DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • DRAGEN TSO 500 and TSO 500 ctDNA Analysis Software
  • DRAGEN TSO 500 Guides
    • DRAGEN TSO 500 v2.6
      • Introduction to DRAGEN TSO 500 Analysis Software v2.6.x
      • Getting Started
        • Installation of 2.6.0 on Standalone DRAGEN Server
        • Installation of 2.6.1 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • RNA Analysis Methods
        • Quality Control
        • Performance Testing
      • Troubleshooting
    • DRAGEN TSO 500 v2.5
      • Introduction to DRAGEN TSO 500 Analysis Software v2.5.x
      • Getting Started
        • Installation of 2.5.3 on Standalone DRAGEN Server
        • Installation of v2.5.4 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
          • Run on Multiple DRAGEN Servers
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 Analysis on ICA
      • Analysis Output
        • DNA Output
        • RNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
          • RNA Expanded Metrics
          • HRD Metrics Report
          • Block List
        • Analysis Methods
          • FASTQ Generation
          • DNA Analysis Methods
          • RNA Analysis Methods
          • Quality Control
          • Performance Testing
      • Troubleshooting
  • DRAGEN TSO 500 ctDNA Guides
    • DRAGEN TSO 500 ctDNA v2.6
      • Introduction to DRAGEN TSO 500 ctDNA Analysis Software v2.6
      • Getting Started
        • Installation of TSO 500 ctDNA v2.6.0 on Standalone DRAGEN Server
        • Installation of TSO 500 ctDNA v2.6.2 on Standalone DRAGEN Server
        • Getting Started on Illumina Connected Analytics
        • Installation of NovaSeq 6000Dx TSO 500 ctDNA Analysis Application
      • Run Planning
        • Sample Sheet Introduction
        • Sample Sheet Requirements
        • Sample Sheet Creation in BaseSpace Run Planning tool
        • NovaSeq 6000Dx Run Set Up
        • Sample Sheet Templates
      • Launching Analysis
        • Analysis Launch on Standalone DRAGEN Server
          • Command-Line Options
        • Analysis Launch on ICA
          • Auto-Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
          • Manual Launch of DRAGEN TSO 500 ctDNA Analysis on ICA
      • Analysis Output
        • DNA Output
        • Combined Variant Output
        • Metrics Output
          • DNA Expanded Metrics
        • Coverage Reports
        • Block List
      • Analysis Methods
        • FastQ Generation
        • DNA Analysis Methods
        • Quality Control
      • Troubleshooting
  • Reference
    • Revision History
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On this page
  • General Troubleshooting on Standalone DRAGEN Server
  • Sample Sheet Validation Failures
  • General troubleshooting for a failed sample sheet:
  • Valid indexes for assay and instrument combinations:
  • Troubleshooting BCL issues:
  • Troubleshooting FASTQs issues:
  • Other Troubleshooting Tips
  • Troubleshooting on ICA

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  1. DRAGEN TSO 500 Guides
  2. DRAGEN TSO 500 v2.5

Troubleshooting

PreviousPerformance TestingNextDRAGEN TSO 500 ctDNA v2.6

Last updated 4 months ago

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General Troubleshooting on Standalone DRAGEN Server

Failure Type
Actions

Software

- Open the log file ./<AnalysisFolder>/Logs_Intermediates/pipeline_trace.txt. This log file displays each pipeline step run by the Nextflow workflow manager software. If a step fails, it is marked as FAILED. Each step generates log files that are stored in step-specific subfolders in the Logs_Intermediates folder. Review the log files in the relevant Logs_Intermediates folder for the step to identify potential sources of error. - Open the errors folder ./<AnalysisFolder>/errors. The workflow creates an error file, error_<NameOfFailedStep>.json, for each step that failed during analysis. For steps that fail per sample, there is a separately labeled file for each sample that failed each step error_<NameOfFailedStep>_<SampleIDIfRelevant>.json. These files contain the command and stdout and stderr from the step.

Samples

Open the combined metrics output results file ./<AnalysisFolder>/Results/<PairId>/MetricsOutput.tsv. If a sample fails an analysis step, the Pair ID that contains the sample shows the failure under FAILED_STEPS in the Analysis Status section, and COMPLETED_ALL_STEPS shows as False. If available, review the individual log files for the failed steps under ./<AnalysisFolder>/Logs_Intermediates to identify potential sources of error.

Multinode Gather

If the following error appears, check if the sample or pair ID was included multiple times during separate node analysis runs, before being gathered together. If the error exists, rerun one of the analyses without the duplicate and reattempt gathering. ERROR:Gather:Destination file ... already exists - check if the same sample ID is in multiple input folders

Sample Sheet Validation Failures

In DRAGEN TruSight Oncology 500 Analysis Software, the analysis fails if a sample sheet is invalid. If an invalid sample sheet in suspected, log files can help troubleshoot a failed analysis. Use the following steps to find the log file for the sample sheet:

  1. Navigate to the following location /<analysis_output>/Logs_Intermediates/SamplesheetValidation.

  2. Open the SamplesheetValidation-.log file

  3. Find a line with the following: SampleSheetValidationTask:NA:1 exited with return code 1 which has not been declared as a valid return code.

  4. Search for errors in the sample sheet validation log and compare with the guidelines and warnings in and the following tables.

General troubleshooting for a failed sample sheet:

Failure Type
Action

Sample Sheet not found

Verify that SampleSheet.csv is present at the top level of the run folder with the name "SampleSheet.csv". If the sample sheet is in a different location, supply the sample sheet using the --sampleSheet option

Indexes are not valid for the sequencer and/or assay

See Valid indexes for assay and instrument combinations for correct indexes for the sequencer and assay.

Pair_ID is not unique

Pair_ID column is required in the TSO500S_Data section of the sample sheet, which pairs at most one RNA and one DNA sample together for analysis. If the sample does not have a pair, use a unique pair ID for single samples.

Sample Sheet is not in v2 format

Verify that the format of the sample sheet is v2. v1 sample sheet is not compatible with DRAGEN TruSight Oncology 500 Analysis Software.

Analysis does not run

Verify the analysis starts from the run folder, and BCLs or FASTQs are in the correct locations as outlined in Starting From BCL Files and Starting From FASTQ Files respectively.

Valid indexes for assay and instrument combinations:

Assay
Index Set ID

TSO 500

  • UP1-UP16

  • CP1-CP16 (DNA Only)

TSO 500 HT

  • UDP0001–UDP0192

Troubleshooting BCL issues:

Failure Type
Action

Lane Column without Values

Ensure that the column is completed. If lane is not applicable to the run, delete the column.

Format of v2 sample sheet is incorrect

HRD analysis is missing

Troubleshooting FASTQs issues:

Failure Type
Action

Sample_ID and/or Sample_Type is not present

Verify that the sample sheet has columns and values for Sample_ID and Sample_Type.

Unique sample IDs

Verify that the Sample_IDs are unique in the sample sheet.

Format of v2 Sample Sheet is incorrect

Verify that the following sections and fields are present in the sample sheet and follow the individual rules in Sample Sheet Requirements. [TS0500S_Data] - Sample_ID - Index_ID - Sample_Type - Pair_ID

Incorrect folder structure

Invalid FASTQ input files

If the FASTQs are invalid, start TSO 500 analysis from BCL files.

HRD analysis missing

Make sure that HRD is in the correct column in the sample sheet.

Other Troubleshooting Tips

Failure Type
Action

The output file directory contains information from previous analyses

If this issue is seen: specify a new target output folder and repeat analysis To prevent this issue: specify an empty directory before starting analysis

Single exon (single probe) genes are still reported in the CNV VCF file, but not the CNV TSV file

No action needed; software is working as expected.

Currently all single probe genes are not emitted to the Copy Number Variants section of our CombinedVariantOutput.tsv. However, you can still find these events in the cnv.vcf.gz.

Due to the single probe nature, accurate CNV calling has not been validated and as such they are emitted as REF

Troubleshooting on ICA

In addition to TSO 500 managed sample sheet validations, ICA managed TSO 500 errors include the following:

Error
Description

Failure type: ValueError: Could not find pipeline ID for app BCLConvert in sample sheet SampleSheet.csv

Verify that the following sections and fields are present in the sample sheet and follow the individual rules in [BCLConvert_Settings] - SoftwareVersion - AdapterRead1 - AdapterRead2 - AdapterBehavior - MinimumTrimmedReadLength - MaskShortReads [BCLConvert_Data] - Sample_ID - index - index2 [TS0500S_Data] - Sample_ID - Index_ID - Sample_Type - Pair_ID - Sample Feature (Optional)

Verify that HRD is in the Sample Feature column in the sample sheet. Refer to for more information.

- Sample Feature (Optional) Verify when FASTQs were generated using the HRD add-kit (Not available in Japan), Sample Feature is added to those DNA Samples. Refer to for more information.

Verify that the FASTQ files are in the correct structure. Refer to for more information.

Action: Ensure StartsFromFastq field is in the [TSO500S_Settings] section, and it is not present in the [BCLConvert_Settings] Section. Refer to for more information.

Sample Sheet Requirements
Sample Sheet Requirements
Sample Sheet Requirements
Sample Sheet Requirements
Sample Sheet Requirements
Starting From FASTQ Files