Option not to check for submit node when using `useGrid=remote`?

[xgrau]

Hi,

I am using the useGrid=remote option in Canu v2.2 so that it prepares qsub submission scripts, which I then execute manually on my local cluster. However, the intermediate steps between the parallelised parts of the pipeline are sometimes a bit computationally intensive (e.g. the seqStore building step), which, due to the configuration of my cluster (which I'm not managing myself), often results in halted jobs due to excess resource usage. In a normal scenario, I would use the useGrid=true option, but this is not possible because my qsub configuration prevents me from launching nested qsub jobs.

A possible workaround to this issue would be running these intermediate steps as independent qsub jobs and keep launching the generated submission scripts manually, but this is apparently only not possible, as the following error appears when launching canu from a compute node:

error: denied: host "XXXX" is neither submit nor admin host

Given that I'm using useGrid=remote and are therefore not interested in using the current node as a submit node, this check seems unnecessary. Is there any way of disasbling it, or any other workaround to this issue? Thanks a lot in advance.

Find my log attached below.

Any tips will be appreciated.

Cheers

Xavi

###
###  Reading options from '/nfs/users2/asebe/xgraubove/Programes/canu-2.2/bin/canu.defaults'
###

# Add site specific options (for setting up Grid or limiting memory/threads) here.

###
###  Reading options from the command line.
###

genomeSize=300m
useGrid=remote
gridEngineResourceOption=-pe smp 16 -l virtual_free=90G,h_rt=720:00:00 -q long-sl7
minReadLength=1000
corOutCoverage=200
batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50
correctedErrorRate=0.105