canu 设置全局#PBS参数问题

https://github.com/marbl/canu/issues/69

有时候，某些程序会在qsub之后自行投递进一步的jobs，比如canu，这时前面设置的-P -l等参数需要传递到后续任务才能成功投递，在canu中gridOptions有这样的功能

• 报错

CRASH: INFO: As you have not specifed whether this job as a personal or project run,
CRASH: INFO: the system will count this as a personal run by default.
CRASH: INFO:
CRASH: INFO: Please use -P Personal or -P <project_id> to properly account for your job.
CRASH: INFO:
CRASH: INFO: Alternatively, in your job submission script please add
CRASH: INFO: #PBS -P Personal or #PBS -P <project_id>
CRASH: INFO: submitting job...
CRASH:
CRASH: qsub: Job has no walltime requested. Rejecting the job

• 解决思路
  to approach the canu software developer and find out a way to include Project ID "-P Personal/<project ID>", and walltime, " -l walltime=01:00:00" arguments.

canu can pass any number of options to the gridOptions flag, in quotes and they will be passed through to the scheduler:

gridOptions="-V -W group_list=xylella -M email -mbea"

There are grid options for each step that will be passed as well as global grid options which will apply to all jobs

canu -options |grep gridOptions
gridOptions                             Grid engine options applied to all jobs
gridOptionsExecutive                    Grid engine options applied to the canu executive script
gridOptionsJobName                      Grid jobs job-name suffix
gridOptionsbat                          Grid engine options applied to unitig construction jobs
gridOptionscns                          Grid engine options applied to unitig consensus jobs
gridOptionscor                          Grid engine options applied to read correction jobs
gridOptionscormhap                      Grid engine options applied to mhap overlaps for correction jobs
gridOptionscormmap                      Grid engine options applied to mmap overlaps for correction jobs
gridOptionscorovl                       Grid engine options applied to overlaps for correction jobs
gridOptionsmeryl                        Grid engine options applied to mer counting jobs
gridOptionsobtmhap                      Grid engine options applied to mhap overlaps for trimming jobs
gridOptionsobtmmap                      Grid engine options applied to mmap overlaps for trimming jobs
gridOptionsobtovl                       Grid engine options applied to overlaps for trimming jobs
gridOptionsoea                          Grid engine options applied to overlap error adjustment jobs
gridOptionsovb                          Grid engine options applied to overlap store bucketizing jobs
gridOptionsovs                          Grid engine options applied to overlap store sorting jobs
gridOptionsred                          Grid engine options applied to read error detection jobs
gridOptionsutgmhap                      Grid engine options applied to mhap overlaps for unitig construction jobs
gridOptionsutgmmap                      Grid engine options applied to mmap overlaps for unitig construction jobs
gridOptionsutgovl                       Grid engine options applied to overlaps for unitig construction jobs

/home/users/00.bin/canu-2.1.1/bin/canu -p LipSX -d /home/users/scratch/01.canu-assembly/ genomeSize=*g -minReadLength=3000 -pacbio /home/users/scratch/00.seqData/SX/subreads.fasta.gz gridOptions="-P Personal -l walltime=24:00:00 -q normal