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-<timestamp>.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 Sample Sheet Requirements and the following tables. |
|
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 present 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 Not in v2 Format |
Verify that the format of the sample sheet is in v2 format. 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. |
|
Assay |
NextSeq 550 |
NextSeq 550 |
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TSO 500 |
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UP1–UP16 |
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TSO 500 HT |
UDP0001–UDP0192 |
UDP0001–UDP0192 |
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Failure Type |
Action |
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|
Lane Column without Values |
Ensure that the column is completed. If lane is not applicable to the run, delete the column. |
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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. [BCLConvert_Settings]
[BCLConvert_Data]
[TS0500S_Data]
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HRD analysis is missing |
Make sure that HRD is in the correct column in the sample sheet. Refer to Sample Sheet Requirements for more information. |
|
Failure Type |
Action |
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Sample_ID and/or Sample_Type is not present |
Verify that the sample sheet has columns and values for Sample_ID and Sample_Type. |
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Unique sample IDs |
Verify that the Sample_IDs are unique in the sample sheet. |
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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]
Make sure that HRD, if needed, is in the correct column in the sample sheet. Refer to Sample Sheet Requirements for more information. |
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Incorrect folder structure |
When starting from FASTQs, the folder structure must be very specific with the correct number of files and subfolders. Refer to Starting From FASTQ Files for more information. |
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Invalid FASTQ input files |
If the FASTQs are invalid, start TSO 500 analysis from BCL files. |
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HRD analysis missing |
Make sure that HRD is in the correct column in the sample sheet. |
