ascatNGS - Tumour Normal cases failing - cannot create R_tmpdir

[karlnyr]

Describe the bug
A clear and concise description of what the bug is.

When running balsamic cases we get the following errors for the rule ascat_tumor_normal:

STDERR: + cut -f 1-3 /{ENVIRONMENT}/cancer/cases/wiredpig/analysis/tmp/de98ctjk/tmpAscat/SnpGcCorrections.tsv
STDERR: + cd /{ENVIRONMENT}/cancer/cases/wiredpig/analysis/tmp/de98ctjk/tmpAscat/ascat
STDERR: + /usr/bin/Rscript /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat/runASCAT.R /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat /{ENVIRONMENT}/cancer/cases/wiredpig/analysis/tmp/de98ctjk/tmpAscat/SnpPositions.tsv /{ENVIRONMENT}/cancer/cases/wiredpig/analysis/tmp/de98ctjk/tmpAscat/SnpGcCorrections.tsv TUMOR TUMOR.count NORMAL NORMAL.count XX 24 /{ENVIRONMENT}/cancer/cases/wiredpig/analysis/tmp/de98ctjk/tmpAscat/ascat/TUMOR.Rdata 'c('\''1'\'','\''10'\'','\''11'\'','\''12'\'','\''13'\'','\''14'\'','\''15'\'','\''16'\'','\''17'\'','\''18'\'','\''19'\'','\''2'\'','\''20'\'','\''21'\'','\''22'\'','\''3'\'','\''4'\'','\''5'\'','\''6'\'','\''7'\'','\''8'\'','\''9'\'','\''X'\'','\''Y'\'')' 'c('\''1'\'','\''10'\'','\''11'\'','\''12'\'','\''13'\'','\''14'\'','\''15'\'','\''16'\'','\''17'\'','\''18'\'','\''19'\'','\''2'\'','\''20'\'','\''21'\'','\''22'\'','\''3'\'','\''4'\'','\''5'\'','\''6'\'','\''7'\'','\''8'\'','\''9'\'','\''X'\'','\''Y'\'')'
STDERR: Fatal error: cannot create 'R_TempDir'
STDERR: Command exited with non-zero status 2
STDERR: 0.49user 0.32system 0:01.07elapsed 75%CPU (0avgtext+0avgdata 4316maxresident)k
STDERR: 6882inputs+0outputs (42major+4041minor)pagefaults 0swaps

To Reproduce
Steps to reproduce the behavior.

Inconsistent error when starting the analysis. Seems to occur for when running wgs cases in general but it is solved by a restart.

If workflow, which rules
If possible, and using the Snakemake workflows, the name of the affected rules and workflows.

ascat_tumor_normal

Version (please complete the following information):
balsamic --version output

Usage: balsamic [OPTIONS] COMMAND [ARGS]...

  BALSAMIC 10.0.2: Bioinformatic Analysis pipeLine for SomAtic MutatIons in
  Cancer

Additional context
Add any other context about the problem here.

We would consider adding a R variable for R_TempDir, perhaps defining it in from the params.tmpdir, and inside the container define an Renviron file as suggested in this post

[khurrammaqbool]

The error does not seem to be specific to R. The relevant portion of the error log is below:

THREAD_EXITED: General output can be found in this file, last 10 lines below: /home/proj/production/cancer/cases/wiredpig/analysis/tmp/de98ctjk/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.out

THREAD_EXITED: Errors can be found in this file, output below: {CASE_FOLER}/analysis/tmp/de98ctjk/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.err


THREAD_EXITED: Wrapper script message:
"{CASE_FOLER}/analysis/tmp/de98ctjk/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.sh 1>  {CASE_FOLER}/analysis/tmp/de98ctjk/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.out 2>  {CASE_FOLER}/analysis/tmp/de98ctjk/tmpAscat/logs/Sanger_CGP_Ascat_Implement_ascat.0.err" unexpectedly returned exit value 2 at /opt/wtsi-cgp/lib/perl5/PCAP/Threaded.pm line 244.
 at /opt/wtsi-cgp/lib/perl5/PCAP/Threaded.pm line 235

This requires further investigation and testing.

[ivadym]

It seems that it has not been reported recently, closing! Feel free to reopen if we encounter these issues again.