VSEARCH on Biowulf
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
References:
- Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016 Oct 18;4
Documentation
Important Notes
- Module Name: vsearch (see the modules page for more information)
- Multithreaded
- Example files in $VSEARCH_EXAMPLES
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive 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 cn3144 are ready for job [user@cn3144 ~]$ module load vsearch [user@cn3144 ~]$ ln -s /usr/local/apps/vsearch/vsearch-data/BioMarKs50k.fsa . [user@cn3144 ~]$ vsearch --cluster_fast BioMarKs50k.fsa --id 0.97 --centroids vsearch.out [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. vsearch.sh). For example:
#!/bin/bash module load vsearch vsearch --usearch_global queries.fsa --db database.fsa --id 0.9 --alnout alnout.txt
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] vsearch.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. vsearch.swarm). For example:
vsearch --usearch_global queries1.fsa --db database.fsa --id 0.9 --alnout alnout1.txt vsearch --usearch_global queries2.fsa --db database.fsa --id 0.9 --alnout alnout2.txt vsearch --usearch_global queries3.fsa --db database.fsa --id 0.9 --alnout alnout3.txt vsearch --usearch_global queries4.fsa --db database.fsa --id 0.9 --alnout alnout4.txt
Submit this job using the swarm command.
swarm -f vsearch.swarm [-g #] [-t #] --module vsearchwhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| -t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
| --module vsearch | Loads the VSEARCH module for each subjob in the swarm |