Troubleshooting
General Troubleshooting on Standalone DRAGEN Server
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:
Navigate to the following location
/<analysis_output>/Logs_Intermediates/SamplesheetValidation.Open the
SamplesheetValidation-.logfileFind a line with the following:
SampleSheetValidationTask:NA:1 exited with return code 1 which has not been declared as a valid return code.Search for errors in the sample sheet validation log and compare with the guidelines and warnings in Sample Sheet Requirements and the following tables.
General troubleshooting for a failed sample sheet:
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:
TSO 500
UP1-UP16
CP1-CP16 (DNA Only)
TSO 500 HT
UDP0001–UDP0192
Troubleshooting BCL issues:
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:
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
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:
Failure type: ValueError: Could not find pipeline ID for app BCLConvert in sample sheet SampleSheet.csv
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