MISO: Warning: cannot parse their job IDs from the cluster submission system
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!!
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What cluster job scheduler are you using?
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.
Try removing the
--use-clustercommand, particularly if you don't already know whatqsubis.when I remove --use-cluster command, I immediately get the warning "WARNING - Thread batch-0 might have failed".