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quast [2017/10/05 20:44]
jokinsey
quast [2017/10/12 18:37]
jokinsey Corrected the job running location in the parallel example
Line 35: Line 35:
  
 cd $PBS_O_WORKDIR cd $PBS_O_WORKDIR
 +cp -r test_data/ /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
  
 python /​share/​apps/​quast/​quast-3.1/​quast.py test_data/​contigs_1.fasta test_data/​contigs_2.fasta -R test_data/​reference.fasta.gz -G test_data/​genes.gff python /​share/​apps/​quast/​quast-3.1/​quast.py test_data/​contigs_1.fasta test_data/​contigs_2.fasta -R test_data/​reference.fasta.gz -G test_data/​genes.gff
 +mv /​scratch/​$PBS_JOBID/​quast_results/​results* $PBS_O_WORKDIR/​quast_results/​
 </​code>​ </​code>​
  
-This script will run Quast on the inputs located in your local ''​$HOME/QUAST-JOBS/test_data''​ directory. If you would like to know more about the values and flags used refer to the manual [[http://​quast.bioinf.spbau.ru/​manual.html|here]].+This script will run Quast on the inputs located in the ''/​scratch/$PBS_JOBID''​ directory. If you would like to know more about the values and flags used refer to the manual [[http://​quast.bioinf.spbau.ru/​manual.html|here]]
 + 
 +The output for the job should be located in ''​$HOME/​QUAST-JOBS/​quast_results/​results_<​when_the_job_was_submitted>''​
  
 All thats left is to submit the job. All thats left is to submit the job.
Line 67: Line 72:
  
 cd $PBS_O_WORKDIR cd $PBS_O_WORKDIR
 +cp -r test_data/ /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
  
-python /​share/​apps/​quast/​quast-3.1/​quast.py --threads ​48 test_data/​contigs_1.fasta test_data/​contigs_2.fasta -R test_data/​reference.fasta.gz -G test_data/​genes.gff+python /​share/​apps/​quast/​quast-3.1/​quast.py --threads ​12 test_data/​contigs_1.fasta test_data/​contigs_2.fasta -R test_data/​reference.fasta.gz -G test_data/​genes.gff 
 +mv /​scratch/​$PBS_JOBID/​quast_results/​results* $PBS_O_WORKDIR/​quast_results/​
 </​code>​ </​code>​
  
-This sets the max thread count at 48 for out set value of 12 virtual processors. You can evaluate the speedup by comparing the completion times of job running in serial job and a job running in parallel ​with the change above.+This changes ​the maximum ​thread count to 12 as we don't want to run more threads on node than their are cores on that node, because ​with hyper-threading turned off any more would kill efficiency.
   ​   ​
  
  
quast.txt · Last modified: 2017/10/12 18:37 by jokinsey