Phylogenetic Assignment of Named Global Outbreak LINeages. pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. It allows a user to assign a SARS-CoV-2 genome sequence the most likely lineage (Pango lineage) to SARS-CoV-2 query sequences.

• pangolin Main Site
• pangolin on GitHub

• Module Name: pangolin (see the modules page for more information)
• pangolin should be run with lscratch and the --tempdir option should be used to make sure that temporary data is written to the correct location. See example below.
• Environment variables set
  • PATH
  • PANGOLIN_TESTDATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive -c4 --mem=8g --gres=lscratch:10
salloc.exe: Pending job allocation 12440727
salloc.exe: job 12440727 queued and waiting for resources
salloc.exe: job 12440727 has been allocated resources
salloc.exe: Granted job allocation 12440727
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0913 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
error: unable to open file /tmp/slurm-spank-x11.12440727.0
slurmstepd: error: x11: unable to read DISPLAY value

[user@cn0913 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0913 12440727]$ module load pangolin
[+] Loading pangolin  2.3.6  on cn0913
[+] Loading singularity  3.7.3  on cn0913

[user@cn0913 12440727]$ cp $PANGOLIN_TESTDATA/* .

[user@cn0913 12440727]$ mkdir tempdir

[user@cn0913 12440727]$ pangolin --tempdir=./tempdir cluster.fasta
Found the snakefile
The query file is:/lscratch/12440727/cluster.fasta
EDB003  sequence too short
EDB004  has an N content of 0.98
Looking in /opt/conda/envs/pangolin/lib/python3.7/site-packages/pangoLEARN/data for data files...

Data files found
Trained model:  /opt/conda/envs/pangolin/lib/python3.7/site-packages/pangoLEARN/data/decisionTree_v1.joblib
Header file:    /opt/conda/envs/pangolin/lib/python3.7/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib
Lineages csv:   /opt/conda/envs/pangolin/lib/python3.7/site-packages/pangoLEARN/data/lineages.metadata.csv
Job counts:
        count   jobs
        1       add_failed_seqs
        1       align_to_reference
        1       all
        1       minimap2_check_distance
        1       overwrite
        1       pangolearn
        1       parse_paf
        1       type_variants_b117
        1       type_variants_b12142
        1       type_variants_b1351
        1       type_variants_p1
        1       type_variants_p2
        1       type_variants_p3
        13
Job counts:
        count   jobs
        1       parse_paf
        1
[M::mm_idx_gen::0.003*1.49] collected minimizers
[M::mm_idx_gen::0.004*1.33] sorted minimizers
[M::main::0.004*1.33] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.004*1.30] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.004*1.28] distinct minimizers: 2952 (100.00% are singletons); average occurrences: 1.000; average spacing: 10.130
warning: using --pad without --trim has no effect
[M::worker_pipeline::0.095*1.00] mapped 8 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -a -x asm5 -t 1 /opt/conda/envs/pangolin/lib/python3.7/site-packages/pangolin-2.3.6-py3.7.egg/pangolin/data/reference.fasta /lscratch/12440727/./tempdir/tmpat6kcm3p/mappable.fasta
[M::main] Real time: 0.096 sec; CPU: 0.096 sec; Peak RSS: 0.003 GB
loading model 04/09/2021, 13:23:32
processing block of 8 sequences 04/09/2021, 13:23:33
complete 04/09/2021, 13:23:34
Job counts:
        count   jobs
        1       add_failed_seqs
        1
Job counts:
        count   jobs
        1       overwrite
        1
Output file written to: /lscratch/12440727/lineage_report.csv

[user@cn0913 12440727]$ cat lineage_report.csv
taxon,lineage,probability,pangoLEARN_version,status,note
EDB001,B.1.1.26,1.0,2021-03-29,passed_qc,
EDB002,B.1.1.26,1.0,2021-03-29,passed_qc,
EDB005,B,1.0,2021-03-29,passed_qc,
EDB006,B.1.1.26,1.0,2021-03-29,passed_qc,
EDB007,B.1.1.26,1.0,2021-03-29,passed_qc,
EDB008,B.1.1.26,1.0,2021-03-29,passed_qc,
EDB009,B.1.1.26,1.0,2021-03-29,passed_qc,
EDB010,B,1.0,2021-03-29,passed_qc,
EDB003,None,0,2021-03-29,fail,seq_len:2997
EDB004,None,0,2021-03-29,fail,N_content:0.98

[user@cn0913 12440727]$ exit
exit
salloc.exe: Relinquishing job allocation 12440727

[user@biowulf ~]$

Create a batch input file (e.g. pangolin.sh). For example:

#!/bin/bash
set -e
module load pangolin
pagolin --tempdir=/lscratch/$SLURM_JOB_ID my.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] [--gres=lscratch:#] pangolin.sh

Create a swarmfile (e.g. pangolin.swarm). For example:

pagolin --tempdir=/lscratch/$SLURM_JOB_ID A.fasta
pagolin --tempdir=/lscratch/$SLURM_JOB_ID B.fasta
pagolin --tempdir=/lscratch/$SLURM_JOB_ID C.fasta
pagolin --tempdir=/lscratch/$SLURM_JOB_ID D.fasta

Submit this job using the swarm command.

swarm -f pangolin.swarm [-g #] [-t #] [--gres=lscratch:#] --module pangolin