Troubleshooting the GenomeStudio Genotyping Module “Length Cannot Be Less Than Zero” Error When Generating a CNV Region Report
The GenomeStudio Genotyping Module is commonly used for Copy Number Variation (CNV) analysis using the CNV Region Report 2.1.1 plug-in.
When generating a Custom Report in GenomeStudio 2.0 using the CNV Region Report 2.1.1 plug-in, modifying the default output file name can cause report generation to fail. This article explains the cause of the error, how it is related to the report file name, and the steps required to successfully generate the report.
Generating the CNV Region Report and Resulting Error Message
To create a CNV report, select the CNV Region Report 2.1.1 plug-in when running the GenomeStudio Report Wizard (Figure 1).
Figure 1. Genotyping Report Wizard configured to generate a Custom Report using the CNV Region Report 2.1.1 plug-in.
On the final screen of the Report Wizard, browse to the Output Path directory where the report will be saved (Figure 2). The Report Name field is automatically populated with the default file name:
<Project Name>_Custom
Figure 2. Final Screen of the Report Wizard showing the default Report Name.
Error
If the default Report Name is modified, for example, by entering a different report name or removing the _Custom suffix, the report generation fails and the following error message is displayed:
Custom Report Execution Failed Length cannot be less than zero. Parameter name: length
Figure 3. Error displayed when the default Custom Report file name is modified.
Resolution
To successfully generate the report:
Return to the final screen of the Report Wizard.
Generate the report using the exact default file name:
<Project Name>_Custom
Alternatively, keep the default file name intact and append additional text to the end of the file name.
Select Finish.
When the report is generated successfully, the confirmation window shown in Figure 4 appears.
Figure 4. Confirmation message displayed after the Custom Report is generated successfully.
Select:
Yes to open the generated text file immediately.
No to review the file later.
The generated <Project Name>_Custom.txt file contains the location of the Standard CNV Report (Figure 5).
Figure 5. Example <Project Name>_Custom.txt file showing the location of the Standard CNV Report.
Additional Information
The CNV Region Report Plug-in Installer package includes the document:
CNV_Region_Report_Plug-in_v2.1.2_for_GSGT-1000000027837-00.pdf
This document provides additional information about the generated reports.
Section 4.1: Standard CNV Report
Outputs all CNV and Loss of Heterozygosity (LOH) regions identified in the selected samples.
Generates the output file: <projectname>_standard_cnv_report.txt
Summary
Modifying the default Custom Report file name during report creation can cause the CNV Region Report plug-in to fail with a "Custom Report Execution Failed" error.
To avoid this issue, files should be saved using the default file name (<Project Name>_Custom) or retain the default file name and append additional characters to the end of the file name. Once the <projectname>_standard_cnv_report.txt file has been generated successfully, the resulting files can be renamed as needed.
References:
For any feedback or questions regarding this article (Illumina Knowledge Article #8305), contact Illumina Technical Support techsupport@illumina.com.
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