metafusion not exiting when error occurs

[anoronh4]

Description of the bug

when Metafusion_forte.sh has errors the script does not exit, instead all following steps are executed. it is possible for the script to exit successfully but still have an invalid result. for example the following showed up in the beginning of a log:

mkdir: cannot create directory ‘.’: File exists
sort: cannot create temporary file in '/scratch': No such file or directory
ename cff
Annotate cff, extract sequence surrounding breakpoint
2346277 annotations from null.metafusion.gene.bed loaded.
13.8489849567 sec. elapsed.
Warning: Input gene annotations include multiple chr, strand, or regions (5Mb away). Skipping current gene annotation.
set([('SNORA81', 'chr18', 'r'), ('SNORA81', 'chr21', 'f'), ('SNORA81', 'chr3', 'f')])
Warning: Input gene annotations include multiple chr, strand, or regions (5Mb away). Skipping current gene annotation.
set([('CKS1B', 'chr1', 'f'), ('CKS1B', 'chr5', 'r')])
Warning: Input gene annotations include multiple chr, strand, or regions (5Mb away). Skipping current gene annotation.

and the script completed, and the process completed with non-zero exit. the output was wrong and the next process failed.
currently we use set +e in the beforeScript directive of all processes, not sure why this is the case. we should add set -e or maybe set -o errexit in the Metafusion_forte.sh script. the mkdir command should also be changed to mkdir -p.

the reason this error occurred was due to TMPDIR in singularity containers not being set correctly on a server that forte has never been configured for. easily fixed with singularity.runOptions = "-B $TMPDIR" but nonetheless, we need a better way to catch the error.

Command used and terminal output

command used is not relevant here

Relevant files

command (2).log

System information

No response