BCL Convert v4.0

The minimum operating requirements for BCL Convert v4.0 are as follows.

Hardware Requirements

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Single multiprocessor or multicore computer

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Minimum 64 GB RAM

Exact storage requirements vary based on throughput and sample count. For more information, refer to the BCL Convert v4.0 pages of the Illumina support center.

Software Requirements

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Linux CentOS 6 or later

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Root access to your computer

BCL Convert v4.0 is installed from an RPM package downloaded from the Illumina support center. To start installation navigate to /usr/local/bin/bcl-convert.

Install the RPM package as follows.

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To install the software in the default location, use the following command:

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To specify a custom install location, use the following commandr:

Run BCL Convert v4.0 as follows.

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Open a command-line window.

2.

Enter the following command and add options as needed:

nohup /usr/local/bin/bcl-convert

For example, the following command populates the output directory with FASTQ files:

nohup /usr/local/bin/bcl-convert -bcl-input-directory

<RunFolder> --output-directory <OutputDirectory>

The Tools and Utilities section of the Illumina DRAGEN Bio-IT Platform documentation provides additional information for using BCL Convert v4.0.

BCL Convert v4.0 produces the following FASTQ and metrics output files. All output files can be found in the Reports folder of the output directory.

For additional information on FASTQ output and directory files and BCL metric output files, refer to the Tools and Utilities section of the Illumina DRAGEN Bio-IT Platform documentation.

FASTQ Output Files

On the Files tab, BCL Convert v4.0 generates one FASTQ data set per sample.

These files are arranged in the following folder structure:

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<Sample ID> data set—Contains complete FASTQ (*.fastq.gz) files for each sample.

Index Metrics Output File

The index metrics output file (IndexMetricsOut.bin) is a binary file in BIN format. The file contains index statistics for each sample and index combination per lane provided to BCL Convert v4.0 in the sample sheet. The content of the file is documented as follows.

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Byte 0: file version number (2)

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The remaining bytes represent records, which are composed of the following information:

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2 bytes: lane number (uint16)

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4 bytes: tile number (uint32)

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2 bytes: read number (uint16)

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2 bytes: indexLength, the length in bytes of index name (uint16)

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indexLength bytes: string representing index name

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8 bytes: number of occurrences of index (uint64)

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2 bytes: sampleLength, the length in bytes of the sample name (uint16)

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sampleLength bytes: string representing sample name

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2 bytes: projectLength, the length in bytes of the project name (uint16)

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projectLength bytes: string representing project name

Use the following to troubleshoot or resolve error conditions experienced while using IlluminaBCL Convert v4.0.

Barcode Collision Error and Solution

Previous versions of BCL Convert allowed the overall concentrated sequence to pass the single index hamming distance rules if the concentration was sufficiently diverse. BCL Convert v3.10.5 and later uses strict barcode collision logic to support increased high-throughput and complex sample pooling. Each index in a dual setup must individually meet the hamming distance requirements set by the BarcodeMismatchesIndex# value. If either i7 or i5 does not meet the hamming distance requirements the program will error.

For default BarcodeMismatchesIndex1 and BarcodeMismatchesIndex2, the following apply:

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Barcodes must differ by at least 3 bases.

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If any two samples in i7 differ by fewer than 3 bases, an error is produced and the run will not proceed, regardless of the samples i5 values.

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If any two samples in i5 differ by fewer than 3 bases, an error is produced and the run will not proceed, regardless of the samples i7 values.

If you receive errors with current versions of DRAGEN or BCL Convert, lower the mismatch tolerance for the index producing the error. To lower mismatch tolerance, use the BarcodeMismatchesIndex1 or BarcodeMismatchesIndex2 sample sheet settings. For additional information on barcode mismatches, refer to the Tools and Utilities section of the Illumina DRAGEN Bio-IT Platform v4.0 documentation.

The BCL Convert v4.0 support pages on the Illumina support center provide additional resources. These resources include training, compatible products, and other considerations. Always check the support center for the latest versions.

Document #	Date	Description of Change
200023259 v00	July 2022	Initial release.