Katuali: Analysis pipelines from Oxford Nanopore Technologies' Research Division

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Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish Oxford Nanopore Technologies' sequencing data.

Documentation

Important Notes

Module Name: Katuali (see the modules page for more information)
Unusual environment variables set
- KATUALI_HOME installation directory
- KATUALI_BIN executables directory
- KATUALI_SRC source code directory
- KATUALI_DATA test data directory

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 

[user@cn3329 ~]$ module load katuali    
[+] Loading singularity  on cn3131
[+] Loading guppy 3.2.2  ...
[+] Loading GD 2.1.1  ...
[+] Loading gnuplot 5.2.2  ...
[+] Loading canu  1.8
[+] Loading nanopolish  0.11.1
[+] Loading Katuali 20190821  ...
[user@cn3329 ~]$  
[user@cn3329 ~]$ cp -r $KATUALI_DATA/* .  
[user@cn3329 ~]$  katuali -s Snakefile --configfile config.yaml 
/usr/local/Anaconda/envs_app/Katuali/20190821/lib/python3.6/site-packages/katuali-0.2.0-py3.6.egg/katuali/__init__.py:76: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  conf = yaml.load(open(args.base_configfile))
Running snakemake -s Snakefile --configfile configs/katuali_2019-09-10_12:07:22-04:00.yaml --restart-times 3 --keep-going
Config saved to configs/katuali_2019-09-10_12:07:22-04:00.yaml
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       version
        1

[Tue Sep 10 12:07:24 2019]
rule version:
    jobid: 0

Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.
Dynamic output is deprecated in favor of checkpoints (see docs). It will be removed in Snakemake 6.0.
Job counts:
        count   jobs
        1       version
        1
katuali version 0.2.0
[Tue Sep 10 12:07:24 2019]
Finished job 0.
1 of 1 steps (100%) done
...

End the interactive session:

[user@cn3329 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226