mkatari-bioinformatics-august-2013-blastnotes
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| mkatari-bioinformatics-august-2013-blastnotes [2013/08/13 15:18] – created mkatari | mkatari-bioinformatics-august-2013-blastnotes [2013/08/13 15:28] – mkatari | ||
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| - | ########################## | + | ====== |
| - | # Run Blast using sbatch | + | |
| - | ########################## | + | |
| - | 1) create | + | - Create |
| - | '' | + | < |
| #!/bin/bash | #!/bin/bash | ||
| #SBATCH -p highmem | #SBATCH -p highmem | ||
| #SBATCH -n 8 | #SBATCH -n 8 | ||
| - | '' | + | </ |
| - | Normally any other # used in a bash script file means a comment follows. However since we are executing the sbatch file using sbatch command (see below) SBATCH knows to look for #SBATCH and use the information that follows. Here we are telling the SBATCH file to use the highmem partition (the mammoth server) and use 8 CPUs to perform the calculation. It is also important to tell that program you are running that it has 8 CPUs available so it will use them, else you will be reserving 8 CPUs but only using one. | + | Normally any other '' |
| - | 2) There are several different job managers and different ways of setting up HPC computer systems. In practice I prefer not to assume that a job that is submitted to a different server will know how to find the different commands or even files. So I like to include the full paths for both. In order to find where the blastx command is located I simply type: | + | - There are several different job managers and different ways of setting up HPC computer systems. In practice I prefer not to assume that a job that is submitted to a different server will know how to find the different commands or even files. So I like to include the full paths for both. In order to find where the '' |
| - | ---------------------------------------------- | + | < |
| module load blast | module load blast | ||
| which blastx # note this will only work if you already have the blast module loaded. | which blastx # note this will only work if you already have the blast module loaded. | ||
| / | / | ||
| - | ---------------------------------------------- | + | </ |
| - | From Alan's Blast sbatch script example on the wiki, I also know where the nr database is | + | From Alan's Blast sbatch script example on [[using-slurm|How to Use Slurm]], I also know where the nr database is |
| - | ----------------------------------------------- | + | < |
| / | / | ||
| - | ----------------------------------------------- | + | </ |
| - | 3) Edit the contigs.fa.nr.sbatch file to include all changes. Final script looks like this: | + | - Edit the '' |
| - | ---------------------------- | + | < |
| #!/bin/bash | #!/bin/bash | ||
| Line 37: | Line 35: | ||
| / | / | ||
| - | ------------------------------ | + | </ |
| - | 4) Run the sbatch file. As soon as you run the file a job id will be assigned to your submission. | + | - Run the sbatch file. As soon as you run the file a job id will be assigned to your submission. |
| - | ----------------------- | + | < |
| sbatch blast.sbatch | sbatch blast.sbatch | ||
| - | ----------------------- | + | </ |
| You can check the status of all jobs on the cluster by typing: | You can check the status of all jobs on the cluster by typing: | ||
| - | ----------------------- | + | < |
| squeue | squeue | ||
| - | ----------------------- | + | </ |
| You can check the details of your specific job by typing: | You can check the details of your specific job by typing: | ||
| - | ---------------------------------------------- | + | < |
| scontrol show job <your jobid> | scontrol show job <your jobid> | ||
| - | ---------------------------------------------- | + | </ |
| You can cancel your job by running | You can cancel your job by running | ||
| - | ---------------------------------------------- | + | < |
| scancel <your jobid> | scancel <your jobid> | ||
| - | ---------------------------------------------- | + | </ |
| The standard output of your job is redirected to a file called | The standard output of your job is redirected to a file called | ||
| - | ---------------------------------------------- | + | < |
| slurm-< | slurm-< | ||
| - | ---------------------------------------------- | + | </ |
mkatari-bioinformatics-august-2013-blastnotes.txt · Last modified: 2015/06/04 12:38 by mkatari