oases pipeline with qsub.

[apallav]

Hi, Following command works perfectly fine, but the one after runs in to errors:

python /production/velvet/1.2.10/oases-master/scripts/oases_pipeline.py -d '-fastq.gz -separate -shortPaired ../SS-49_1.fastq.gz ../SS-49_2.fastq.gz' -m 21 -M 99 -s 2 -o SS-49_H7M3LBCXX_2_AAGGACAC_unstranded -p '-ins_length 150'

with qsub :

qsub -cwd -v PATH -S /bin/bash -b y -j y /production/velvet/1.2.10/oases-master/scripts/oases_pipeline.py -d '-fastq.gz -separate -shortPaired ../SS-49_1.fastq.gz ../SS-49_2.fastq.gz' -m 21 -M 99 -s 2 -o SS-49_H7M3LBCXX_2_AAGGACAC_unstranded -p '-ins_length 150'

gets me following error:

Usage: oases_pipeline.py [options] --data "velveth file descriptors"

oases_pipeline.py: error: option -s: invalid integer value: 'eparate'

No matter how I change it complains about something or the other.

Here was how I compiled velvet and oases:

make 'CATEGORIES=57' 'MAXKMERLENGTH=101' 'BIGASSEMBLY=1' 'LONGSEQUENCES=1' 'OPENMP=1'

Can you please help?