Cactus is a reference-free whole-genome multiple alignment program.

References:

• Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251.

• Cactus Main Site: GitHub

• Module Name: cactus (see the modules page for more information)
• Environment variables set:
• CACTUS_HOME
• Example files in $CACTUS_HOME/examples

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4 --gres=lscratch:8
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 cn4224 are ready for job

[user@cn4224 ~]$ module load cactus
[+] Loading cactus  1.2.3  on cn4224 
[+] Loading singularity  3.7.0  on cn4224

[user@cn4224 ~]$ cd /lscratch/${SLURM_JOB_ID}
[user@cn4224 ~]$ export SINGULARITYENV_TMPDIR=/lscratch/${SLURM_JOB_ID}
[user@cn4224 ~]$ wget https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt

[user@cn4224 ~]$ cactus /lscratch/${SLURM_JOB_ID}/jobStore \
       /lscratch/${SLURM_JOB_ID}/evolverMammals.txt \
       /data/${USER}/evolverMammals.hal \
       --root mr \
       --binariesMode local
[...]
Workflow Progress 100%||||||||||||||||||||||| 379/379 (0 failures) [19:08<00:00, 0.33 jobs/s]
[2020-12-23T13:47:39-0500] [MainThread] [I] [toil.common] Successfully deleted the job store: FileJobStore(/lscratch/46116226/jobStore)
[2020-12-23T13:47:39-0500] [MainThread] [I] [cactus.progressive.cactus_progressive] Cactus has finished after 1156.1930517529836 seconds

[user@cn4224 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226

[user@biowulf ~]$

Create a batch input file (e.g. cactus.sh) similar to the following.

#! /bin/bash

set -e

module load cactus

cd /lscratch/${SLURM_JOB_ID}
export SINGULARITYENV_TMPDIR=/lscratch/${SLURM_JOB_ID}
cactus /lscratch/${SLURM_JOB_ID}/jobStore \
       /lscratch/${SLURM_JOB_ID}/evolverMammals.txt \
       /data/${USER}/evolverMammals.hal \
       --root mr \
       --binariesMode local

Submit these jobs using the Slurm sbatch command.

Create a swarmfile for the first step of the pipeline (e.g. cactus.swarm). For example:

cd /lscratch/${SLURM_JOB_ID}; \
export SINGULARITYENV_TMPDIR=/lscratch/${SLURM_JOB_ID}; \
cactus /lscratch/${SLURM_JOB_ID}/jobStore \
       /lscratch/${SLURM_JOB_ID}/file1.txt \
       /data/${USER}/file1.hal \
       --root mr \
       --binariesMode local
cd /lscratch/${SLURM_JOB_ID}; \
export SINGULARITYENV_TMPDIR=/lscratch/${SLURM_JOB_ID}; \
cactus /lscratch/${SLURM_JOB_ID}/jobStore \
       /lscratch/${SLURM_JOB_ID}/file2.txt \
       /data/${USER}/file2.hal \
       --root mr \
       --binariesMode local

Submit this job using the swarm command.

swarm -f cactus.swarm [-g #] --module cactus