BionanoSolve-Sapelo2 - Revision history

Shtsai at 02:40, 16 September 2021

2021-09-16T02:40:35Z

← Older revision		Revision as of 22:40, 15 September 2021
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	[[Category:~~Sapelo2old~~]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]

	=== Category ===		=== Category ===

Moses at 12:34, 15 April 2021

2021-04-15T12:34:07Z

Show changes

Moses at 14:46, 14 April 2021

2021-04-14T14:46:45Z

← Older revision		Revision as of 10:46, 14 April 2021
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	Sample job submission script (sub.sh) to run hybridScaffold.pl from BionanoSolve/3.6.1-11162020 in a batch job:		Sample job submission script (sub.sh) to run hybridScaffold.pl from BionanoSolve v3.6.1-11162020 in a batch job:

	<pre class="gscript">		<pre class="gscript">
Line 49:		Line 49:
	#SBATCH --partition=batch		#SBATCH --partition=batch
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
	#SBATCH --cpus-per-task=8		#SBATCH --cpus-per-task=2
	#SBATCH --mem=20gb		#SBATCH --mem=20gb
	#SBATCH --time=120:00:00		#SBATCH --time=120:00:00
Line 57:		Line 57:
	#SBATCH --mail-type=ALL		#SBATCH --mail-type=ALL

	cd $~~PBS_O_WORKDIR~~		cd $SLURM_SUBMIT_DIR
	~~module load BionanoSolve/3.2.1-04122018-foss-2016b~~
	~~perl $EBROOTBIONANOSOLVE/HybridScaffold/04122018/hybridScaffold.pl [options]~~
	~~</pre>~~

	~~Sample job submission script (sub.sh) to run pipelineCL.py from~~ BionanoSolve/3.2.1-~~04122018 in a batch job:~~		module load BionanoSolve/3.6.1-11162020-foss-2019b

	~~<pre class="gscript">~~		perl ${EBROOTBIONANOSOLVE}/HybridScaffold/11162020/hybridScaffold.pl [options]
	~~#PBS -S /bin/bash~~		</pre>
	~~#PBS -q batch~~
	~~#PBS -N job_hybridScaffold~~
	~~#PBS -l nodes=1:ppn=48~~
	~~#PBS -l walltime=12:00:00~~
	~~#PBS -l mem=10g~~
	~~#PBS -j oe~~

	~~cd $PBS_O_WORKDIR~~
	~~ml BionanoSolve/3.2.1-04122018-foss-2016b~~
	~~python~~ $EBROOTBIONANOSOLVE/~~Pipeline~~/~~04122018~~/~~pipelineCL~~.~~py -T 48 -j 48~~ [options]
	</pre>

	Sample job submission script (sub.sh) to run ~~hybridScaffold~~.pl from BionanoSolve/3.2.2-~~08222018~~ in a batch job:		Sample job submission script (sub.sh) to run pipelineCL.py from BionanoSolve v3.6.1-11162020 in a batch job:

	<pre class="gscript">		<pre class="gscript">
	#~~PBS -S~~ /bin/bash		#!/bin/bash
	#~~PBS~~ -q batch		#SBATCH --job-name=job_hybridScaffold
	#~~PBS~~ -~~N job_hybridScaffold~~		#SBATCH --partition=batch
	#~~PBS~~ -~~l nodes~~=1~~:ppn~~=2		#SBATCH --nodes=1
	#~~PBS~~ -~~l walltime~~=12:00:00		#SBATCH --ntasks=1
	#~~PBS~~ -~~l mem~~=~~10g~~		#SBATCH --cpus-per-task=32
	#~~PBS~~ -j oe		#SBATCH --mem=40gb
			#SBATCH --time=120:00:00
			#SBATCH --output=log.%j.out
			#SBATCH --error=log.%j.err
			#SBATCH --mail-user=username@uga.edu
			#SBATCH --mail-type=ALL

	cd $~~PBS_O_WORKDIR~~		cd $SLURM_SUBMIT_DIR
	~~module load BionanoSolve/3.2.2-08222018-foss-2016b~~
	~~perl $EBROOTBIONANOSOLVE/HybridScaffold/08222018/hybridScaffold.pl [options]~~
	~~</pre>~~

	~~Sample job submission script (sub.sh) to run pipelineCL.py from~~ BionanoSolve/3.2.~~2-08222018 in a batch job:~~		module load BionanoSolve/3.6.1-11162020-foss-2019b

	~~<pre class="gscript">~~
	~~#PBS -S /bin/bash~~
	~~#PBS -q batch~~
	~~#PBS -N job_hybridScaffold~~
	~~#PBS -l nodes=~~1~~:ppn=48~~
	~~#PBS~~ -~~l walltime=12:00:00~~
	~~#PBS~~ -~~l mem=10g~~
	~~#PBS~~ -~~j oe~~

	~~cd $PBS_O_WORKDIR~~		python ${EBROOTBIONANOSOLVE}/Pipeline/11162020/pipelineCL.py -T 32 -j 32 [options]
	~~module load BionanoSolve/3.2.2-08222018-foss-2016b~~
	python $EBROOTBIONANOSOLVE/Pipeline/~~08222018~~/pipelineCL.py -T 48 -j 48 [options]
	</pre>		</pre>

	where EBROOTBIONANOSOLVE is the environmental variable storing BionanoSolve installation path on cluster; [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.		where EBROOTBIONANOSOLVE is the environmental variable storing BionanoSolve installation path on the cluster; [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.

	'''Please note:''' BionanoSolve needs to use Distributed Resource Management Application API (DRMAA http://www.drmaa.org/) and a properly configured "clusterArgument.xml" file to run a distributed parallel job on cluster. Currently DRMAA is not available on Sapelo2 cluster; therefore, please run BionanoSolve pipelineCL.py on a single node. Please do not run the pipeline using "-C <cluster argument.xml file>" option. We are sorry for the inconvenience.		'''Please note:''' BionanoSolve needs to use Distributed Resource Management Application API (DRMAA http://www.drmaa.org/) and a properly configured "clusterArgument.xml" file to run a distributed parallel job on the cluster. Currently DRMAA is not available on Sapelo2 cluster; therefore, please run BionanoSolve pipelineCL.py on a single node. Please do not run the pipeline using "-C <cluster argument.xml file>" option. We are sorry for the inconvenience.


	Example of job submission		Example of job submission
	<pre class="gcommand">		<pre class="gcommand">
	~~qsub~~ sub.sh		sbatch sub.sh
	</pre>		</pre>

Moses at 14:31, 14 April 2021

2021-04-14T14:31:55Z

← Older revision		Revision as of 10:31, 14 April 2021
Line 31:		Line 31:


	Pipeline is at $EBROOTBIONANOSOLVE/Pipeline/11162020		Pipeline is at ${EBROOTBIONANOSOLVE}/Pipeline/11162020

	HybridScaffold is at $EBROOTBIONANOSOLVE/HybridScaffold/11162020		HybridScaffold is at ${EBROOTBIONANOSOLVE}/HybridScaffold/11162020

	RefAligner is at $EBROOTBIONANOSOLVE/RefAligner/11442.11643rel		RefAligner is at ${EBROOTBIONANOSOLVE}/RefAligner/11442.11643rel

	VariantAnnotation is at $EBROOTBIONANOSOLVE/VariantAnnotation/11162020		VariantAnnotation is at ${EBROOTBIONANOSOLVE}/VariantAnnotation/11162020

	FSHD is at $EBROOTBIONANOSOLVE/FSHD/11162020		FSHD is at ${EBROOTBIONANOSOLVE}/FSHD/11162020


Line 45:		Line 45:

	<pre class="gscript">		<pre class="gscript">
	#~~PBS -S~~ /bin/bash		#!/bin/bash
	#~~PBS~~ -q batch		#SBATCH --job-name=job_hybridScaffold
	#~~PBS~~ -~~N job_hybridScaffold~~		#SBATCH --partition=batch
	#~~PBS~~ -~~l nodes~~=~~1:ppn~~=2		#SBATCH --ntasks=1
	#~~PBS~~ -~~l walltime~~=12:00:00		#SBATCH --cpus-per-task=8
	#~~PBS~~ -~~l mem~~=~~10g~~		#SBATCH --mem=20gb
	#~~PBS~~ -j oe		#SBATCH --time=120:00:00
			#SBATCH --output=log.%j.out
			#SBATCH --error=log.%j.err
			#SBATCH --mail-user=username@uga.edu
			#SBATCH --mail-type=ALL

	cd $PBS_O_WORKDIR		cd $PBS_O_WORKDIR

Moses at 14:29, 14 April 2021

2021-04-14T14:29:20Z

← Older revision		Revision as of 10:29, 14 April 2021
Line 8:		Line 8:

	=== Version ===		=== Version ===
	3.2.1-~~04122018, 3.2.2-08222018, 3.3-10252018, 3.4-06042019~~		3.6.1-11162020

	=== Author / Distributor ===		=== Author / Distributor ===
Line 21:		Line 21:
	For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.		For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

	*Version 3.2.1-~~04122018~~, installed in ~~/usr/local~~/apps/eb/BionanoSolve/3.2.1-~~04122018-foss-2016b~~		*Version 3.6.1-11162020, installed in /apps/eb/BionanoSolve/3.6.1-11162020-foss-2019b
	*Version 3.2.2-08222018, installed in /usr/local/apps/eb/BionanoSolve/3.2.2-08222018-foss-2016b
	*Version 3.3-10252018, installed in /usr/local/apps/eb/BionanoSolve/3.3-10252018-foss-2016b
	*Version 3.4-06042019, installed in /usr/local/apps/eb/BionanoSolve/3.4-06042019-foss-~~2016b~~

	To use BionanoSolve/3.2.1-~~04122018~~ pipelines, please first load the module with		To use BionanoSolve v3.6.1-11162020 pipelines, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	module load BionanoSolve/3.2.1-~~04122018~~-foss-~~2016b~~		module load BionanoSolve/3.6.1-11162020-foss-2019b
	</pre>		</pre>

	~~To use BionanoSolve/3.2.2-08222018 pipelines, please first load the module with~~		Once you loaded the module, an environmental variable called EBROOTBIONANOSOLVE is exported. It stores BionanoSolve installation path on the cluster, i.e., /apps/eb/BionanoSolve/3.6.1-11162020-foss-2019b/ . Using EBROOTBIONANOSOLVE, BionanoSolve components can be easily found, for example:
	~~<pre class="gscript">~~
	~~module load BionanoSolve/3.2.2-08222018-foss-2016b~~
	~~</pre>~~

	~~To use BionanoSolve/3.3-10252018 pipelines, please first load the module with~~
	~~<pre class="gscript">~~
	~~module load BionanoSolve/3.3-10252018-foss-2016b~~
	~~</pre>~~

	~~To use BionanoSolve/3.4-06042019 pipelines, please first load the module with~~
	~~<pre class="gscript">~~
	~~module load BionanoSolve/3.4-06042019-foss-2016b~~
	~~</pre>~~

	Once you loaded the module, an environmental variable called EBROOTBIONANOSOLVE is ~~created for storing~~ BionanoSolve installation path on cluster (i.e. ~~/usr/local~~/apps/eb/BionanoSolve/3.2.1-~~04122018~~-foss-~~2016b for version 3.2.1-04122018; /usr/local/apps/eb/BionanoSolve~~/~~3.2.2-08222018-foss-2016b for version 3.2.2-08222018; /usr/local/apps/eb/BionanoSolve/3.3-10252018-foss-2016b for version 3.2.2-08222018)~~. Using EBROOTBIONANOSOLVE, BionanoSolve components can be easily found, for example:

	*Version 3.2.1-04122018:

	~~Pipeline is put in $EBROOTBIONANOSOLVE/Pipeline/04122018~~

	~~HybridScaffold is put in $EBROOTBIONANOSOLVE/HybridScaffold/04122018~~

	~~RefAligner is put in $EBROOTBIONANOSOLVE/RefAligner/7437.7523rel~~

	~~VariantAnnotation is put in $EBROOTBIONANOSOLVE/VariantAnnotation/04122018~~

	*Version 3.2.2-08222018:

	~~Pipeline is put in $EBROOTBIONANOSOLVE/Pipeline/08222018~~

	~~HybridScaffold is put in $EBROOTBIONANOSOLVE/HybridScaffold/08222018~~

	~~RefAligner is put in $EBROOTBIONANOSOLVE/RefAligner/7782.7865rel~~

	~~VariantAnnotation is put in $EBROOTBIONANOSOLVE/VariantAnnotation/08222018~~

	*Version 3.3-10252018:

	~~Pipeline is put in $EBROOTBIONANOSOLVE/Pipeline/10252018~~

	~~HybridScaffold is put in $EBROOTBIONANOSOLVE/HybridScaffold/10252018~~

	~~RefAligner is put in $EBROOTBIONANOSOLVE/RefAligner/7915.7989rel~~

	~~VariantAnnotation is put in $EBROOTBIONANOSOLVE/VariantAnnotation/10252018~~

	*Version 3.4-06042019:		Pipeline is at $EBROOTBIONANOSOLVE/Pipeline/11162020

	~~Pipeline~~ is ~~put in~~ $EBROOTBIONANOSOLVE/~~Pipeline~~/~~06042019~~		HybridScaffold is at $EBROOTBIONANOSOLVE/HybridScaffold/11162020

	~~HybridScaffold~~ is ~~put in~~ $EBROOTBIONANOSOLVE/~~HybridScaffold~~/~~06042019~~		RefAligner is at $EBROOTBIONANOSOLVE/RefAligner/11442.11643rel

	~~RefAligner~~ is ~~put in~~ $EBROOTBIONANOSOLVE/~~RefAligner~~/~~8949.9232rel~~		VariantAnnotation is at $EBROOTBIONANOSOLVE/VariantAnnotation/11162020

	~~VariantAnnotation~~ is ~~put in~~ $EBROOTBIONANOSOLVE/~~VariantAnnotation~~/~~06042019~~		FSHD is at $EBROOTBIONANOSOLVE/FSHD/11162020


	Sample job submission script (sub.sh) to run hybridScaffold.pl from BionanoSolve/3.2.1-~~04122018~~ in a batch job:		Sample job submission script (sub.sh) to run hybridScaffold.pl from BionanoSolve/3.6.1-11162020 in a batch job:

	<pre class="gscript">		<pre class="gscript">

Moses: Created page with "Category:Sapelo2oldCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 3.2.1-04122018, 3.2.2-0..."

2021-04-14T14:14:23Z

Created page with "Category:Sapelo2old Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 3.2.1-04122018, 3.2.2-0..."

New page

[[Category:Sapelo2old]][[Category:Software]][[Category:Bioinformatics]]

=== Category ===
Bioinformatics

=== Program On ===
Sapelo2

=== Version ===
3.2.1-04122018, 3.2.2-08222018, 3.3-10252018, 3.4-06042019

=== Author / Distributor ===
Details are at [https://bionanogenomics.com/support-page/bionano-solve/ Bionano Solve]

=== Description ===
From [https://bionanogenomics.com/support-page/bionano-solve/ Bionano Solve]: "Bionano Solve™ is an analysis pipeline for Bionano data processing, optimized for Bionano Compute and IrysSolve Compute Servers. A de novo assembly of a human genome can be completed in about 28 hours. Bionano Tools contains various tools and scripts, including the Bionano Solve analysis pipeline. These tools together perform computation jobs on Saphyr and IrysSolve Compute Servers."

=== Running Program ===
Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

*Version 3.2.1-04122018, installed in /usr/local/apps/eb/BionanoSolve/3.2.1-04122018-foss-2016b
*Version 3.2.2-08222018, installed in /usr/local/apps/eb/BionanoSolve/3.2.2-08222018-foss-2016b
*Version 3.3-10252018, installed in /usr/local/apps/eb/BionanoSolve/3.3-10252018-foss-2016b
*Version 3.4-06042019, installed in /usr/local/apps/eb/BionanoSolve/3.4-06042019-foss-2016b

To use BionanoSolve/3.2.1-04122018 pipelines, please first load the module with
<pre class="gscript">
module load BionanoSolve/3.2.1-04122018-foss-2016b
</pre>

To use BionanoSolve/3.2.2-08222018 pipelines, please first load the module with
<pre class="gscript">
module load BionanoSolve/3.2.2-08222018-foss-2016b
</pre>

To use BionanoSolve/3.3-10252018 pipelines, please first load the module with
<pre class="gscript">
module load BionanoSolve/3.3-10252018-foss-2016b
</pre>

To use BionanoSolve/3.4-06042019 pipelines, please first load the module with
<pre class="gscript">
module load BionanoSolve/3.4-06042019-foss-2016b
</pre>

Once you loaded the module, an environmental variable called EBROOTBIONANOSOLVE is created for storing BionanoSolve installation path on cluster (i.e. /usr/local/apps/eb/BionanoSolve/3.2.1-04122018-foss-2016b for version 3.2.1-04122018; /usr/local/apps/eb/BionanoSolve/3.2.2-08222018-foss-2016b for version 3.2.2-08222018; /usr/local/apps/eb/BionanoSolve/3.3-10252018-foss-2016b for version 3.2.2-08222018). Using EBROOTBIONANOSOLVE, BionanoSolve components can be easily found, for example:

*Version 3.2.1-04122018:

Pipeline is put in $EBROOTBIONANOSOLVE/Pipeline/04122018

HybridScaffold is put in $EBROOTBIONANOSOLVE/HybridScaffold/04122018

RefAligner is put in $EBROOTBIONANOSOLVE/RefAligner/7437.7523rel

VariantAnnotation is put in $EBROOTBIONANOSOLVE/VariantAnnotation/04122018

*Version 3.2.2-08222018:

Pipeline is put in $EBROOTBIONANOSOLVE/Pipeline/08222018

HybridScaffold is put in $EBROOTBIONANOSOLVE/HybridScaffold/08222018

RefAligner is put in $EBROOTBIONANOSOLVE/RefAligner/7782.7865rel

VariantAnnotation is put in $EBROOTBIONANOSOLVE/VariantAnnotation/08222018

*Version 3.3-10252018:

Pipeline is put in $EBROOTBIONANOSOLVE/Pipeline/10252018

HybridScaffold is put in $EBROOTBIONANOSOLVE/HybridScaffold/10252018

RefAligner is put in $EBROOTBIONANOSOLVE/RefAligner/7915.7989rel

VariantAnnotation is put in $EBROOTBIONANOSOLVE/VariantAnnotation/10252018

*Version 3.4-06042019:

Pipeline is put in $EBROOTBIONANOSOLVE/Pipeline/06042019

HybridScaffold is put in $EBROOTBIONANOSOLVE/HybridScaffold/06042019

RefAligner is put in $EBROOTBIONANOSOLVE/RefAligner/8949.9232rel

VariantAnnotation is put in $EBROOTBIONANOSOLVE/VariantAnnotation/06042019

Sample job submission script (sub.sh) to run hybridScaffold.pl from BionanoSolve/3.2.1-04122018 in a batch job:

<pre class="gscript">
#PBS -S /bin/bash
#PBS -q batch
#PBS -N job_hybridScaffold
#PBS -l nodes=1:ppn=2
#PBS -l walltime=12:00:00
#PBS -l mem=10g
#PBS -j oe

cd $PBS_O_WORKDIR
module load BionanoSolve/3.2.1-04122018-foss-2016b
perl $EBROOTBIONANOSOLVE/HybridScaffold/04122018/hybridScaffold.pl [options]
</pre>

Sample job submission script (sub.sh) to run pipelineCL.py from BionanoSolve/3.2.1-04122018 in a batch job:

<pre class="gscript">
#PBS -S /bin/bash
#PBS -q batch
#PBS -N job_hybridScaffold
#PBS -l nodes=1:ppn=48
#PBS -l walltime=12:00:00
#PBS -l mem=10g
#PBS -j oe

cd $PBS_O_WORKDIR
ml BionanoSolve/3.2.1-04122018-foss-2016b
python $EBROOTBIONANOSOLVE/Pipeline/04122018/pipelineCL.py -T 48 -j 48 [options]
</pre>

Sample job submission script (sub.sh) to run hybridScaffold.pl from BionanoSolve/3.2.2-08222018 in a batch job:

<pre class="gscript">
#PBS -S /bin/bash
#PBS -q batch
#PBS -N job_hybridScaffold
#PBS -l nodes=1:ppn=2
#PBS -l walltime=12:00:00
#PBS -l mem=10g
#PBS -j oe

cd $PBS_O_WORKDIR
module load BionanoSolve/3.2.2-08222018-foss-2016b
perl $EBROOTBIONANOSOLVE/HybridScaffold/08222018/hybridScaffold.pl [options]
</pre>

Sample job submission script (sub.sh) to run pipelineCL.py from BionanoSolve/3.2.2-08222018 in a batch job:

<pre class="gscript">
#PBS -S /bin/bash
#PBS -q batch
#PBS -N job_hybridScaffold
#PBS -l nodes=1:ppn=48
#PBS -l walltime=12:00:00
#PBS -l mem=10g
#PBS -j oe

cd $PBS_O_WORKDIR
module load BionanoSolve/3.2.2-08222018-foss-2016b
python $EBROOTBIONANOSOLVE/Pipeline/08222018/pipelineCL.py -T 48 -j 48 [options]
</pre>

where EBROOTBIONANOSOLVE is the environmental variable storing BionanoSolve installation path on cluster; [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.

'''Please note:''' BionanoSolve needs to use Distributed Resource Management Application API (DRMAA http://www.drmaa.org/) and a properly configured "clusterArgument.xml" file to run a distributed parallel job on cluster. Currently DRMAA is not available on Sapelo2 cluster; therefore, please run BionanoSolve pipelineCL.py on a single node. Please do not run the pipeline using "-C <cluster argument.xml file>" option. We are sorry for the inconvenience.

Example of job submission
<pre class="gcommand">
qsub sub.sh
</pre>

=== Documentation ===

Details are at [https://bionanogenomics.com/support-page/bionano-solve/ BionanoSolve]

A user manual for running BionanoSolve pipeline on command-line can be found at [https://bionanogenomics.com/wp-content/uploads/2018/04/30205-Guidelines-for-Running-Bionano-Solve-Pipeline-on-Command-Line.pdf BionanoSolve guide]

<pre class="gcommand">
module load BionanoSolve/3.2.2-08222018-foss-2016b
perl $EBROOTBIONANOSOLVE/HybridScaffold/08222018/hybridScaffold.pl -h

Usage: perl hybridScaffold.pl <-h> <-n ngs_file> <-b bng_cmap_file> <-c hybrid_config_xml> <-o output_folder> <-B conflict_filter_level> <-N conflict_filter_level> <-f>
<-m molecules_bnx> <-p de_novo_pipeline> <-q de_novo_xml> <-v> <-x> <-y> <-e noise_param><-z tar_zip_file><-S>
-h : This help message
-n : Input NGS FASTA [required]
-b : Input BioNano CMAP [required]
-c : Merge configuration file [required]
-o : Output folder [required]
-r : RefAligner program [required]
-B : conflict filter level: 1 no filter, 2 cut contig at conflict, 3 exclude conflicting contig [required if not using -M option]
-N : conflict filter level: 1 no filter, 2 cut contig at conflict, 3 exclude conflicting contig [required if not using -M option]
-f : Force output and overwrite any existing files
-x : Flag to generate molecules to hybrid scaffold alignment and molecules to genome map alignment [optional]
-y : Flag to generate chimeric quality score for the Input BioNano CMAP [optional]
-m : Input BioNano molecules BNX [optional; only required for either the -x or -y option]
-p : Input de novo assembly pipeline directory [optional; only required for -x option]
-q : Input de novo assembly pipeline optArguments XML script [optional; only required for -x option]
-e : Input de novo assembly noise parameter .errbin or .err file [optional; recommended for -y option but not required]
-v : Print pipeline version information
-M : Input a conflict resolution file indicating which NGS and BioNano conflicting contigs to be cut [optional]
-z : Name of a zipped file to archive the essential output files [optional]
-S : Only run hybridScaffold up to before Merge steps [optional]
-w : Name of the status text file needed by IrysView [optional]
-t : Perform pre-pairmerge sequence to pre-pairmerge genome map alignment [optional]
-u : Sequence of enzyme recognition site (overrides what has been specified in config XML file, for IrysView only) [optional]

python $EBROOTBIONANOSOLVE/Pipeline/08222018/pipelineCL.py -h

usage: pipelineCL.py [-h] [-T T] [-j MAXTHREADS] [-jp MAXTHREADSPW] [-N N]
[-G BED] [-i ITER] [-b BNX] [-l LOCAL] [-t TOOLS]
[-B BYPASS] [-e EXP] [-r REF] [-x] [-c CLEANUP] [-C CXML]
[-w] [-a XML] [-p PERF] [-d] [-u] [-U [GROUPCONTIGS]]
[-v [VERSION]] [-V RUNSV] [-A] [-y] [-m] [-H [H]]
[-f [F]] [-J J] [-z] [-E] [-W W] [-F F] [-R [R]]
[-cd CONTROLDIR] [-pd PARAMDIR] [-op OUTLIERP]

Pipeline for de novo assembly - BioNano Genomics

optional arguments:
-h, --help show this help message and exit
-T T Available threads per Node [default 1]
-j MAXTHREADS Max Threads per job [default -T]
-jp MAXTHREADSPW Max Threads per pairwise or stage0 job [default -T arg]
-N N Minimum number of split bnx files (actual number is
multiple of this) (optional, default 2)
-G BED Bed file for gaps, used in structural variation (SV)
detection to check for SV overlap with reference gaps
-i ITER Number of extension and merge iterations (default=1, must
be in range [0,20], use 0 to skip)
-b BNX Input molecule (.bnx) file, required
-l LOCAL Location of output files root directory, required, will
be created if does not exist; if does exist, will
overwrite contents (may be error-prone)
-t TOOLS Location of executable files (RefAligner and Assembler,
required)
-B BYPASS Skip steps, using previous result. <= 0:None,
1:ImgDetect, 2:NoiseChar/Subsample, 3:Pairwise,
4:Assembly, 5:RefineA, 6:RefineB, 7:merge0,
8+(i-1)*2:Ext(i), 9+(i-1)*2:Mrg(i), N+1:alignmol
-e EXP Output file prefix (optional, default = exp)
-r REF Reference file (must be .cmap), to compare resulting
contigs (optional)
-x Exit after auto noise (noise characterization), do not
preform de novo assembly
-c CLEANUP Remove contig results (0 - keep all (default), 1 - remove
intermediate files, 2 - store in sqlite, 3 - store in
sqlite and remove)
-C CXML Run on cluster, read XML file for submission arguments
(optional--will not use cluster submission if absent)
-w Wipe clean previous contig results
-a XML Read XML file for parameters (required)
-p PERF Log performance in pipelineReport 0=None, 1=time, 2=perf,
3=time&perf (default=1)
-d Retired option (contig subdirectories), always enabled.
-u Do not perform final refinement (not recommended).
-U [GROUPCONTIGS] Group contigs in refinement and extension stages: always
ON, this argument has no effect (retained for backward
compatibility)
-v [VERSION] Print version; exit if argument > 1 supplied.
-V RUNSV Detect structural variations. Default: run after final
stage (normally refineFinal); if argument 0, disable.
-A Align molcules to final contigs (ON by default, use this
to turn off).
-y Automatically determine noise parameters (requires
reference; optional, default off)
-m Disable molecule vs reference alignments (default on with
reference)
-H [H] Use HG19 (human genome) as reference, loaded from
Analysis/SV/CopyNumberProfiles/DATA. Overrides -r
argument. Use HG38 if argument 2 is supplied. [Default
OFF]
-f [F] Run this fraction of grouped jobs on host (0.2 if no arg)
[default 0]
-J J Number of threads on host for grouped jobs (has no effect
without -f) [default 48]
-z Zip pipeline results (default ON, use this to turn off).
-E ReCheck stdout completeness for completed jobs (default
ON, use this to turn off).
-W W Multiply group sizes by this factor to reduce number of
jobs (for Genomes larger than Human). Use value under 1
to increase number of jobs
-F F Color channel: replace -usecolor X in optArgs with this,
must be either 1 or 2 [default OFF]
-R [R] Rough assembly: denovo assembly used as autoNoise
reference for re-assembly; sequence may be optionally
specified as -r, if supplied, will be used for global
scaling and SV calls, but not for autoNoise (optional,
default off, optional argument 0.2-0.9 for fraction of
rough assembly which must align to sequence for
rescaling)
-cd CONTROLDIR Control data directory for copy number profiles
[optional]
-pd PARAMDIR Parameters directory for copy number profiles [optional]
-op OUTLIERP Outlier Probability for copy number profile (optional)
</pre>

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=== Installation ===

source code from [https://bionanogenomics.com/support/software-downloads/ BionanoSolve download]

=== System ===
64-bit Linux