MISO --run error

Question

[Govardhan Anande]

Hello,

I have installed miso using root. Now i am trying to execute command and got error every time...

miso --run ~/miso_annotations_hg19_v2/indexed_SE_events/ ~/Sample.sort.bam --output-dir OUT/ --read-len 49 --paired-end=147 27 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt

Error==Waiting on 4 threads...

Then I increased number of threads but still ended in errors.

After that I started job in cluster mode using following command but still I got following error.

miso --run ~/miso_annotations_hg19_v2/indexed_SE_events/ ~/Sample.sort.bam --output-dir OUT/ --read-len 49 --paired-end=147 27 --use-cluster --chunk-jobs 50 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt

WARNING - Asked to wait on cluster jobs but cannot parse their job IDs from the cluster submission system.

Any suggestion is appreciated. I saw few related posts on similar issue and tried almost everything but still getting error.

Thanks in advance.

[weihaichao1985]

I met the same questions as yours. Have you solved it? Could you tell how to do this? Thank you！

[Govardhan Anande]

When you get this issue try to run following command stead.

python ~misopy/run_miso.py --compute-genes-from-file "~batch-genes/batch-0_genes.txt" ~/Sample.sort.bam ~OUT/ --read-len 49 --paired-end 147.0 27.0 --settings-filename miso_settings.txt

Answer 1

[Govardhan Anande]

Hi,

When you get this issue try to run following command stead.

python ~misopy/run_miso.py --compute-genes-from-file "~batch-genes/batch-0_genes.txt" ~accepted_hits.bam ~MISO_Out --read-len 49 --paired-end 147.0 27.0 --settings-filename miso_settings.txt

Correct me if I am wrong.

Thanks