Unrecognized error during reading timsTOF file

[plyush1993]

Hello there, I use a predefined workflow (LFQ workflow, for a DDA experiment. IM-MS data) and I'm pretty sure all parameters and the files conversion are correct (.d format). Moreover, other files from this instrument passed without errors.

• The relevant snippet from the log file is: Operating on slice 1 of 1: Fragment index slice generated in 1.51 s
  1. Serum_Aptamer_15m_1.d There are multiple scan modes: 0,8. Will only use the scans with mode 8 (PASEF). ​
  2. Serum_Aptamer_15m_1.d loading 45% Could not load file Y:\Members\Ivan\TIMS-TOF_data\2024_01_28_HSA_10k_d_15_30_45_60min\Serum_Aptamer_15m_1.d. The file may be corrupted. java.util.concurrent.ExecutionException: umich.ms.fileio.exceptions.FileParsingException: org.sqlite.SQLiteException: [SQLITE_BUSY] The database file is locked (database is locked) at java.base/java.util.concurrent.FutureTask.report(Unknown Source) at java.base/java.util.concurrent.FutureTask.get(Unknown Source) at edu.umich.andykong.msfragger.MSRun.readAsTimsTof(MSRun.java:524) at edu.umich.andykong.msfragger.MSRun.loadScans(MSRun.java:115) at edu.umich.andykong.msfragger.MSFraggerCore.(MSFraggerCore.java:93) at edu.umich.andykong.msfragger.MSFragger.main1(MSFragger.java:821) at edu.umich.andykong.msfragger.MSFragger.main0(MSFragger.java:207) at edu.umich.andykong.msfragger.MSFragger.main(MSFragger.java:75) Caused by: umich.ms.fileio.exceptions.FileParsingException: org.sqlite.SQLiteException: [SQLITE_BUSY] The database file is locked (database is locked) at umich.ms.fileio.filetypes.bruker.BrukerTdfFileBase.readMs1AsPasef(BrukerTdfFileBase.java:116) at edu.umich.andykong.msfragger.MSRun.lambda$readAsTimsTof$6(MSRun.java:353) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: org.sqlite.SQLiteException: [SQLITE_BUSY] The database file is locked (database is locked) at org.sqlite.core.DB.newSQLException(DB.java:1179) at org.sqlite.core.DB.newSQLException(DB.java:1190) at org.sqlite.core.DB.execute(DB.java:985) at org.sqlite.jdbc3.JDBC3PreparedStatement.lambda$executeQuery$1(JDBC3PreparedStatement.java:89) at org.sqlite.jdbc3.JDBC3Statement.withConnectionTimeout(JDBC3Statement.java:459) at org.sqlite.jdbc3.JDBC3PreparedStatement.executeQuery(JDBC3PreparedStatement.java:84) at umich.ms.fileio.filetypes.bruker.BrukerTdfSql.sqlReadPrecursorById(BrukerTdfSql.java:302) at umich.ms.fileio.filetypes.bruker.BrukerTdfFileBase.readMs1AsPasef(BrukerTdfFileBase.java:102) ... 5 more

[fcyu]

Your .d folder has been corrupted. And also, something seems not right: "There are multiple scan modes: 0,8. Will only use the scans with mode 8 (PASEF)."

Best,

Fengchao

[plyush1993]

Your .d folder has been corrupted. And also, something seems not right: "There are multiple scan modes: 0,8. Will only use the scans with mode 8 (PASEF)."

Best,

Fengchao

Thank you for your quick reply. multiple scan modes is not a problem, for other files the same modes run without error. I also can't identify any corruption in files. Maybe you could provide other suggestions/potential solutions?

With best regards, Ivan

[fcyu]

It seems to be related to the tdf file. Could you make sure that there is no other program reading or writing the .d, and try again?

Best,

Fengchao

[plyush1993]

I noticed that each time it gaves error on different stage of loading the first processed file, like: 39 %, next 67 %, etc. I mean it is not completely reproducible. Maybe this will help somehow too

[fcyu]

Yeah, something was wrong with your operating system or file system. Please troubleshoot locally. I don't think we can help much here.

Best,

Fengchao

[plyush1993]

Ok thanks