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optimusmoose / jsms

A modular JavaScript viewer for mass spectrometry data
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msViz hangs at 99% imported #1

Open glycoaddict opened 4 years ago

glycoaddict commented 4 years ago

image Thanks for the nice work. Came across your software from your PlosOne and Bioinformatics papers. This is on your 2.0 commit (d9f366a) as I couldn't work out how to run your Xflow commit.

I opened an mzml file, and the progress % went up but eventually hung at 99% for 45 min, at which point I closed it. The viewer loads but nothing is loaded so it just gives me a blank grid. Do you have example data I can test on?

Thanks.

glycoaddict commented 4 years ago

update: tried a second file with only MS1 and it get to 100% but still not loading. JRE 8, MZML 1.1 using msconvert from Thermo orbitrap fusion .raw.

image

optimusmoose commented 4 years ago

Hi Matthew, There is a bit of heavy lifting after the load process.

Did you increase from the default memory size using the command line arguments in the readme?

Thanks, Rob

On Tue, Dec 3, 2019 at 3:05 AM Matthew Choo notifications@github.com wrote:

update: tried a second file with only MS1 and it get to 100% but still not loading. JRE 8, MZML 1.1 using msconvert from Thermo orbitrap fusion .raw.

[image: image] https://user-images.githubusercontent.com/19943098/70041066-74dd7f80-15f7-11ea-831f-6031563744f4.png

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glycoaddict commented 4 years ago

Hi Rob, I changed it to -Xmx4g and tried again. The file seems to have gone to 100% and I notice that the axes in the viewer have the correct ranges (in my case 20-40 min, m/z 300-2500).

But the plot is empty and the screen shows:

<html><body><h2>500 Internal Server Error</h2></body></html>
0 Pending Updates
0 points. Progress: unknown (press A to recompute)
No trace or envelope selected.
MZ: [589.839, 599.839]
RT: [19.903, 40.097]
INT: [Infinity, 0]
[ No point near mouse ]

The console displays this message if I press the key "a":

Dec 04, 2019 2:29:43 PM edu.msViz.mzTree.MzTree ensurePointIDs
WARNING: Failed to retrieve points for node. Future query results may be incomplete.
java.lang.NullPointerException
    at edu.msViz.mzTree.storage.HybridStorage$SQLEngine.selectPointIDsByNode(HybridStorage.java:767)
    at edu.msViz.mzTree.storage.HybridStorage.getNodePointIDs(HybridStorage.java:177)
    at edu.msViz.mzTree.MzTree.ensurePointIDs(MzTree.java:826)
    at edu.msViz.mzTree.MzTree.collectPointsWithinBounds(MzTree.java:800)
    at edu.msViz.mzTree.MzTree.query(MzTree.java:703)
    at edu.msViz.msHttpApi.MsDataServer.getPoints(MsDataServer.java:184)
    at spark.RouteImpl$1.handle(RouteImpl.java:72)
    at spark.http.matching.Routes.execute(Routes.java:61)
    at spark.http.matching.MatcherFilter.doFilter(MatcherFilter.java:130)
    at spark.embeddedserver.jetty.JettyHandler.doHandle(JettyHandler.java:50)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1568)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132)
    at org.eclipse.jetty.server.Server.handle(Server.java:530)
    at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:347)
    at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:256)
    at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279)
    at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102)
    at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140)
    at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131)
    at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:382)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:708)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:626)
    at java.lang.Thread.run(Unknown Source)
optimusmoose commented 4 years ago

If you aren't get a file loaded message in the server console, it hasn't loaded fully yet. Like I said, there is quite a long wait period at the very end of the file load as the data structures are being built. Give it as much memory as you can spare and some more time and see if it resolves the issue. How large is the file in MB/GB?

On Tue, Dec 3, 2019 at 11:32 PM Matthew Choo notifications@github.com wrote:

Hi Rob, I changed it to -Xmx4g and tried again. The file seems to have gone to 100% and I notice that the axes in the viewer have the correct ranges (in my case 20-40 min, m/z 300-2500).

But the plot is empty and the screen shows:

500 Internal Server Error

0 Pending Updates 0 points. Progress: unknown (press A to recompute) No trace or envelope selected. MZ: [589.839, 599.839] RT: [19.903, 40.097] INT: [Infinity, 0] [ No point near mouse ]

The console displays this message if I press the key "a":

Dec 04, 2019 2:29:43 PM edu.msViz.mzTree.MzTree ensurePointIDs WARNING: Failed to retrieve points for node. Future query results may be incomplete. java.lang.NullPointerException at edu.msViz.mzTree.storage.HybridStorage$SQLEngine.selectPointIDsByNode(HybridStorage.java:767) at edu.msViz.mzTree.storage.HybridStorage.getNodePointIDs(HybridStorage.java:177) at edu.msViz.mzTree.MzTree.ensurePointIDs(MzTree.java:826) at edu.msViz.mzTree.MzTree.collectPointsWithinBounds(MzTree.java:800) at edu.msViz.mzTree.MzTree.query(MzTree.java:703) at edu.msViz.msHttpApi.MsDataServer.getPoints(MsDataServer.java:184) at spark.RouteImpl$1.handle(RouteImpl.java:72) at spark.http.matching.Routes.execute(Routes.java:61) at spark.http.matching.MatcherFilter.doFilter(MatcherFilter.java:130) at spark.embeddedserver.jetty.JettyHandler.doHandle(JettyHandler.java:50) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1568) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:132) at org.eclipse.jetty.server.Server.handle(Server.java:530) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:347) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:256) at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:279) at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:102) at org.eclipse.jetty.io.ChannelEndPoint$2.run(ChannelEndPoint.java:124) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce(EatWhatYouKill.java:247) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.produce(EatWhatYouKill.java:140) at org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run(EatWhatYouKill.java:131) at org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run(ReservedThreadExecutor.java:382) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:708) at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:626) at java.lang.Thread.run(Unknown Source)

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glycoaddict commented 4 years ago

I used msconvert to take a subset of my larger file so its a smaller size at 184 MB. I gave it an hour over lunch. I also tried loading the .mzTree file. The export tab is clickable but shows no entries, if that helps.

optimusmoose commented 4 years ago

Is there any way we can get your input file to troubleshoot it? Alternatively, you could see if you could reproduce it with a publicly available file and send me the link.

Thanks, Rob

On Wed, Dec 4, 2019 at 3:37 AM Matthew Choo notifications@github.com wrote:

I used msconvert to take a subset of my larger file so its a smaller size at 184 MB. I gave it an hour over lunch. I also tried loading the .mzTree file. The export tab is clickable but shows no entries, if that helps.

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glycoaddict commented 4 years ago

Hi Rob, you can find the file here https://hcpacrc.fugu-sg.org/u/78ZVbxdGVWn9xlVt/101a%20-%20HEK-AXL_500ng_OT_HCD30EThcD.mzML?l

This is the snippet from a replicate run to the raw file at https://www.ebi.ac.uk/pride/archive/projects/PXD009222/files namely: https://www.ebi.ac.uk/pride/data/archive/2019/05/PXD009222/101a%20-%20HEK-AXL_500ng_OT_HCD30EThcD.raw

I hope this helps!

optimusmoose commented 4 years ago

Hi Matthew, I'm sorry for the delay. I was traveling.

I just downloaded your file. I made sure I had the up to date release. I followed the build instructions in the readme notes, then opened your file. I didn't change the default memory size. It loaded in about three minutes on my laptop, and the viewer launched successfully.

On Wed, Dec 4, 2019 at 4:59 AM Matthew Choo notifications@github.com wrote:

Hi Rob, you can find the file here https://hcpacrc.fugu-sg.org/u/78ZVbxdGVWn9xlVt/101a%20-%20HEK-AXL_500ng_OT_HCD30EThcD.mzML?l

This is the snippet from a replicate run to the raw file at https://www.ebi.ac.uk/pride/archive/projects/PXD009222/files namely: https://www.ebi.ac.uk/pride/data/archive/2019/05/PXD009222/101a%20-%20HEK-AXL_500ng_OT_HCD30EThcD.raw

I hope this helps!

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glycoaddict commented 4 years ago

It works! Previously I didn't do the build step as it seemed optional, but after installing JDK 8 and Maven, adding JDK 8 and Maven to path, the build worked. Prob my noob error in not building for my system.

Thanks so much!