Cytoscape stuck at "finalize" when opening session file

[Jan Baumann]

Hi all,

the title pretty much says it all: Cytoscape hangs at the stage of "finalize" when opening a session file. CPU load for the java process goes up to around 100% and stays there. This happens in Cytoscape 3.0.2 and 3.1 but 2.8.2 seems to work fine (but of course the session file is different for 2.8.2, but both were generated using the appropriate version of Metscape).

I run Xubuntu 13.10 and I have tried open-jdk6, open-jdk7, oracle-java-6 and oracle-java-7 but that doesn't seem to make a difference.

Any help would be greatly appreciated!

Cheers,

Jan

[Tim Hull]

Do you have a sample session file that exhibits this problem? Also, are you using the final release of 3.1.0 or a beta? I ask that because this sounds somewhat like a bug that we had in the 3.1.0 beta and fixed for the final release... 

Tim

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[Jan Baumann]

Hi Tim,

thanks for taking a shot at this. I am using the final release of 3.1.0, I just went through the download link on the front page. I am attaching the network file that is giving me problems.
The network was generated in 3.0.2. Both 3.1.0 and 3.0.2 get stuck at "finalize" when trying to open the file.

Again, thanks for your help!

Jan

On Thursday, March 6, 2014 1:59:14 PM UTC-5, Tim Hull wrote:

Do you have a sample session file that exhibits this problem? Also, are you using the final release of 3.1.0 or a beta? I ask that because this sounds somewhat like a bug that we had in the 3.1.0 beta and fixed for the final release... 

Tim

On Thu, Mar 6, 2014 at 6:51 AM, Jan Baumann <haeusl...@gmail.com> wrote:

Hi all,

the title pretty much says it all: Cytoscape hangs at the stage of "finalize" when opening a session file. CPU load for the java process goes up to around 100% and stays there. This happens in Cytoscape 3.0.2 and 3.1 but 2.8.2 seems to work fine (but of course the session file is different for 2.8.2, but both were generated using the appropriate version of Metscape).

I run Xubuntu 13.10 and I have tried open-jdk6, open-jdk7, oracle-java-6 and oracle-java-7 but that doesn't seem to make a difference.

Any help would be greatly appreciated!

Cheers,

Jan

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[Tim Hull]

I just tested on Ubuntu 13.10 with Cytoscape 3.1.0, and I'm not seeing this issue. How much memory do you have, and how much memory does Cytoscape show as available (click the green button in the lower-right corner in Cytoscape)? I'm wondering fi you may be low on memory...

Tim

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[Jan Baumann]

Memory is not the issue, it goes to about 18% used when trying to load the network. I have 12GB of RAM and allow Cytoscape to use 10. Interesting note: I tried opening the same network in Windows 7, Cytoscape 3.1.0 and it worked flawlessly...

On Friday, March 7, 2014 2:28:09 PM UTC-5, Tim Hull wrote:

I just tested on Ubuntu 13.10 with Cytoscape 3.1.0, and I'm not seeing this issue. How much memory do you have, and how much memory does Cytoscape show as available (click the green button in the lower-right corner in Cytoscape)? I'm wondering fi you may be low on memory...

Tim

On Fri, Mar 7, 2014 at 5:09 AM, Jan Baumann <haeusl...@gmail.com> wrote:

Hi Tim,

thanks for taking a shot at this. I am using the final release of 3.1.0, I just went through the download link on the front page. I am attaching the network file that is giving me problems.
The network was generated in 3.0.2. Both 3.1.0 and 3.0.2 get stuck at "finalize" when trying to open the file.

Again, thanks for your help!

Jan

On Thursday, March 6, 2014 1:59:14 PM UTC-5, Tim Hull wrote:

Do you have a sample session file that exhibits this problem? Also, are you using the final release of 3.1.0 or a beta? I ask that because this sounds somewhat like a bug that we had in the 3.1.0 beta and fixed for the final release... 

Tim

On Thu, Mar 6, 2014 at 6:51 AM, Jan Baumann <haeusl...@gmail.com> wrote:

Hi all,

the title pretty much says it all: Cytoscape hangs at the stage of "finalize" when opening a session file. CPU load for the java process goes up to around 100% and stays there. This happens in Cytoscape 3.0.2 and 3.1 but 2.8.2 seems to work fine (but of course the session file is different for 2.8.2, but both were generated using the appropriate version of Metscape).

I run Xubuntu 13.10 and I have tried open-jdk6, open-jdk7, oracle-java-6 and oracle-java-7 but that doesn't seem to make a difference.

Any help would be greatly appreciated!

Cheers,

Jan

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[Tim Hull]

What kind of CPU/how many cores do you have? Thinking this may be a very system configuration-specific issue...

Tim

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[Jan Baumann]

Intel Core i7 3630QM, 4 cores, if I am not mistaken.

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[Jan Baumann]

Ok, I finally got it to work. The culprit was the folder "CytoscapeConfiguration". I renamed it CytoscapeConfiguration.old and started cytoscape 3.1, which recreated the folder. After installing Metscape the network opens without any issues.

[Mike]

I had the same issue and deleting the "CytoscapeConfiguration" folder fixed the problem for me as well. 

It came about when I was using OSX 10.6.8. 2.2GHz Intel Core i7. I had no issues on the same machine when using Linux Mint or Windows 7. I had multiple versions of Cytoscape (2.8.3, 3.1.0, 3.0.?) in OSX so the issue may relate to that. 

It was frustrating as I had a task that worked a lot better in Cytoscape 3 so I was very glad to find Jan's fix.

Cheers Jan.

Mike

[Jan Baumann]

I am glad it helped someone. I also had multiple versions of cytoscape installed, so the issue is probably related to that. For anyone new to this problem I recommend to backup the config folder before you delete it, just in case...

Cheers,

Jan

[Thiago Jacomasso]

Thanks for the information! Had exactly the same issue, and the solution worked for me as well.

Cheers!

[Nafiz Haidi]

Hi Mike and Jan,

Sorry if I barge in a little too late but I had also encountered the same problem as you guys but able to fix it based on Jan's solution. But I just want to confirm whether deleting that specific files will cause any repercussions when opening a cytoscape file as I was not able to access some of the downloaded app feature on my previous sessions?

Appreciate any feedbacks from you guys.

Cheers!

Nafiz

[Scooter Morris]

Hi Nafiz,

Yes, when you delete your CytoscapeConfiguration directory, you also delete all of the installed apps.  My suggestion would be to delete the directory, then install your apps one at a time -- it's possible that one of the apps might be causing a problem.

-- scooter