Error when submitting as grid job

[callumjethomas]

When I try and submit a job which I want to run on multiple computation nodes with USE_GRID=true, I get the following error:

2025-03-20 23:54:20 [Info] Sumbit command: qsub -j oe -d `pwd` -N cns_pprr.sh -l nodes=1:ppn=30 -o /rds-d7/project/rds-fT31urweTx0/projects/project_BSF_Nanopore/run_2/results/necat/scripts/cns_pprr.sh.log  /rds-d7/project/rds-fT31urweTx0/projects/project_BSF_Nanopore/run_2/results/necat/scripts/cns_pprr.sh
Unknown option: d
Usage:
    qsub [-a start_time] [-A account] [-b y|n] [-e err_path] [-I] [-l
    resource_list] [-m mail_options] [-M user_list] [-N job_name] [-o
    out_path] [-p priority] [-pe shm task_cnt] [-P wckey] [-q destination]
    [-r y|n] [-v variable_list] [-V] [-wd workdir] [-W
    additional_attributes] [-h] [script]

2025-03-20 23:54:20 [Info] Failed to sumbit command

This seems to indicate there is a bug in the PBS grid script at line 57, where the option -d is incorrectly set.

Is it possible this should be -wd instead?

NECAT/src/pipeline/Plgd/GridPbs.pm

Line 57 in 0c5fc85

$cmd = $cmd . " -d `pwd`" if ($isPro == 0);