signalp6.rst

Signalp6

Introduction ~~~~~~~~ SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.

For more information, please check:
Home page: https://services.healthtech.dtu.dk/service.php?SignalP

Versions

• 6.0-fast
• 6.0-slow

Commands ~~~~~~~ - signalp6

Example job for fast mode ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run signalp6 on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --job-name=signalp6
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load signalp6/XXXX ### you can run *module avail signalp6* to check all available versions

signalp6 --write_procs 8 --fastafile proteins_clean.fasta  \
         --organism euk --output_dir output_fast  \
         --format txt --mode fast

Example job for slow mode ~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run signalp6 on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --job-name=signalp6
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load signalp6/XXXX ### you can run *module avail signalp6* to check all available versions

signalp6 --write_procs 8 --fastafile proteins_clean.fasta  \
         --organism euk --output_dir output_slow  \
         --format txt --mode slow

signalp6 --write_procs 8 --fastafile proteins_clean.fasta  \
         --organism euk --output_dir output_slow-sequential  \
         --format txt --mode slow-sequential