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Optional Arguments

The following arguments are optional additions to a Bases2Fastq execution command. Arguments that affect run parameters default to the value recorded in the RunParameters.json file from the sequencing run.

--chemistry-version​

Use --chemistry-version to overwrite the sequencing kit version in RunParameters.json with one of the following valid values:

  • Cloudbreak for a Cloudbreak kit
  • CloudbreakFS for a Cloudbreak Freestyle kit
  • CloudbreakUQ for a Cloudbreak UltraQ kit
  • Trinity for a Trinity kit
bases2fastq /input /output --chemistry-version Cloudbreak

--demux-only​

Use --demux-only or -d to enable demultiplexing-only mode, which performs demultiplexing and outputs index metrics without generating any FASTQ files.

bases2fastq /input /output --d
bases2fastq /input /output --demux-only

--detect-adapters​

Use --detect-adapters to detect adapter sequences and override any sequences present in the run manifest. For more information, see Adapter Trimming.

bases2fastq /input /output --detect-adapters

--error-on-missing​

Use --error-on-missing to make an execution terminate when a non-critical file is missing, rather than the default behavior of skipping the file and continuing the execution.

bases2fastq /input /output --error-on-missing

--exclude-tile​

Use --exclude-tile or -e to specify a subset of tiles to exclude from processing. The argument uses regex to identify the tiles. To specify multiple subsets, enter the argument multiple times.

The following examples exclude the tiles from lane 1.

bases2fastq /input /output -e 'L1R..C..S.'
bases2fastq /input /output --exclude-tile 'L1R..C..S.'

--filter-mask​

Use --filter-mask to apply a custom base mask to specify the cycles that determine if a read passes filter. Separate each read section with a hyphen. The argument is only compatible with Cloudbreak or Cloudbreak Freestyle chemistry. The default values are R1:Y15N* and R2:Y15N*. In AVITI OS, the Filter Mask setting for the Advanced Run Settings add-on can modify the default values.

The following example applies a filter mask with the base mask I1:Y4N*, which refers to the first four cycles of the Index 1 read.

bases2fastq /input /output --filter-mask I1:Y4N*

The following example applies a filter mask with the base masks R1:Y18N* and R2:Y18N*, which refer to the first 18 cycles of both Read 1 and Read 2.

bases2fastq /input /output --filter-mask R1:Y18N*-R2:Y18N*

--flowcell-id​

Use --flowcell-id to overwrite the flow cell ID in RunParameters.json with another flow cell ID. You can use this argument to add a missing flow cell ID.

The following example updates the flow cell ID to 123abc123.

bases2fastq /input /output --flowcell-id 123abc123

--force-index-orientation​

Use --force-index-orientation to perform demultiplexing without detecting the index sequence orientation. When used, Bases2Fastq applies the orientation recorded in the run manifest.

bases2fastq /input /output --force-index-orientation

--group-fastq​

Use --group-fastq to group all generated sample FASTQ files at the root of the project folder.

bases2fastq /input /output --group-fastq

When used with --no-projects, Bases2Fastq groups all generated sample FASTQ files in the Samples folder.

bases2fastq /input /output --group-fastq --no-projects

--help​

Use --help or -h to display the usage statement for Bases2Fastq.

bases2fastq -h
bases2fastq --help

--i1-cycles​

Use --i1-cycles to overwrite the number of cycles in Index 1 in RunParameters.json with another value.

bases2fastq /input /output --i1-cycles 16

--i2-cycles​

Use --i2-cycles to overwrite the number of cycles in Index 2 in RunParameters.json with another value.

bases2fastq /input /output --i2-cycles 16

--include-tile​

Use --include-tile or -i to specify a subset of tiles to include in the execution. To include specific tiles, you must first exclude all tiles with the --exclude-tile or -e argument. The argument uses regex to identify the selected tiles. To specify multiple subsets, enter the argument multiple times.

The following example includes the subset of tiles L1R..C..S2 after excluding all tiles.

bases2fastq /input /output --exclude-tile 'L.*R..C..S.' --include-tile 'L1R..C..S2'

The following example includes the additional subset of tiles L2R..C..S1.

bases2fastq /input /output -e 'L.*R..C..S.' -i 'L1R..C..S2' -i 'L2R..C..S1'

--input-remote​

Use --input-remote to set the rclone remote name that points to the input files.

bases2fastq /input /output --input-remote '<input-name>'

--kit-configuration​

Use --kit-configuration to overwrite the kit configuration in RunParameters.json with one of the following valid values:

  • 150Cycles for a 2 x 75 kit
  • 300Cycles for a 2 x 150 kit
  • 600Cycles for a 2 x 300 kit
bases2fastq /input /output --kit-configuration 300Cycles

--legacy-fastq​

Use --legacy-fastq to apply a legacy file naming convention to FASTQ files, such as SampleName_S1_L001_R1_001.fastq.gz. Some secondary analysis software might require this naming convention.

Note:

The --legacy-fastq argument is not compatible with lane merging. When you use the --legacy-fastq argument, Bases2Fastq writes the FASTQ files as split lanes. Therefore, if you combine the --split-lanes and --legacy-fastq arguments, the --legacy-fastq argument takes precedence, and Bases2Fastq displays a warning message before proceeding with the execution.

bases2fastq /input /output --legacy-fastq

--log-level​

Use --log-level or -l to specify the minimum level required to log an event. Use one of the following valid values. The default value is INFO.

  • INFO
  • DEBUG
  • WARNING
  • ERROR
bases2fastq /input /output -l DEBUG
bases2fastq /input /output --log-level WARNING

--no-error-on-invalid​

Use --no-error-on-invalid to skip non-critical files that Bases2Fastq identifies as invalid.

bases2fastq /input /output --no-error-on-invalid

--no-projects​

Use --no-projects to organize the output file directory without project folders and instead use the standard, sample-based folder structure.

bases2fastq /input /output --no-projects

--num-threads​

Use --num-threads or -p to specify the number of threads to use for processing, with a minimum value of 1 and a maximum value that depends on your system. The default value is 1.

bases2fastq /input /output -p 8
bases2fastq /input /output --num-threads 8

--num-unassigned​

Use --num-unassigned to specify a value ≤ 1000 that indicates the maximum number of unassigned sequences to support. The default value is 30.

bases2fastq /input /output --num-unassigned 20

--output-remote​

Use --output-remote to set the rclone remote name that points to the output files.

bases2fastq /input /output --output-remote '<output-name>'

--preparation-workflow​

Use --preparation-workflow to overwrite the library prep workflow in RunParameters.json with one of the following valid values:

  • Adept
  • Elevate
  • ThirdParty
bases2fastq /input /output --preparation-workflow Elevate

--qc-only​

Use --qc-only to enable QC-only mode, which generates a representative view of run metrics on one tile and no FASTQ files. Executions in QC-only mode are faster than executions with demultiplexing and can support the following scenarios:

  • Troubleshooting parameters applied to execution
  • Troubleshooting execution issues for specific tiles
  • Quickly obtaining QC metrics for a run
bases2fastq /input /output --qc-only

You can use --include-tile to execute QC-only mode on more than one tile. The following example executes QC-only mode on all tiles in lane 1.

bases2fastq /input /output --qc-only --include-tile 'L1R..C..S.'

--r1-cycles​

Use --r1-cycles to overwrite the number of cycles for Read 1 in RunParameters.json with another value.

bases2fastq /input /output --r1-cycles 48

--r2-cycles​

Use --r2-cycles to overwrite the number of cycles for Read 2 in RunParameters.json with another value.

bases2fastq /input /output --r2-cycles 48

--run-manifest​

Use --run-manifest or -r to define the location of an alternate run manifest for the execution instead of the RunManifest.csv file output by the instrument. For information on corrected run manifests, see the Run Manifest Documentation.

bases2fastq /input /output -r /input/<corrected_manifest_filename.csv>
bases2fastq /input /output -run-manifest /input/<corrected_manifest_filename.csv>

--settings​

Use --settings to overwrite run manifest settings. Entering the argument for each setting you want to overwrite. For more information on available settings, see the Run Manifest Documentation.

The following example changes the run manifest setting for generating an Index 1 FASTQ file to True.

bases2fastq /input /output --settings 'I1Fastq,True'

If you want to overwrite two different settings, you can use --settings twice. The following example also changes the Index 1 base mask to I1:N3Y*.

bases2fastq /input /output --settings 'I1Fastq,True' --settings 'I1Mask,I1:N3Y*'

--skip-qc-report​

Use --skip-qc-report to skip the creation of an HTML QC report.

bases2fastq /input /output --skip-qc-report

--split-lanes​

Use --split-lanes to divide FASTQ files by flow cell lane.

Note:

When you use the --legacy-fastq argument, Bases2Fastq writes the FASTQ files as split lanes. Therefore, if you combine the --split-lanes and --legacy-fastq arguments, the --legacy-fastq argument takes precedence, and Bases2Fastq displays a warning message before proceeding with the execution.

bases2fastq /input /output --split-lanes

--strict​

Use --strict or -s to enable strict mode, which prevents processing when any input files are invalid. When you do not enable strict mode, Bases2Fastq warns you that files are missing or corrupt but continues processing.

bases2fastq /input /output -s
bases2fastq /input /output --strict

--version​

Use --version or -v to display the current version of Bases2Fastq. Bases2Fastq logs the version at the start of any execution on the command line and in the log file.

bases2fastq -v
bases2fastq --version
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