slapnap on Biowulf
Description The slapnap container is a tool for using the Compile, Analyze and Tally NAb Panels (CATNAP; Yoon et al. 2015) database to develop predictive models of HIV-1 neutralization sensitivity to one or several broadly neutralizing antibodies (bnAbs).
References:
- Magaret A Prediction of VRC01 Neutralization Sensitivity by HIV-1 gp160 Sequence Features. PLoS Computational Biology 15 (4): e1006952.
- Yoon Hyejin CATNAP: A Tool to Compile, Analyze and Tally Neutralizing Antibody Panels. Nucleic Acids Research 43 (W1): W213–W219
Documentation
Important Notes
- Module Name: slapnap (see the modules page for more information)
- This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load slapnap [user@cn3144 ~]$ cp -r /usr/local/apps/slapnap/20210507/libexec/lib/ . [user@cn3144 ~]$ mkdir -p ./output/ ./dat/analysis ./slfits [user@cn3144 ~]$ export SINGULARITYENV_nab="PGT135;CH01" [user@cn3144 ~]$ export SINGULARITYENV_outcomes="ic50" [user@cn3144 ~]$ run_analysis.sh Starting SLAPNAP Messages, warnings, and errors (if any) will appear in your output directory under VRC01_26Feb2024.log Checking options Building analytic data set from CATNAP database Fitting learners Compiling results using R Markdown Returning requested objects Closing down SLAPNAP. Check your output directory for requested objects. [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
The result html will be in ./output/ dir.
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. slapnap.sh). For example:
#!/bin/bash set -e module load slapnap slapnap < slapnap.in > slapnap.out
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] slapnap.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. slapnap.swarm). For example:
slapnap < slapnap.in > slapnap.out slapnap < slapnap.in > slapnap.out slapnap < slapnap.in > slapnap.out slapnap < slapnap.in > slapnap.out
Submit this job using the swarm command.
swarm -f slapnap.swarm [-g #] [-t #] --module slapnapwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| -t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
| --module slapnap | Loads the slapnap module for each subjob in the swarm |