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minimap2 on Biowulf

Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.

References:

Documentation
Important Notes

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@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 minimap2
[+] Loading minimap2, version 2.2...
[user@cn3144 ~]$ man minimap2 # read the documentation
[user@cn3144 ~]$ minimap2 -ax map10k $MINIMAP2_HOME/test/MT-human.fa $MINIMAP2_HOME/test/MT-orang.fa > test.sam
[M::mm_idx_gen::0.005*1.16] collected minimizers
[M::mm_idx_gen::0.007*1.24] sorted minimizers
[M::main::0.007*1.24] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.008*1.19] mid_occ = 3
[M::mm_idx_stat] kmer size: 19; skip: 10; is_HPC: 1; #seq: 1
[M::mm_idx_stat::0.008*1.27] distinct minimizers: 2127 (99.95% are singletons); average occurrences: 1.000; average spacing: 7.786
[M::worker_pipeline::0.035*1.03] mapped 1 sequences
[M::main] Version: 2.2-r409
[M::main] CMD: minimap2 -ax map10k /usr/local/apps/minimap2/2.2/test/MT-human.fa /usr/local/apps/minimap2/2.2/test/MT-orang.fa
[M::main] Real time: 0.036 sec; CPU: 0.037 sec
[user@cn3144 ~]$ 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. minimap2.sh). For example:

#!/bin/bash
set -e
module load minimap2
minimap2 -ax map10k $MINIMAP2_HOME/test/MT-human.fa $MINIMAP2_HOME/test/MT-orang.fa > test.sam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] minimap2.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. minimap2.swarm). For example:

minimap2 -ax map10k reference.fa reads1.fa > out1.sam
minimap2 -ax map10k reference.fa reads2.fa > out2.sam
minimap2 -ax map10k reference.fa reads3.fa > out3.sam
minimap2 -ax map10k reference.fa reads4.fa > out4.sam

Submit this job using the swarm command.

swarm -f minimap2.swarm [-g #] [-t #] --module minimap2
where
-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 minimap2 Loads the minimap2 module for each subjob in the swarm