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I suspect what is happening is that args[5] is returning NA causing issues. However, if that was the case I don't think this script would be working for anybody. I'm clearing missing something with how this script was written. Will try investigate it further by looking at runs that work, but I've already cleared out my cache for previously successful tumor-only runs.
Description of the bug
Ran into this controlfreec error trying to run sarek in paired mode:
I noticed that 4 files were supplied to the R script in this order:
I am a bit confused by the contents of the R script, it seems to only take two tables as args and for some reason is calling from args[5] and args[4]:
I suspect what is happening is that
args[5]
is returningNA
causing issues. However, if that was the case I don't think this script would be working for anybody. I'm clearing missing something with how this script was written. Will try investigate it further by looking at runs that work, but I've already cleared out my cache for previously successful tumor-only runs.Command used and terminal output
No response
Relevant files
controlfreec_assesssignificance_bug.zip
System information
System information
23.10.1
,23.04.5
Linux m3-login2 3.10.0-1160.71.1.el7.x86_64 #1 SMP Tue Jun 28 15:37:28 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
3.4.0
,3.3.2
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