Argument "PBS/Torque" isn't numeric in numeric eq (==) at /Canu/20210423-GCCcore-6.4.0/bin/../lib/site_perl/canu/Grid_PBSTorque.pm line 76.

[Enorya]

Hello, I'm trying to use Canu on multiple fastq files using PBS/Torque '6.1.3':

canu useGrid=true gridOptions='-l walltime=72:00:00 -A llp_lbeg' -p coral -d /staging/leuven/stg_00026/Coral-DNA_MinION/canu/Coral-assembly genomeSize=458.6m -nanopore /staging/leuven/stg_00026/Coral-DNA_MinION/kraken2_analysis/coral-sequences/*.fastq java=/apps/leuven/skylake/2018a/software/Java/13.0.2/bin/java

But I end up with this error:

-- Detected Java(TM) Runtime Environment '1.8.0_162' (from '/apps/leuven/skylake/2018a/software/Java/1.8.0_162/bin/java') with -d64 support.
-- Detected gnuplot version '4.6 patchlevel 2   ' (from 'gnuplot') and image format 'png'.
--
-- Detected 36 CPUs and 378 gigabytes of memory on the local machine.
--
-- Detected PBS/Torque '6.1.3' with 'pbsnodes' binary in /usr/bin/pbsnodes.
Argument "PBSPro" isn't numeric in numeric eq (==) at /vsc-hard-mounts/leuven-apps/skylake/2018a/software/Canu/20210423-GCCcore-6.4.0/bin/../lib/site_perl/canu/Grid_PBSTorque.pm line 76.
Argument "PBS/Torque" isn't numeric in numeric eq (==) at /vsc-hard-mounts/leuven-apps/skylake/2018a/software/Canu/20210423-GCCcore-6.4.0/bin/../lib/site_perl/canu/Grid_PBSTorque.pm line 76.
-- Detecting PBSPro resources.
pbsnodes: invalid option -- 'v'
usage:  pbsnodes [-{c|d|l|o|p|r}] [-s server] [-n] [-N "note"] [-A "append note"] [-q] [-m standby|suspend|sleep|hibernate|shutdown] node ...
        pbsnodes [-{a|x}] [-s server] [-q] [node]
--
-- PBSPro support detected.  Resources available:

ABORT:
ABORT: canu snapshot v2.2-development +110 changes (r10219 8ae77e7d96e0bdd42348b19108bcdafff1b8e868)
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting.  If that doesn't work, ask for help.
ABORT:
ABORT:   invalid useGrid (1) and gridEngine (PBSPRO); found no execution hosts - is grid available from this host?.
ABORT:

The Canu version I'm using is the following one: canu snapshot v2.2-development +110 changes (r102198ae77e7d96e0bdd42348b19108bcdafff1b8e868)

Do you know from where comes the problem?

[brianwalenz]

Argh!

It's a simple fix. Edit src/pipelines/canu/Grid_PBSTorque.pm and change line 76 from

        setGlobal("gridEngine", ($name == "PBSPro") ? "PBSPRO" : "PBS");

to

        setGlobal("gridEngine", ($name eq "PBSPro") ? "PBSPRO" : "PBS");

The change is also committed to github.

Unfortunately, we have no way to test the PBS support. :-(

[skoren]

You could alternatively add gridEngine=PBS as a workaround to bypass this code.

[Enorya]

Thank you both for your quick answers!