IGV session save/reload error

[Heewoong Lim]

Hi, I would like to report an error that I am experiencing in recent version.

1. IGV 2.3.52

2. Starting with blank session, loaded one bed file (simple bed file containing 10 regions only for testing), and saved the session.

But after that, trying reloading the saved session has failed.

3. I expected to open the saved session normally, because I've just made the session.

4. Error message & freeze of IGV

Here are detailed log and save session file.

One thing that should noted here is I am using symbolic link for data management, i.e.

/home/myID/Research is actually a symbolic link to /media/Disk2/Research2/

It has worked well with this environment but doesn't work since I upgraded IGV using relative paths.

Thank you.

#######################################

## IGV log

#######################################

### IGV open => load Test/test.bed file => save session

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/home/myID/Temp

INFO [2015-05-07 13:35:50,862]  [DirectoryManager.java:149] [main]  IGV Directory: /home/myID/igv

INFO [2015-05-07 13:35:50,862] [DirectoryManager.java:149]  IGV Directory: /home/myID/igv

INFO [2015-05-07 13:35:50,869]  [Main.java:85] [main]  Startup  IGV Version 2.3.52 (67)05/04/2015 01:14 PM

INFO [2015-05-07 13:35:50,870]  [Main.java:86] [main]  Java 1.7.0_79

INFO [2015-05-07 13:35:50,870]  [DirectoryManager.java:58] [main]  Fetching user directory... 

INFO [2015-05-07 13:35:50,973]  [Main.java:87] [main]  Default User Directory: /home/myID

INFO [2015-05-07 13:35:50,973]  [Main.java:88] [main]  OS: Linux

INFO [2015-05-07 13:36:12,554]  [GenomeManager.java:130] [main]  Loading genome: /home/myID/igv/genomes/mm9.genome

INFO [2015-05-07 13:36:14,655]  [GenomeManager.java:177] [main]  Genome loaded.  id= mm9

INFO [2015-05-07 13:36:14,959]  [CommandListener.java:88] [Thread-6]  Listening on port 60151

INFO [2015-05-07 13:36:37,385]  [IGV.java:1639] [pool-1-thread-2]  Loading 1 resources.

INFO [2015-05-07 13:36:37,387]  [TrackLoader.java:112] [pool-1-thread-2]  Loading resource, path /home/myID/Research/2.IGV_Session/Test/test.bed

### Trying reloading saved session => Error

INFO [2015-05-07 13:37:23,712]  [TrackLoader.java:112] [Thread-10]  Loading resource, path /media/Disk2/Research2/2.IGV_Session/Test/test.bed

INFO [2015-05-07 13:37:23,768]  [IGVSessionReader.java:1053] [pool-1-thread-2]  Warning.  No tracks were found with id: /home/myID/Research/2.IGV_Session/Test/test.bed in session file

INFO [2015-05-07 13:37:23,824]  [MessageUtils.java:60] [pool-1-thread-5]  Error loading features for interval: chr9:43230698-70914667 <br>java.lang.NullPointerException

ERROR [2015-05-07 13:37:50,392]  [FeatureTrack.java:904] [pool-1-thread-5]  Error loading features for interval: chr9:43230698-70914667 <br>java.lang.NullPointerException

java.lang.NullPointerException

at org.broad.igv.track.FeatureTrack$1.run(FeatureTrack.java:882)

at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:57)

at java.util.concurrent.FutureTask.run(FutureTask.java:262)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)

at java.lang.Thread.run(Thread.java:745)

############################################

### Saved Session file

############################################

<?xml version="1.0" encoding="UTF-8" standalone="no"?>

<Session genome="mm9" hasGeneTrack="true" hasSequenceTrack="true" locus="chr9:43230699-70914667" path="/home/myID/Research/2.IGV_Session/0.test.xml" version="8">

    <Resources>

        <Resource path="Test/test.bed"/>

    </Resources>

    <Panel height="578" name="FeaturePanel" width="1131">

        <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/>

        <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;226.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="mm9_genes" name="Refseq genes" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">

            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="226.0" minimum="0.0" type="LINEAR"/>

        </Track>

        <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;1.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="/home/myID/Research/2.IGV_Session/Test/test.bed" name="test.bed" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">

            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>

        </Track>

    </Panel>

    <PanelLayout dividerFractions="0.010186757215619695"/>

    <HiddenAttributes>

        <Attribute name="NAME"/>

        <Attribute name="DATA FILE"/>

        <Attribute name="DATA TYPE"/>

    </HiddenAttributes>

</Session>

[Jim Robinson]

Hi,

Does this work in some previous version?  If so which one, if you know?

The problem is related to the symbolic link.

Thanks

Jim

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[Heewoong Lim]

Hi Jim:

Thank you for quick response.

I've tried a couple of different version tracking back,

and found that IGV_2.3.40 works well.

And I tried a couple of different testing, and got error only if symbolic link is included in the path toward the track file.

It worked well if I load the track file by absolute path starting from / without including any symbolic link.

Here is the session file generated by 2.3.40.

Thank you.

-Lim

#####################################################3

<?xml version="1.0" encoding="UTF-8" standalone="no"?>

<Session genome="mm9" hasGeneTrack="true" hasSequenceTrack="true" locus="All" version="8">

    <Resources>

        <Resource path="/home/heewlim/Research/2.IGV_Session/Test/test.bed"/>

    </Resources>

    <Panel height="549" name="FeaturePanel" width="1129">

        <Track altColor="0,0,178" autoScale="false" color="0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="Reference sequence" name="Reference sequence" sortable="false" visible="true"/>

        <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;226.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" height="35" id="mm9_genes" name="Refseq genes" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">

            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="226.0" minimum="0.0" type="LINEAR"/>

        </Track>

        <Track altColor="0,0,178" autoScale="false" clazz="org.broad.igv.track.FeatureTrack" color="0,0,178" colorScale="ContinuousColorScale;0.0;1.0;255,255,255;0,0,178" displayMode="COLLAPSED" featureVisibilityWindow="-1" fontSize="10" id="/home/heewlim/Research/2.IGV_Session/Test/test.bed" name="test.bed" renderer="BASIC_FEATURE" sortable="false" visible="true" windowFunction="count">

            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="1.0" minimum="0.0" type="LINEAR"/>

        </Track>

    </Panel>

    <PanelLayout dividerFractions="0.010714285714285714"/>

    <HiddenAttributes>

        <Attribute name="NAME"/>

        <Attribute name="DATA FILE"/>

        <Attribute name="DATA TYPE"/>

    </HiddenAttributes>

</Session>

[Jim Robinson]

OK,  I'll enter a bug report on github.   This will require a software fix, apologies.

Jim

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/99075581-bc47-4aa7-a021-bf02bbf8da34%40googlegroups.com.

[Heewoong Lim]

Thanks a lot, Jim!

[Atul Kakrana]

Hi Jim,

I get same error when I use IGV on Ubuntu Linux and Fedora server. Is there any place I can get old binary version of IGV?

AK

[Jim Robinson]

There is a link to the archive from the downloads page. 

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/e5a4cf26-ed9a-4f90-b797-e1fb25ca72be%40googlegroups.com.

[Jim Robinson]

Hi,  the latest release (2.3.60) might resolve this issue.    I have t

[Heewoong Lim]

Wow, I almost forgot about this.

I've just tested my previous session, now it works. 

I also see that now we can decide whether to use 'relative path' or not, GREAT!.

Thank you so much.