Command Line Options

Use the following options to control BCL Convert.

Option

Description

Default

--bcl-input-directory

A main command-line option that indicates the path to the run folder directory.

Not applicable

--output-directory

A required command-line option that indicates the path to demultuplexed FASTQ output. The directory must not exist, unless -f, force is specified.

Not applicable

-f --force

[Optional] Allows for the directory specified by the --output- directory option to exist already.

Not applicable

--sample-sheet

[Optional] Indicates the path to the sample sheet to specify the sample sheet location and name, if different from the default.

<--bcl-input-directory>/SampleSheet.csv

--bcl-only-lane

[Optional] Converts only the specified lane number. The value must be less than or equal to the number of lanes specified in the RunInfo.xml. Must be a single integer value.

All lanes as specified in the RunInfo.xml

--first-tile-only

[Optional]

If true, the option only processes the first title of the first swath of the top surface of each lane specified in the sample sheet.

 

If false, the option processes all titles in each lane, as specified in the sample sheet.

true

false

--strict-mode

[Optional]

If true, the option aborts the program if any filter, LOCSlocs, BCLbcl, or BCIbci lane files are missing or corrupt.

 

If false, the option continues processing if any filter, LOCSlocs, BCLbcl, or BCIbci lane files are missing. Returns a warning message for each missing or corrupt file.

false

--bcl-sampleproject-subdirectories

[Optional]

If true, the option allows creation of Sample_Project subdirectories as specified in the sample sheet. To use the Sample_Project column in the data section, this option must be set to true for the Sample_Project column in the data section to be used.

false

-h,
--help

Produces a help message and exits the application.

Not applicable

-V,
--version

Produces a help message and exits the application.

Not applicable

--no-lane-splitting

Consolidates FASTQ files across lanes. : Eeach sample is provided into the same file on a per read basis.

• Must be true or false.
• Only allowed when Lane column is excluded from the Sample Sheet.

false

The following options can be used to manually control performance. Only use the options to reduce core count when BCL Convert is running on a shared machine . In all other instances, use the default settings.

Total CPU heavy threads should be less than the number of HW cores you want to use for other processes. The following formula gives the total number of CPU heavy threads used by BCL Convert:

(--bcl-num-parallel-tiles * --bcl-num-conversion-threads + --bcl-num-compression-threads + --bcl-num-decompression-threads)

Option

Description

Default

--bcl-num-parallel-tiles

Specifies number of tiles being converted to FASTQ files in parallel. Must be between 1 and available hardware threads, inclusive.

For 32 CPU threads use --bcl-num-parallel -tiles 2.

Determined dynamically.

If using CBCI input, the value is 4.

If using aggregate BCL input, the value is 1.

--bcl-conversion-threads

Specifies number of threads used for conversion per tile. Must be between 1 and available hardware threads, inclusive.

For 32 CPU threads use

--bcl-num-conversion-threads 4.

Determined dynamically.

If > 10,000 samples, the value is 1.

If < 10,000 samples, the value is nproc / #parallel-tiles.

--bcl-num-compression-threads

Specifies number of CPU threads used for compression of output FASTQ files. Must be between 1 and available hardware threads, inclusive.

For 32 CPU threads use

--bcl-num-compression-threads 16.

Determined dynamically

--bcl-num-decompression-threads

Specifies number of CPU threads used for decompression of input base call files. Must be between 1 and available hardware threads, inclusive.

For 32 CPU threads use

--bcl-num-decompression-threads 8.

Determined dynamically

--shared-thread-odirect-output

Uses experimental shared-thread file output code, which requires O_DIRECT mode. Must be true or false.

This file output method is optimized for sample counts greater than 100,000. The optionIt is not recommended for lower sample counts or if using a distributed file system target such as GPFS or Lustre.

false