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

[Yu Gao]

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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