MISO: Warning: cannot parse their job IDs from the cluster submission system
0
0
Entering edit mode
8.4 years ago
ag1194 • 0

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!!

RNA-Seq MISO • 2.5k views
ADD COMMENT
0
Entering edit mode

What cluster job scheduler are you using?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2093 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6