Biowulf High Performance Computing at the NIH
pomoxis on Biowulf

Pomoxis contains convenience wrappers around nanopore tools.

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 --gres=lscratch:50 --cpus-per-task=6 --mem=12g
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]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ ml pomoxis
[+] Loading minimap2, version 2.17...
[+] Loading miniasm 0.3.r179  ...
[+] Loading samtools 1.9  ...
[+] Loading racon 1.3.2  ...
[+] Loading seqkit  0.10.2
[+] Loading porechop  0.2.4
[+] Loading pomoxis  0.2.3

[user@cn3144]$ cp -L $POMOXIS_TEST_DATA/* .
[user@cn3144]$ ls -lh
total 906M
-rw-r----- 1 wresch staff 4.5M Sep 12 09:12 NC_000913.3.fasta
-rw-r----- 1 wresch staff 901M Sep 12 09:12 R9_Ecoli_K12_MG1655_lambda_MinKNOW_0.51.1.62.all.fasta

The ecoli reads used in these examples were obtained from the Loman Labs. The mini_align script uses minimap2 to align reads and runs some common post-alignment processing steps like sorting and aligning the resulting bam file.


[user@cn3144]$ mini_align -r NC_000913.3.fasta \
                     -i R9_Ecoli_K12_MG1655_lambda_MinKNOW_0.51.1.62.all.fasta \
                     -t $SLURM_CPUS_PER_TASK -p ecoli
Constructing minimap index.
[M::mm_idx_gen::0.178*1.01] collected minimizers
[M::mm_idx_gen::0.220*1.38] sorted minimizers
[M::main::0.274*1.31] loaded/built the index for 1 target sequence(s)
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.286*1.29] distinct minimizers: 838542 (98.18% are singletons); average occurrences: 1.034; average spacing: 5.352
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -I 16G -x map-ont -d NC_000913.3.fasta.mmi NC_000913.3.fasta
[M::main] Real time: 0.292 sec; CPU: 0.376 sec; Peak RSS: 0.049 GB
[samfaipath] build FASTA index...
[M::main::0.070*1.02] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.086*1.01] mid_occ = 12
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.097*1.01] distinct minimizers: 838542 (98.18% are singletons); average occurrences: 1.034; average spacing: 5.352
[M::worker_pipeline::128.218*5.37] mapped 72602 sequences
[M::worker_pipeline::203.551*5.30] mapped 59810 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x map-ont -t 6 -a NC_000913.3.fasta.mmi R9_Ecoli_K12_MG1655_lambda_MinKNOW_0.51.1.62.all.fasta
[M::main] Real time: 203.564 sec; CPU: 1078.051 sec; Peak RSS: 3.832 GB
[bam_sort_core] merging from 0 files and 6 in-memory blocks...

De novo assembly with miniasm

[user@cn3144]$ mini_assemble -i R9_Ecoli_K12_MG1655_lambda_MinKNOW_0.51.1.62.all.fasta \
                     -o ecoli_assm -t $SLURM_CPUS_PER_TASK  -m 1 -c
...much output...
[user@cn3144]$ assess_assembly -r NC_000913.3.fasta \
                     -i  ecoli_assm/reads_final.fa -t $SLURM_CPUS_PER_TASK
...
  name     mean     q10      q50      q90
 err_ont  2.033%   1.783%   1.925%   2.332%
 err_bal  2.052%   1.797%   1.942%   2.357%
    iden  0.320%   0.257%   0.296%   0.344%
     del  0.821%   0.721%   0.788%   0.913%
     ins  0.913%   0.764%   0.858%   1.079%

#  Q Scores
  name     mean      q10      q50      q90
 err_ont  16.92    17.49    17.16    16.32
 err_bal  16.88    17.46    17.12    16.28
    iden  24.95    25.89    25.29    24.64
     del  20.85    21.42    21.03    20.40
     ins  20.40    21.17    20.67    19.67


[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. pomoxis.sh), which uses the input file 'pomoxis.in'. For example:

#!/bin/bash
wd=$PWD
module load pomoxis/0.2.3 || exit 1
cd /lscratch/$SLURM_JOB_ID
cp -L $POMOXIS_TEST_DATA/R9_Ecoli_K12_MG1655_lambda_MinKNOW_0.51.1.62.all.fasta .
mini_assemble -i R9_Ecoli_K12_MG1655_lambda_MinKNOW_0.51.1.62.all.fasta \
    -o ecoli_assm -t $SLURM_CPUS_PER_TASK  -m 1 -c
mv ecoli_assm $wd

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=10g pomoxis.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. pomoxis.swarm). For example:

mini_align -r NC_000913.3.fasta -i expt1.fastq -t $SLURM_CPUS_PER_TASK -p expt1
mini_align -r NC_000913.3.fasta -i expt2.fastq -t $SLURM_CPUS_PER_TASK -p expt2
mini_align -r NC_000913.3.fasta -i expt3.fastq -t $SLURM_CPUS_PER_TASK -p expt3

Submit this job using the swarm command.

swarm -f pomoxis.swarm -g 10 -t 6 --module pomoxis/0.2.3
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 pomoxis Loads the pomoxis module for each subjob in the swarm