Cannot open data files in BiopharmaLynx - WKB22208

SYMPTOMS

• Processing data gives a file-specific error message.

• Opening raw data also results in an error in the results browser similar to the one shown below.

• C:/Biopharmalynx1.3.5/log/browser.txt contains an error message as shown below. The bold text shows the important parts of the message, but there is no bold text in the actual log file.

Severity : 30 (Error)
Time : 13/02/18 11:52:37
Type : java.lang.InterruptedException: sleep interrupted [sleep interrupted]

[trace..]
  1   java.lang.Thread.sleep(Native Method)
  2   uk.co.micromass.processor.ProcessorManager.processJobs(Unknown Source)
  3   uk.co.micromass.processor.ProcessorManager.process2DRawData(Unknown Source)
  4   uk.co.micromass.UserInterface.ProteinLynx.results.rawdatadisplay.RawDataWorkerThread.doInBackground(Unknown Source)
  5   uk.co.micromass.UserInterface.ProteinLynx.results.rawdatadisplay.RawDataWorkerThread.doInBackground(Unknown Source)
  6   javax.swing.SwingWorker$1.call(Unknown Source)
  7   java.util.concurrent.FutureTask.run(Unknown Source)
  8   javax.swing.SwingWorker.run(Unknown Source)
  9   java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
  10   java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
  11   java.lang.Thread.run(Unknown Source)

ENVIRONMENT

• Reported in BiopharmaLynx 1.3.5
• May also affect previous versions of BiopharmaLynx

CAUSE

RawDataWorkerThread runs in the background when a BiopharmaLynx project is first opened. It reads data from the MassLynx raw data folder to display on screen in the BiopharmaLynx chromatograms and spectra displays if the user switches to the raw data displays. If the data is large, this process can take a while and could cause processing to slow if the user reprocesses data while this process is running. In other words, if you try to process the data before rawdataworkerthread has finished loading the data, you get a processing error.

FIX or WORKAROUND

There are two things the user can try:
1. Wait until the read is done before reprocessing. Switch to the raw data displays and wait for traces to appear.
2. Open Task Manager and look for a process called, "raw_extract.exe." This process is executed about six times by BiopharmaLynx to read data for each of the raw data displays. Stop each of these processes. The raw data displays no longer show data, but the browser and processing should be faster.

ADDITIONAL INFORMATION