[miso-users] Problem with "cluster jobs"?

[Yarden Katz]

Hi,

Which cluster system do you use?  What does a typical cluster submission command look like in your system, and what does the job status program (e.g. "bjobs") produce?

This error generally means that MISO could not parse the job ID after submitting the job, and therefore cannot wait on that job to finish.

Yarden


On Mar 5, 2015, at 1:03 PM, Yu Gao <ygao000 at gmail.com> wrote:

> Hi all,
> I am a new miso user and I run miso like this:
> Preparing the alternative isoforms annotation
> 
> "
> index_gff --index ensGene.gff3 indexed/
> "
> Computing expression estimates (“Psi” / Ψ values)
> 
> 
> "
> miso --run indexed/ ~/mbd1rnaseq/3549WT.genome.sorted.bam --output-dir my_output1/ --paired-end 250 15 --read-len 101 --use-cluster --prefilter
> "
> It seems the running is fine, but I got a WARNING:
> 
> "WARNING: Asked to wait on cluster jobs but cannot parse their job IDs from the cluster submission system."
> When I check the generated files under"my_sample_output", I could not find subdirectories by chromosomes:
> like"
>   chr1/
>   chr2/
>   ...
>   chrX/
> 
> "
> Instead, I got four folders under "my_sample_output":
> "
> batch-logs
> scripts_output
> batch-genes
> cluster_scripts
> 
> "
> Anybody know how to solve this?
> Thanks in advance.
> Best, Yu
> 
> 
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