SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species.

References:

• Cosentino, Salvatore, and Wataru Iwasaki. "SonicParanoid: fast, accurate and easy orthology inference." Bioinformatics 35.1 (2019): 149-151.

• SonicParanoid Main Site
• SonicParanoid on GitLab
• SonicParanoid on PyPi

• Module Name: sonicparanoid (see the modules page for more information)
• This application is multi-threaded. Control the number of threads with the "--threads N" option/argument pair.
• Example files can be obtained using the command sonicparanoid-get-test-data. (See examples below.)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive -c16 --mem=32g --gres=lscratch:10
salloc.exe: Pending job allocation 59415428
salloc.exe: job 59415428 queued and waiting for resources
salloc.exe: job 59415428 has been allocated resources
salloc.exe: Granted job allocation 59415428
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3201 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn3201 ~]$ module load sonicparanoid
[+] Loading sonicparanoid  1.3.2  on cn3201
[+] Loading singularity  3.5.3  on cn3201

[user@cn3201 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3201 59415428]$ sonicparanoid-get-test-data --output-directory .
/lscratch/59415428/sonicparanoid_test/
INFO: all test files were succesfully copied to
/lscratch/59415428/sonicparanoid_test/

Go inside the directory
/lscratch/59415428/sonicparanoid_test/
and type

sonicparanoid -i ./test_input -o ./test_output -m fast -t 4

[user@cn3201 59415428]$ cd sonicparanoid_test/

[user@cn3201 sonicparanoid_test]$ tree
.
|-- test_input
|   |-- chlamydia_trachomatis
|   |-- deinococcus_radiodurans
|   |-- gloeobacter_violaceus
|   `-- thermotoga_maritima
`-- test_output
    `-- README.txt

2 directories, 5 files

[user@cn3201 sonicparanoid_test]$ sonicparanoid \
    --input-directory ./test_input \
    --output-directory ./test_output  \
    --mode fast \
    --threads $SLURM_CPUS_ON_NODE

Run START:      Mon Jun  8 17:13:53 2020
SonicParanoid 1.3.2 will be executed with the following parameters:
Run ID: sonic_8620171353_fast_16cpus_ml05
Run directory: /lscratch/59415428/sonicparanoid_test/test_output/runs/sonic_8620171353_fast_16cpus_ml05
Input directory: /lscratch/59415428/sonicparanoid_test/test_input/
Input proteomes: 4
Output directory: /lscratch/59415428/sonicparanoid_test/test_output
Alignments directory: /lscratch/59415428/sonicparanoid_test/test_output/alignments/
Pairwise tables directory: /lscratch/59415428/sonicparanoid_test/test_output/runs/sonic_8620171353_fast_16cpus_ml05/pairwise_orthologs/
Directory with ortholog groups: /lscratch/59415428/sonicparanoid_test/test_output/runs/sonic_8620171353_fast_16cpus_ml05/ortholog_groups/
Pairwise tables database directory: /lscratch/59415428/sonicparanoid_test/test_output/orthologs_db/
Runs directory: /lscratch/59415428/sonicparanoid_test/test_output/runs/
Update run:     False
Create pre-filter indexes:      True
Complete overwrite:     False
Re-create ortholog tables:      False
Threads:        16
Memory per thread (Gigabytes):  15.73
Minimum memory per thread (Gigabytes):  1.75
Run mode:       fast (MMseqs2 s=2.5)
MCL inflation:  1.50
/usr/local/lib/python3.6/dist-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.22.2.post1 when using version 0.23.1. This might lead to breaking code or invalid results. Use at your own risk.
  UserWarning)
/usr/local/lib/python3.6/dist-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator AdaBoostClassifier from version 0.22.2.post1 when using version 0.23.1. This might lead to breaking code or invalid results. Use at your own risk.
  UserWarning)

For the 4 input species 6 combinations are possible.

16 MMseqs2 alignments will be performed...
Creating 4 MMseqs2 databases...

MMseqs2 databases creation elapsed time (seconds):      4.195

All-vs-all alignments elapsed time (seconds):   8.272

Predicting 6 ortholog tables...
Ortholog tables creation elapsed time (seconds):        0.26

Creating ortholog groups...

Creating orthology matrixes...
Ortholog matrixes creation elapsed time (seconds):      0.072

Merging inparalog matrixes...
Inparalogs merging elapsed time (seconds):      0.071

Creating input matrix for MCL...
MCL graph creation elapsed time (seconds):      0.091

Running MCL...
MCL execution elapsed time (seconds):   3.461

Generating final output files...
Elapsed time for the creation of final output (seconds):        0.673

Ortholog groups creation elapsed time (seconds):        4.408

Total elapsed time (seconds):   18.217

[user@cn3201 sonicparanoid_test]$ exit
exit
salloc.exe: Relinquishing job allocation 59415428
salloc.exe: Job allocation 59415428 has been revoked.

[user@biowulf ~]$ 

Create a batch input file (e.g. sonicparanoid.sh). For example:

#!/bin/bash
set -e
module load sonicparanoid
sonicparanoid \
    --input-directory ./test_input \
    --output-directory ./test_output  \
    --mode fast \
    --threads $SLURM_CPUS_ON_NODE

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] sonicparanoid.sh

Create a swarmfile (e.g. sonicparanoid.swarm). For example:

sonicparanoid -i ./test_input1 -o ./test_output1 -m fast -t $SLURM_CPUS_ON_NODE
sonicparanoid -i ./test_input2 -o ./test_output2 -m fast -t $SLURM_CPUS_ON_NODE
sonicparanoid -i ./test_input3 -o ./test_output3 -m fast -t $SLURM_CPUS_ON_NODE
sonicparanoid -i ./test_input4 -o ./test_output4 -m fast -t $SLURM_CPUS_ON_NODE

Submit this job using the swarm command.

swarm -f sonicparanoid.swarm [-g #] [-t #] --module sonicparanoid