IGV is running slow on a server with X11 forwarding for trio sequencing (H.sapiens)

[Matthew Oldach]

On our server IGV 2.4.8 is installed for all users so I tried using this first (even though it's an older version). Unfortunately I found that it had very slow performance.  Therefore I also tried to download the latest version (2.8.2).

Starting the IGV gui the recommended way (using igv.sh, according to the readme.txt) takes about 2 minutes from: `/export/common/program/IGV_2.4.8/igv.sh` (same with the latest version).

Loading three BAM files (mother/father/proband) takes around 1 minute.
I load the VCF file (proband) and when trying simple operations like clicking "File" or hovering over items (eg. SNP) the box that contains information will often take ~30 seconds to pop-up.

Have others experienced slow performance from IGV when X11 forwarding on servers? What can be done to speed things up?

Some more information that may be helpful

Server:

currently consists of 16 general compute nodes each with 28 cores (56 threads) and 256 GB of memory attached to a 1.5 PB file-system. This server is set up for user to run interactive jobs on (as opposed to batch submission with a scheduler) so I believe memory is not a limiting factor.

The readme.txt suggests another way of calling IGV via Java where you can explicitly set memory,  however, I get an error when trying:

(base) [IGV_Linux_2.8.2]$ java --module-path=lib -Xmx4g @igv.args --module=org.igv/org.broad.igv.ui.Main
Unrecognized option: --module-path=lib
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

Any idea why this isn't working?

The size of the bam files are ~40-50GB each
The number of alignments contained in that file are ~655,250,000

Thanks for developing IGV, it is a very useful tool for our lab!

[James Robinson]

Hi, first we don't recommend using IGV with a remote server and x11 forwarding, performance is very bad as you have discovered.   A large amount of time has been spent investigating this with no solution.    We recommend users install local copies.  

BAM file size is really not relevant,  only small slices of the bam are loaded at any one time.     The sizes you quote are typical of WGS, not particularly large.

WRT the error, the most likely cause for that is you are not running Java 11.  Track checking the java version from the command line.

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[James Robinson]

Sorry, correction, you mention that you are using IGV 2.4,  so disregard the java 11 comment.  However the command line you are using IS for the Java 11 version, so that is not going to work.     Open the igv.sh file that came with the distribution you are running, it will have the correct command line.

[Matthew Oldach]

Hi James and thank you for your prompt response.

Okay so you suggest running a local copy then. I'm wondering about getting the data into IGV from the server?

Copying three BAM files, each ~50Gb, from the server to the laptop to run locally takes a lot of time.

I know that you can load BAM files from Google Cloud Storage if you were working in the cloud. https://software.broadinstitute.org/software/igv/LoadData

Do you know if there is a way to set up links to files from a server instead?

Thanks,
Matt

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[James Robinson]

Have you considered serving them from a web server (by URL)?     For example Apache, nginx, or even Flask properly configured?

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[James Robinson]

Hi Matt, I omitted the obvious suggestion, if this is an institute file server can it be mounted as a drive on the end user's machine?   Then you just load from the file menu.

On Fri, Jun 5, 2020 at 2:04 PM Matthew Oldach <molda...@gmail.com> wrote: