Error with batch execution in cluster

[mgabriell1]

Hi,
First of all thanks for this tools!
I'm writing here as I'm having some problems running it in batch mode using a PBS-based cluster.
I've installed InterProScan and run the initial setup as shown in the guide and I've tested it on the examples provided and everything seems to work.
I then tried to annotate my protein files and I've run in a bunch of java errors (see log attached). It seems that IPS it is trying to use a temporary folder in a non-existent folder whose name is related to the one of the PBS submitted job. For example:

Could not execute bin/prosite/pfscanV3 --matrix-only -o4 -L-1 /scratch/4706233[2].sched-torque.pace.gatech.edu/ps971869-1.tmp /scratch/4706233[2].sched-torque.pace.gatech.edu/ps971869-3.tmp

This happens even when I set the temp folder using an abosute path.

Running it manually on the login nodes using the same command does not result in any errors, probably because it does not try to use those folders.

IPS is at version 5.56-89, JDK is v12.0.2 and Python is v3.7.4. The command that I'm using is :

tempdir=`pwd`"/temp"
./interproscan.sh -i predRedRedund_prot.fasta.clean.fas --goterms -b ips_annotations -T $tempdir

log_InterProScan_protein_annotation.txt