Thermo server timeout

[fabianegli]

Describe the issue or question:

I see an error message and don't know if that indicates that the analysis will be erroneous. #484 indicates that the analysis should not be affected by what underlies that error message.

Excerpt from the log

Checking spectral files...
[pool-1-thread-2] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Did not get port information from server output within timeout.
[pool-2-thread-1] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess - Error while scanning stream
java.lang.InterruptedException: sleep interrupted
    at java.base/java.lang.Thread.sleep(Native Method)
    at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.scanStreamForPattern(ThermoGrpcServerProcess.java:307)
    at com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess.lambda$start$7(ThermoGrpcServerProcess.java:248)
    at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.base/java.lang.Thread.run(Unknown Source)
C:\path\to\raw\measurement-1.raw: Scans = 34000
C:\path\to\raw\measurement-2.raw: Scans = 34100
C:\path\to\raw\measurement-3.raw: Scans = 34200
C:\path\to\raw\measurement-4.raw: Scans = 34300
C:\path\to\raw\measurement-5.raw: Scans = 34400
C:\path\to\raw\measurement-6.raw: Scans = 34500

• Judging from the continuation after FragPipe, it seems that the error does not persist and is somehow remedied. Could the resolution of the error be reason enough not to put it in the log?
• Can this error message be ignored by the user?
• Could it be that a little bit longer timeout would prevent the error? Judging from the error message, it seems the Thermo server goes into a sleep mode and takes some time to become responsive again and that this takes longer than the FragPipe timeout allows.

[reynoldsanthony]

Is there a solution to this issue? I'm getting the same error message, but the analysis by FragPipe is aborted after a few minutes of trying to run. Thanks!

[fcyu]

Most likely, your computer has the security configuration or antivirus that block the Thermo parser. You need to troubleshoot locally with your IT people.

Best,

Fengchao

[guoci]

Please see https://github.com/Nesvilab/FragPipe/issues/1448#issuecomment-1943034114. Future versions will not have this problem. The interprocess communication no longer uses a localhost port.