MISO: Warning: cannot parse their job IDs from the cluster submission system

Question

[ag1194]

Hi,

I am running MISO and getting following warning:

WARNING - Asked to wait on cluster jobs but cannot parse their job IDs from the cluster submission system.

And in mysample.output/ directory, instead of having MISO run output, I have:

batch-genes , batch--logs, cluster_scripts, logs, scripts_output folders.

My command line is following:

miso --run /MISO/mm9/ALE.indexed /tophat_out/accepted_hits.bam --output-dir /MISO/mysample.output --read-len 60 --paired-end 149 7.9 --use-cluster

Has anybody got the same warning before? Any suggestion going to be helpful

Thanks!!

[GenoMax]

What cluster job scheduler are you using?

[ag1194]

I am very new at MISO. MISO manual says "MISO comes with basic functionality for running on a cluster" . While running MISO, command line says "executing: qsub" I suppose this is for cluster job scheduler. Other than that, I have no idea.

[Devon Ryan]

Try removing the --use-cluster command, particularly if you don't already know what qsub is.

[ag1194]

when I remove --use-cluster command, I immediately get the warning "WARNING - Thread batch-0 might have failed".