problems to open IGV ([CommandListener.java:83])

[noa.b...@gmail.com]

I'm using IGV Version 2.2.5 on Linux machine for couple of month.

In the last few days when I'm trying to open IGV, I get the following:

 

noab@complex1:/data2/noab/programs/IGV_2.2.5$ java -Xmx750m -jar igv.jar
INFO [2013-12-19 12:59:57,419]  [DirectoryManager.java:149] [main]  IGV Directory: /ph2users/noab/igv
INFO [2013-12-19 12:59:57,423]  [Main.java:72] [main]  Startup  IGV Version 2.2.5 (7)01/25/2013 02:05 PM
INFO [2013-12-19 12:59:57,423]  [Main.java:73] [main]  Java 1.6.0_24
Fetching user directory... INFO [2013-12-19 12:59:57,519]  [Main.java:74] [main]  Default User Directory: /ph2users/noab
INFO [2013-12-19 12:59:59,107]  [GenomeManager.java:113] [main]  Loading genome: http://igv.broadinstitute.org/genomes/hg19.genome
INFO [2013-12-19 13:00:01,583]  [GenomeManager.java:143] [main]  Genome loaded.  id= hg19
INFO [2013-12-19 13:00:01,607]  [CommandListener.java:80] [Thread-6]  Listening on port 60151
 

and then its stuck and the IGV program does not open...

 

I tried to download the newest version (Version 2.3.25), but I get the same:

noab@complex1:/data2/noab/programs/IGV_2.3.25$ java -Xmx750m -jar igv.jar
INFO [2013-12-19 13:03:19,996]  [DirectoryManager.java:149] [main]  IGV Directory: /ph2users/noab/igv
INFO [2013-12-19 13:03:20,000]  [Main.java:72] [main]  Startup  IGV Version 2.3.25 (29)11/25/2013 11:20 AM
INFO [2013-12-19 13:03:20,000]  [Main.java:73] [main]  Java 1.6.0_24
Fetching user directory... INFO [2013-12-19 13:03:20,087]  [Main.java:74] [main]  Default User Directory: /ph2users/noab
INFO [2013-12-19 13:03:21,500]  [GenomeManager.java:134] [main]  Loading genome: http://igv.broadinstitute.org/genomes/hg19.genome
INFO [2013-12-19 13:03:23,789]  [GenomeManager.java:178] [main]  Genome loaded.  id= hg19
INFO [2013-12-19 13:03:24,003]  [CommandListener.java:83] [Thread-6]  Listening on port 60151

 

and I saw here that someone recomended to try the latest snapshot build, tried it also, but got also the same

noab@complex1:/data2/noab/programs/IGV_Snapshot$ java -Xmx750m -jar igv.jar
WARN [2013-12-19 13:06:00,093]  [Globals.java:147] [main]  Development mode is enabled
INFO [2013-12-19 13:06:00,095]  [DirectoryManager.java:149] [main]  IGV Directory: /ph2users/noab/igv
INFO [2013-12-19 13:06:00,118]  [Main.java:74] [main]  Startup  IGV Version Snapshot (977 (2013-12-19_00-00-38))12/19/2013 12:15 AM
INFO [2013-12-19 13:06:00,118]  [Main.java:75] [main]  Java 1.6.0_24
Fetching user directory... INFO [2013-12-19 13:06:00,259]  [Main.java:76] [main]  Default User Directory: /ph2users/noab
INFO [2013-12-19 13:06:00,259]  [Main.java:77] [main]  OS: Linux
INFO [2013-12-19 13:06:01,561]  [GenomeManager.java:130] [main]  Loading genome: http://igv.broadinstitute.org/genomes/hg19.genome
INFO [2013-12-19 13:06:03,732]  [GenomeManager.java:174] [main]  Genome loaded.  id= hg19
INFO [2013-12-19 13:06:03,922]  [CommandListener.java:85] [Thread-6]  Listening on port 60151

Does anyone know what is the problem?

 

Thanks a lot,

Noa.

 

[Jim Robinson]

Hi,

I don't see any errors here, the log looks normal.   What do you see in the window, if anything?   Does the main window, or any window open?

Jim

On Thursday, December 19, 2013 5:07:17 AM UTC-5, noa.b...@gmail.com wrote:

I'm using IGV Version 2.2.5 on Linux machine for couple of month.

In the last few days when I'm trying to open IGV, I get the following:

 

no...@complex1:/data2/noab/programs/IGV_2.2.5$ java -Xmx750m -jar igv.jar

INFO [2013-12-19 12:59:57,419]  [DirectoryManager.java:149] [main]  IGV Directory: /ph2users/noab/igv
INFO [2013-12-19 12:59:57,423]  [Main.java:72] [main]  Startup  IGV Version 2.2.5 (7)01/25/2013 02:05 PM
INFO [2013-12-19 12:59:57,423]  [Main.java:73] [main]  Java 1.6.0_24
Fetching user directory... INFO [2013-12-19 12:59:57,519]  [Main.java:74] [main]  Default User Directory: /ph2users/noab
INFO [2013-12-19 12:59:59,107]  [GenomeManager.java:113] [main]  Loading genome: http://igv.broadinstitute.org/genomes/hg19.genome
INFO [2013-12-19 13:00:01,583]  [GenomeManager.java:143] [main]  Genome loaded.  id= hg19
INFO [2013-12-19 13:00:01,607]  [CommandListener.java:80] [Thread-6]  Listening on port 60151
 

and then its stuck and the IGV program does not open...

 

I tried to download the newest version (Version 2.3.25), but I get the same:

no...@complex1:/data2/noab/programs/IGV_2.3.25$ java -Xmx750m -jar igv.jar

INFO [2013-12-19 13:03:19,996]  [DirectoryManager.java:149] [main]  IGV Directory: /ph2users/noab/igv
INFO [2013-12-19 13:03:20,000]  [Main.java:72] [main]  Startup  IGV Version 2.3.25 (29)11/25/2013 11:20 AM
INFO [2013-12-19 13:03:20,000]  [Main.java:73] [main]  Java 1.6.0_24
Fetching user directory... INFO [2013-12-19 13:03:20,087]  [Main.java:74] [main]  Default User Directory: /ph2users/noab
INFO [2013-12-19 13:03:21,500]  [GenomeManager.java:134] [main]  Loading genome: http://igv.broadinstitute.org/genomes/hg19.genome
INFO [2013-12-19 13:03:23,789]  [GenomeManager.java:178] [main]  Genome loaded.  id= hg19
INFO [2013-12-19 13:03:24,003]  [CommandListener.java:83] [Thread-6]  Listening on port 60151

 

and I saw here that someone recomended to try the latest snapshot build, tried it also, but got also the same

no...@complex1:/data2/noab/programs/IGV_Snapshot$ java -Xmx750m -jar igv.jar

WARN [2013-12-19 13:06:00,093]  [Globals.java:147] [main]  Development mode is enabled
INFO [2013-12-19 13:06:00,095]  [DirectoryManager.java:149] [main]  IGV Directory: /ph2users/noab/igv
INFO [2013-12-19 13:06:00,118]  [Main.java:74] [main]  Startup  IGV Version Snapshot (977 (2013-12-19_00-00-38))12/19/2013 12:15 AM
INFO [2013-12-19 13:06:00,118]  [Main.java:75] [main]  Java 1.6.0_24
Fetching user directory... INFO [2013-12-19 13:06:00,259]  [Main.java:76] [main]  Default User Directory: /ph2users/noab
INFO [2013-12-19 13:06:00,259]  [Main.java:77] [main]  OS: Linux
INFO [2013-12-19 13:06:01,561]  [GenomeManager.java:130] [main]  Loading genome: http://igv.broadinstitute.org/genomes/hg19.genome
INFO [2013-12-19 13:06:03,732]  [GenomeManager.java:174] [main]  Genome loaded.  id= hg19
INFO [2013-12-19 13:06:03,922]  [CommandListener.java:85] [Thread-6]  Listening on port 60151

[noa.b...@gmail.com]

 

Hi Jim,

 

On the screen I see the "bar" of <Initializing...>, then <Loading Genome...>, and then it disappears and nothing happens for hours (not in the screen and not in the terminal).

(i.e. the main windows of IGV does not displayed on the screen. when I used it before it opened in few seconds).

 

Thanks,

Noa.