Updated 2023-03-31
Run Scythe on the Cluster¶
Summary¶
- Currently,
Scythe/0.994
is available on the Cluster - Load Scythe with
module load scythe
- In your
SBATCH
script, the lines to execute Scythe must go after the lines to load scythe - The general command to run Scythe is:
scythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq
- For more options when running scythe, enter the command
scythe
or visit the github page
Walkthrough: Run RAxML on the Cluster¶
- To create a
SBATCH
script on the cluster, enter the folder you want to use then typevim <name.sbatch>
. Name the file whatever you want, but keep.sbatch
at the end.Vim
is a text editor that is reliable and effecient to use on Linux. illumina_adapters.fasta
can be found heresequences.fastq
can be found hereSBATCH
Script can be found here- You can transfer the files to your account on the cluster to follow along. The file transfer guide guide may be helpful.
Example SBATCH Script¶
#!/bin/bash
#SBATCH -Jscythejob
#SBATCH -A [Account]
#SBATCH -N2 --ntasks-per-node=8
#SBATCH -t2
#SBATCH -qinferno
#SBATCH -oReport-%j.out
cd $SLURM_SUBMIT_DIR
module load scythe/0.994
srun scythe -a illumina_adapters.fasta -o trimmed_sequences.fasta sequences.fastq
- The
#SBATCH
directives are standard, requesting 2 hours of walltime and 2 node with 8 cores per node. More on#PBS
directives can be found in the Using Slurm on Phoenix Guide $SBATCH_SUBMIT_DIR
is simply a variable that represents the directory you submit the SBATCH script from. Make sure the.fastq
&.fasta
files you want to use are in the same directory you put theSBATCH
script. This line tells the cluster to enter this directory where you have stored the files for the job, so it has access to all the files it needs- Output Files, will also show up in the same directory as the
SBATCH
script. module load scythe
loads scythescythe -a adapter_file.fasta -o trimmed_sequences.fasta sequences.fastq
runs scythe
Submit Job & Check Job Status¶
- Make sure you're in the directory that contains the
SBATCH
script and the.fasq
and.fasta
files - Submit as normal, with
sbatch < script name>
. In this casesbatch samtools.sbatch
- Check job status with
squeue --job <jobID>
, replacing with the jobid returned after running sbatch - You can delete the job with
scancel <jobID>
, replacing with the jobid returned after running sbatch
Collect Results¶
- All files created will be in the same folder where your
SBATCH
script is (same directory you ransbatch
from) - The
Report-<jobID>.out
file will be found here as well. It contains the results of the job, as well as diagnostics and a report of resources used during the job. If the job fails or doesn't produce the result your were hoping for, theReport-<jobID>.out
file is a great debugging tool. - The
trimmed_sequences.fasta
file that gets generated can be found here Report-<jobID>.out
should look like this:
---------------------------------------
Begin Slurm Prolog: Jan-26-2023 14:55:15
Job ID: 593270
User ID: svangala3
Account: phx-pace-staff
Job name: scythejob
Partition: cpu-small
QOS: inferno
---------------------------------------
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
prior: 0.300
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
Adapter Trimming Complete
contaminated: 1329, uncontaminated: 8671, total: 10000
contamination rate: 0.132900
---------------------------------------
Begin Slurm Epilog: Jan-26-2023 14:55:17
Job ID: 593270
Array Job ID: _4294967294
User ID: svangala3
Account: phx-pace-staff
Job name: scythejob
Resources: cpu=16,mem=16G,node=2
Rsrc Used: cput=00:00:48,vmem=288K,walltime=00:00:03,mem=0,energy_used=0
Partition: cpu-small
QOS: inferno
Nodes: atl1-1-02-014-19-2,atl1-1-02-014-20-2
---------------------------------------
- You can transfer the resulting files off the cluster using scp or a file transfer service