search

mrvollger / SDA

Segmental Duplication Assembler (SDA).
MIT License
44 stars 6 forks source link

qsub command line incompatible with PBS Pro #13

Closed ptrebert closed 1 year ago

ptrebert commented 4 years ago

Hi Mitchell,

the below way of constructing the qsub call is not compatible with PBS Pro, which only supports the non-default values oe and eo for merging stdout/stderr (-j):

https://github.com/mrvollger/SDA/blob/1fbe948f3d8cde6ae6b8c49b33f4220053755718/SDA#L119

Best, Peter

mrvollger commented 4 years ago

Hi Peter,

Sorry about this issue, should have foreseen this one. I will get on a fix as soon as I have time. In the mean time if you are in a rush you could just change the way log is setup on that one line for your cluster as I don't think it will be used anywhere else.

Best, Mitchell

SergejN commented 3 years ago

Hi @mrvollger to follow up on that, I also had to modify the script (starting at line 118 of SDA) in order to make it work with SLURM:

    elif( args.cluster ):
        if 'sbatch' in args.cluster:
            cmd += f' --cluster " {args.cluster} --output {LOG} " '
        else:
            cmd += f' --cluster " {args.cluster} -j y -o {LOG} " '

Best Sergej

SergejN commented 3 years ago

I'm sorry, I just realized that the outputs are not written. The correct code for SLURM should be

elif( args.cluster ):
    if 'sbatch' in args.cluster:
        cmd += f' --cluster " {args.cluster} --output {LOG}/slurm-%j.out --error {LOG}/slurm-%j.err " '
    else:
        cmd += f' --cluster " {args.cluster} -j y -o {LOG} " '