shmlast is a reimplementation of the Conditional Reciprocal Best Hits algorithm for finding potential orthologs between a transcriptome and a species-specific protein database. It uses the LAST aligner and the pydata stack to achieve much better performance while staying in the Python ecosystem.

References:

• Bo Li, Nathanael Fillmore, Yongsheng Bai, Mike Collins, James A. Thomson, Ron Stewart, and Colin N. Dewey.
  Evaluation of de novo transcriptome assemblies from RNA-Seq data
  Genome Biology 2014, 15:553
  

• shmlast project home page
• shmlast github page

• Module Name: shmlast (see the modules page for more information)
• Unusual environment variables set
  • SHMLAST_HOME  installation directory
  • SHMLAST_BIN       executable directory
  • SHMLAST_DATA  sample data directory

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

[user@biowulf]$ sinteractive --mem=4g
[user@@cn3200 ~]$module load shmlast  
[+] Loading singularity  3.10.0  on cn1113
[+] Loading shmlast  1.6
[user@biowulf]$ shmlast
usage: shmlast [-h] [--version] {rbl,crbl} ...

shmlast is a reimplementation of the Conditional Reciprocal Best
Hits algorithm for finding potential orthologs between
a transcriptome and a species-specific protein database. It uses the LAST
aligner and the pydata stack to achieve much better performance while staying in the Python ecosystem. 

positional arguments:
  {rbl,crbl}

optional arguments:
  -h, --help  show this help message and exit
  --version   show program's version number and exit
[user@biowulf]$ 
shmlast 1.2.1 -- Camille Scott, 2016
------------------------------------
subcommand: Conditional Reciprocal Best LAST
doit action: run

--- Begin Task Execution ---
.  rename:/usr/local/apps/shmlast/1.2.1/sample_data/test-transcript.fa:
    * Python: rename_input
.  rename:/usr/local/apps/shmlast/1.2.1/sample_data/test-protein.fa:
    * Python: rename_input
.  translate:.test-transcript.fa:
    * Python: function translate_fastx
.  lastdb:.test-transcript.fa.pep:
    * Cmd: `/usr/local/apps/shmlast/1.2.1/bin/lastdb -p -w3 .test-transcript.fa.pep .test-transcript.fa.pep`
.  lastdb:.test-protein.fa:
    * Cmd: `/usr/local/apps/shmlast/1.2.1/bin/lastdb -p -w3 .test-protein.fa .test-protein.fa`
.  lastal:.test-protein.fa.x.test-transcript.fa.pep.maf:
    * Cmd: `cat .test-protein.fa | /usr/local/apps/parallel/20171222/bin/parallel --round-robin --pipe -L 2 -N 10000 --gnu -j 1 -a .test-protein.fa /usr/local/apps/shmlast/1.2.1/bin/lastal -D100000.0 .test-transcript.fa.pep > .test-protein.fa.x.test-transcript.fa.pep.maf`
.  lastal:.test-transcript.fa.pep.x.test-protein.fa.maf:
    * Cmd: `cat .test-transcript.fa.pep | /usr/local/apps/parallel/20171222/bin/parallel --round-robin --pipe -L 2 -N 10000 --gnu -j 1 -a .test-transcript.fa.pep /usr/local/apps/shmlast/1.2.1/bin/lastal -D100000.0 .test-protein.fa > .test-transcript.fa.pep.x.test-protein.fa.maf`
.  fit_and_filter_crbl_hits:
    * Python: do_crbl_fit_and_filter

[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
#SBATCH --mem=4g
module load shmlast
cd /data/$USER         
shmlast crbl -q $SHMLAST_DATA/test-transcript.fa -d  $SHMLAST_DATA/test-protein.fa     

Submit this job using the Slurm sbatch command.

sbatch shmlast.sh 

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

#!/bin/bash
module load shmlast
cd /data/$USER
shmlast crbl -q $SHMLAST_DATA/test-transcript.fa -d  $SHMLAST_DATA/test-protein.fa

Submit this job using the swarm command.

swarm -f shmlast.swarm -g 4