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

• slapnap Main Site

• 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.

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.

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

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 slapnap