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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
BSD 3-Clause Clear License
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FALCON_unzip reverts to job_type=local #58

Closed roblehmann closed 7 years ago

roblehmann commented 7 years ago

Hi, I'm trying to run FALCON_unzip on the ecoli example. I have set:

[General]
job_type = SLURM

However, it only runs in local mode: 

[INFO]job_type='local', job_queue='UNSPECIFIED_QUEUE', sge_option=None, use_tmpdir=None, squash=False`

Interestingly, e.g. the 3-unzip/reads/task.json states the job_type is SLURM.

The revisions: FALCON_unzip: 38de578054fc62ba6087ab6c596371fb85417c1e FALCON-integrate: cd3770021fa1884caa141953fc27a79918930ade FALCON: 3b90cca3af5435b2a3b11e5f529befe718191368

thanks in advance

pb-jchin commented 7 years ago

FALCON_unzip for non-SGE is not tested much. If your genome is small, local mode might be the way to go for now.

pb-cdunn commented 7 years ago

I think this is fixed with the latest pypeflow and FALCON_unzip.