Pomoxis contains convenience wrappers around nanopore tools.

• pomoxis on GitHub
• pomoxis Documentation

• Module Name: pomoxis (see the modules page for more information)
• Some pomoxis tools are multithreaded. Please match the number of allocated CPUs and the number of threads
• Example files in $POMOXIS_TEST_DATA

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/0.3.15
[+] Loading singularity  4.0.1  on cn4299
[+] Loading pomoxis  0.3.15

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

Create a batch input file (e.g. pomoxis.sh), which uses the input file 'pomoxis.in'. For example:

#!/bin/bash
wd=$PWD
module load pomoxis/0.3.15 || exit 1
cd /lscratch/$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 --gres=lscratch:50 --mem=10g pomoxis.sh

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