User Tools

Site Tools


quast

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Last revision Both sides next revision
quast [2017/10/05 20:44]
jokinsey
quast [2017/10/12 18:30]
jokinsey Corrected the serial job running location
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.
quast.txt · Last modified: 2017/10/12 18:37 by jokinsey