INSTALLATION MANUAL. GenoProof Mixture 3. Version /03/2018 qualitype GmbH Dresden. All rights reserved.

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1 INSTALLATION MANUAL GenoProof Mixture 3 Version /03/2018 qualitype GmbH Dresden. All rights reserved. qualitype GmbH Moritzburger Weg Dresden Germany Tel +49 (0) Fax +49 (0) ticketsystem@qualitype.de qualitype.de

2 2 Production and sales: qualitype GmbH Moritzburger Weg Dresden, Germany Tel.: +49 (0) Legal Information and Trademarks This document is property of qualitype GmbH and protected by copyright. The content of this document must not be reproduced in whole or in part, translated, transmitted, stored or disclosed to third parties without prior written approval by qualitype GmbH. The qualitype GmbH continually develops and enhances its products. Hence, the information in this document may be changed without prior notice due to product improvements, standardizations or technical reasons. Some products referred to in the documentation are trademarks or registered trademarks of qualitype GmbH. Other mentioned product names or company names may be trademarks, trade names or registered trademarks of their respective owners. For further information please read the Terms and Conditions and the Software License Terms of qualitype GmbH.

3 3 TABLE OF CONTENTS 1 Installing the software Technical specifications Installation by download Installation procedure Licence agreement Choose install location Choose start menu folder Choose components Copying of data Storage configuration Troubleshooting Questions and problems before the calculation has started Questions and problems during the calculation Questions during the analysis of the convergence diagnostics Index 0

4 4 1 Installing the software This chapter explains how to install GenoProof Mixture and guides you through the installation process, starting from the download of the software to choosing the components you want to install. 1.1 Technical specifications The listed parameters are used to guarantee the necessary technical specifications and preferences are fulfilled. It is possible to use the application in a different environment, but the performance cannot be guaranteed. > System environment - Client Windows 7 Professional/Ultimate/Enterprise, 64 Bit Windows 10 Pro/Enterprise, 64 Bit Modern multi-core processor (4 cores) 4 GB internal memory Full-HD resolution (1920 x 1080 pixel) 200 MB free memory on the installation medium 1 GBit network connection For correct visualisation, the monitor scaling needs to be set to 100 % Note: The available internal memory has a direct effect on the number of possible input parameters for calculations. > System environment - Database Windows Server 2012 R2, 64 Bit Windows Server 2016, 64 Bit Modern multi-core processor (4 cores) 4 GB internal memory for the application server and the database 200 MB free memory for the installation, storage memory depends on the usage High data transfer (SSD recommended) 1 GBit network connection

5 5 Note: It is recommended to install the database on a central server. If the database is installed on the client computer, the specifications for internal memory and medium add up. In this case, the network connection specifications are redundant. 1.2 Installation by download When you have downloaded GenoProof from our website, you can directly start the installation process. Double click on the GenoProof3Setup.exe file. Please continue reading the chapter installation procedure. 1.3 Installation procedure After you have launched the installation procedure, a security warning may pop up. This depends on the security settings of your operating system and secures that only trustworthy and familiar applications are executed. Check the displayed information and confirm the execution of the installation. The installation wizard will open. To get from one to the next screen page, press Next. The language of the installation wizard will automatically be set according to your computer language system. 1.4 Licence agreement The installation wizard shows the licence agreement for GenoProof Mixture. Please read it carefully. Only continue with the installation, when all listed terms and conditions apply. Select I Agree to continue the installation process.

6 6 Figure 1: Licence agreement for GenoProof Mixture. 1.5 Choose install location The install location determines the location on your computer, where GenoProof Mixture will be installed. We recommend to use the pre set installation location, but you can install GenoProof Mixture at any place (e.g. a different drive). Select Browse and choose the install location. Confirm your selection by clicking on Next. Figure 2: Choose Install Location of GenoProof Mixture.

7 7 1.6 Choose start menu folder On the next page you can choose a folder for GenoProof Mixture. Confirm your selection by pressing Next. Figure 3: Choose start menu folder. 1.7 Choose components On this page you can choose the components of GenoProof Mixture, which will be installed. For the correct function of GenoProof Mixture all components are necessary, but you can choose to install the central components on a database. For single-user licences please choose the recommended default setting Desktop. Depending on the intended use, you have several options to install GenoProof Mixture: 1. Desktop All components of GenoProof Mixture are installed on a single computer. Therefore GenoProof Mixture can only be used by one user at a time, but you can create multiple users and take turns in using the program. 2. Client When choosing this type, only the application without the database will be installed on your computer. This options is useful, when the program is installed on multiple computers with different users working at the same time. In addition, you need to install the database on a

8 8 separate computer. When logging in to GenoProof Mixture you need to enter the name of the database. 3. Database This option installs the central database. Multiple users can log on to the database and work at the same time 4. Custom This option gives you more options in deciding which components will be installed. Detailed technical knowledge of the infrastructure may be required. Continue the installation by clicking Install. Figure 4: Selection of the components of GenoProof Mixture. 1.8 Copying of data You have now selected all preferences and the installation wizard will start copying the data to the install location. Additional windows may open when necessary to install additional components. Figure 5 shows the progress of the installation and will close independently.

9 9 Figure 5:Installing of GenoProof Mixture. Please wait until the installation is completed. Depending on your computer, this may take a few minutes. When the installation is finished, press Next. Figure 6: Completing of the installation. Now the installation is completed. Press Finish to close the installation wizard.

10 10 2 Storage configuration For mixture calculations, GenoProof Mixture needs a certain amount of working memory on your computer. This is orientated on the installed working memory, so that the program reserves a proportion of it. This means the more working memory you have installed on your computer, the more memory is available to GenoProof Mixture. When performing extensive calculations, it is possible that the program runs out of working memory. In this case, the error Java Heap Space will be displayed. To avoid this problem, you can configure GenoProof Mixture to use more than the standard proportion of the available working memory. Nevertheless, you should consider that is impossible to assign the complete working memory of you computer to one program, as your system software and other running programs also need a certain amount of the memory. In general, it is possible to assign more memory to GenoProof Mixture than is installed on your computer. In this case, your system software will use the hard drive to provide more memory. This may result in reduced speed of GenoProof Mixture, you system software and other programs. To configure the working memory availability follow these steps: 1. Terminate GenoProof Mixture. 2. Look for the file GenoProof Mixture 3.ini in the installation directory of GenoProof Mixture. The installation directory is usually named: C:\Program Files\qualitype\GenoProof Mixture Open the file to edit with the program Notepad. 4. Add the following lines at the end of the file to configure the memory to the maximum of 8 GB (you can also choose a different value): -vmargs -Xmx8g 5. Save the file. Please note that you may need administrator rights to complete this step. Please ask your system administrator if you need any help. The easiest possibility to edit the file is to copy it to your desktop and edit it there. Then you can copy the edited file in the installation directory of GenoProof Mixture. Your system software will ask you for administrator rights at this point. 6. Start GenoProof Mixture again.

11 11 3 Troubleshooting This chapter describes questions and problems that may arise when calculating the LR according to the fully continuous approach, their causes and potential solutions. 3.1 Questions and problems before the calculation has started 1. Are the default settings suitable for my analysis? Background: Default settings cover a wide range of stain qualities. In particular cases or depending on laboratory conditions (e.g. allele variance constant (9.1.3) or detection limit (9.1.5)), an adaption of parameter values might be useful. Potential solutions: We recommend running calculations with default settings first. Observed problems (issues and ) and analysis of convergence diagnostics (issue ) may indicate useful adaptions of parameter settings. 2. The parameter degradation is set to 0 (default value). Does this mean that degradation is not considered in the calculation? Background: In samples with low or moderate degradation, the parameter degradation competes with the amplification efficiency during the MCMC process. Thus, low and moderate degradation is considered via the amplification efficiency. Potential solutions: We recommend running calculations with a degradation of 0 first. If problems occur (issues ), degradation can be set up to In this case, please consider issue Which factors determine the allele variance constant and should I change its default settings? Background: The allele peak height variance especially depends on the number of PCR cycles of the amplification of the stain. The allele peak height variance exponentially increases with a higher number of PCR cycles. Potential solutions: Working with relatively low numbers of PCR cycles (e.g ), the upper limit can be set to approximately 15. This adaption results in a faster calculation. Issues and indicate whether an adaption of this parameter is useful.

12 12 4. The error message "No relevant genotype constellations could be generated for marker [marker name]" is displayed after starting the calculation (Figure 7). Figure 7. Background: There are alleles in the stain that cannot be explained. This can occur whenever the number of contributors or the dropin limit is set too low. Potential solutions: Please check the number of contributors or the dropin settings. 5. The error message "Alleles with a smaller peak height than the configured detection limit were detected" is displayed after starting the calculation (Figure 8). Figure 8. Background: The detection limit in the preferences should be consistent with the applied detection limit (minimum peak height until which peaks are labeled as alleles) for raw data analysis. The detection limit is applied to calculate the probability of matching between estimated and observed peak heights during the MCMC process in case of dropouts. Potential solutions: Please adjust the parameter detection limit in the preferences. 3.2 Questions and problems during the calculation 1. The calculation takes a long time. Background: Depending on stain quality, number of contributors, number of replicates and parameter settings, calculations can take several hours in particular cases.

13 13 Potential solutions: Please wait. Another option is to cancel the calculation and to analyse the preliminary convergence diagrams (issues ), which may indicate useful adaptions of parameters (9.1.1). 2. The calculation does not come to an end or the progress bar of the calculation is not moving anymore. Background: One of the markov chains is stuck in an unfavourable parameter space. Potential solutions: Cancel the calculation and analyse the preliminary convergence diagrams (issue ), which may indicate useful adaptions of parameters (9.1.1). 3.3 Questions during the analysis of the convergence diagnostics 1. The Gelman-Rubin-value is higher than Background: The converging of the markov chain has not been completed. Therefore, a steady state of parameters has not been established yet. Potential solutions: Increase the iteration steps (e.g. doubling of burn-in and iteration accepts). 2. The graph in the running mean plot is not parallel to the x-axis yet (Figure 9). Figure 9. Background: The converging of the markov chain has not been completed. Therefore, a steady state of parameters has not been established yet. Potential solutions: Increase the iteration steps (e.g. doubling of burn-in and iteration accepts). 3. The graph in the trace plot resides at the top or at the bottom of the diagram (Figure 10).

14 14 Figure 10. Background: The parameter range is too restricted. Potential solutions: Extend the corresponding parameter range in the preferences (in the example: increase the upper limit of the allele variance constant). 4. The graph in the trace plot diagram displays irregularities (Figure 11). Figure 11. Background: Irregularities indicate poor mixing of the parameters and therefore, wrong parameterisation or problems with the MCMC-process. Potential solutions: Please contact the customer support. 5. The graphs in the trace plot diagrams are restricted to a certain area of the diagram (Figure 12). Figure 12. Background: The parameter range is too wide. Potential solutions: Restrict the corresponding parameter in the preferences (in the example: restriction of the upper limit of the allele variance constant from 33 to 20). This will result in increased calculation speed.

15 15 6. The graphs in the running mean plot differ greatly between markov chains (Figure 13). Figure 13. Background: Diverging optimal solutions in the parameter space have been found. This may be caused by competing parameters. Potential solutions: Check the parameter settings in the preferences (e.g. reduce the degradation to 0, see 9.1.2).