Falcon Unzip Concurrents are not working

[AfterRain]

Dear Developer,

I am using SGE and run Falcon-Unzip. However, every time It is using only 8 concurrent jobs.

unzip cfg files are like below,

[Unzip] input_fofn= input.fofn input_bam_fofn= input_bam.fofn

smrt_bin=/shared2/smrtlink/install/smrtlink-release_5.0.1.9585/bundles/smrttools/smrtcmds/bin

jobqueue = bigmem sge_phasing= -pe smp 8 -q %(jobqueue)s sge_quiver= -pe smp 16 -q %(jobqueue)s sge_track_reads= -pe smp 8 -q %(jobqueue)s sge_blasr_aln= -pe smp 8 -q %(jobqueue)s sge_hasm= -pe smp 8 -q %(jobqueue)s unzip_concurrent_jobs = 120 quiver_concurrent_jobs = 60

I ran it with this command "fc_unzip.py fc_unzip.cfg" However, it doesn't work It looks always try to run with default queue and 8 concurrent.

Do you have any idea how I can increase unzip_concurrent setting?

Thank you,

[cschin]

Do you know if you system has a queue called "bigmem"?

[AfterRain]

@cschin

Thank you fo your answer!

Yes, I have bigmem queue I made one script run_example.sh which has configure programs and called "fc_unzip.py fc_unzip.cfg" in that script.

And I run that script just using qsub run_example.sh

It is coming like below,

job-ID prior name user state submit/start at queue slots ja-task-ID

  5 0.50500 run_exampl smrtanalysis r     08/31/2017 13:43:04 all.q@master                       1
  6 0.60500 P1a25507e4 smrtanalysis r     08/31/2017 13:43:19 default@master                     8

[AfterRain]

after this It is supposed to have multiple jobs processing, but It is coming only 8 * 8 jobs are in the queue with default queue. and when I checked log, It is showing concurrent = 8.

[AfterRain]

@cschin

It looks working fine now, I just added below two line in the unzip.cfg file. I am not so sure It is directly related but I just comment for information.

unzip_blasr_concurrent_jobs = 120 unzip_phasing_concurrent_jobs = 120

However, queue is still coming as "default" queue.

Thank you so much!