Frequently asked questions

 

We keep an online request list and discussion here: >>> You may want to check out this request list too.

 

Topics related to the SVA project

Q[1]. What reference genome and gene catalog does SVA use?

A: In the current release SVA is based on NCBI human genome assembly build 36.3 (specifically, RefSeq and GeneBank build 36.3), and Ensembl build 50. In SVA release 1.01beta onwards, all the entries in the gene catalog are also matched to HuGO Gene Nomenclature Committee (HGNC) approved database for a 'canonical gene set'.

It is critical that SVA users use the same human genome assembly build.

The data sources of SVA can be conveniently updated, and in the future we will release newer supporting databases on our website.

Q[2]. What level of technical support can I get from the SVA development team?

A: SVA is a very important and central part of our work. We will provide the highest level of technical support as we can.

Q[3]. Will SVA stay free?

A: Yes. SVA will stay available to the research community, both in academia and in industry, free of charge .

 

Topics related to using the software

Q[1]. I am getting a 'Configuration error' message, and the program won't start.

A: This is most frequently caused by the setup of JAVA environment installed on your workstation. JAVA has to be correctly installed, which means that JAVA is correctly added into your system path. Otherwise, SVA will throw a "Configuration error" exception and will not start.

In other words, if you do not add JAVA into your system path, you cannot start SVA by executing this command by directly calling JAVA path:

[YOUR JAVA PATH]/java -jar SequenceVariantAnalyzer.jar

 

Q[2].The fonts of SVA are weird.

[AND/OR]

The program is not responding to me.

[AND/OR]

The program does not seem to work properly at all!

A: This is most frequently caused by the setup of JAVA environment installed on your workstation. SVA is compiled using the Sun JAVA (http://www.java.com/). It is known that it does not run properly in an OpenJDK environment.

 

Q[3]. SVA automatically assign 1024MB of RAM to itself and starts. This amount of RAM won't allow me to do any annotation or analysis.

A: This is most frequently caused by the amount of RAM assigned by you exceeds the amount that the operating system can grant. For example, if the maximum RAM available in the system is 32GB, and you are trying to allocate 40GB to SVA, SVA will fail. What the program tries to do next is to start in a 'safe mode' with the minimum amount of RAM ( 1024MB), allowing a chance to re-configure the memory through menu 'Options->Memory allocation'. This minimum amount in the 'safe mode' will not allow you to do anything meaningful rather than just re-allocating the memory.

 

Q[4]. I have more than 4GB of RAM insalled in my computer. But SVA won't let me allocate more than around 3700MB (or 4GB) of RAM to itself.

A: This is caused by a 32-bit JAVA in your system.

Type in command

java -version

If you have installed a 64-bit JAVA, you will see something like:


Java(TM) SE Runtime Environment (build 1.6.0_17-b04)
Java HotSpot(TM) 64-Bit Server VM (build 14.3-b01, mixed mode)


If you have installed a 32-bit JAVA, you will see something like:


Java(TM) SE Runtime Environment (build 1.6.0_17-b04)
Java HotSpot(TM) Server VM (build 14.3-b01, mixed mode)


To solve this problem, you need to install a 64-bit JAVA from:

http://www.java.com/en/download/index.jsp

Q[5]. The annotation process is slow.

A: We have two recommendations. (1) You will need a powerful workstation for using SVA. (2) In SVA release 1.01beta onwards, there is an option in the .gsap project file that allows you to use previously annotated project as an 'SVA dictionary' which SVA can look up, so that it's not necessary to re-annotate the function of every single variant from scratch.

This option is:

[SVADICTIONARY]= {your preciously annotated SVA output file}

Our experience with the workstation specified here is that it requires about one full day to annotate 50 genomes from scratch, and it requires about one night to annotate with an SVA dictionary. Please note when number of genomes increases, the time required is not increasing linearly. It will be less that a linear prediction because a large proportion of human genomic variants overlap.

The annotation time is also affected by computer models and intranet/internet speed if the data is not stored locally.

 

Q[6]. I cannot navigate to external resources, for example NCBI, from SVA genome browser.

A: By default SVA calls internet browser using this command: htmlview. This can be changed in your .gsap project file with an option:

[UNIXINTERNETBROWSER]= {your command to start internet browser}

Make sure your command to start internet browser works. For example, you can test this in your terminal:

{your command to start internet browser} www.

This should bring up your browser and direct to .