[zhoufan]

Hi,
I am trying Jelly 13.10.22 version on ubuntu 10.04 with smrtanalysis 2.0.1 . I am trying the sample data and the support stage have no result with no error. Has anyone met this kind of situation?

[HenrivdGeest]

Yes,I also encounter this.
I think there is a small bug in the sample scripts in the latest release of pbjelly(13.10.22). The mapping quality of the reads is lower than the default filtering settings of the support stage. If you run the support stage with lower settings it should work:
Jelly.py support Protocol.xml -x "--minMapqv=45" # the qv of mapped reads in the sample = 50.
( I got this more or less from the documentation from the pbjelly website at sourceforge)

[bio_d]

Running PBJELLY on SLURM

How do I submit PBJELLY script in a cluster(SLURM)?

I mean slurm doesn't allow job submission at head node whereas PBJELLY says the script will itself submit jobs according to the specifications in the <cluster></cluster> tag of the Protocol.xml file.