on my cluster, and for some reasons, java couldn't be found (I also tried to specify the path to java, like "/usr/share/java", but still without luck.

Any suggestions would be appreciated - would be nice to calculate the SHM rate with mixcr.

Many thanks, Andy

vickreiner commented 2 years ago

Hi! Can you leave the custom.cmd.call blank ("") and try to call MIXCR without invoking Java first. Depending on your MIXCR installation this may work. Otherwise I would try to use a terminal on your cluster to find a command that can reliably call mixcr and then translate that into the R function using the custom.cmd.call.