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ThermoRawFileParser Error

Open drboothtj opened this issue 1 year ago • 0 comments

Having an issue with the ThermoRawFileParser.


Standard output: Running: mono .snakemake/conda/5624a2a9a937aa833db817288853595e_/bin/ThermoRawFileParser.exe -i=data/raw/20231113_Ac-C18_POS_UMETAB404_Blank_02.raw --output_file=data/mzML/20231113_Ac-C18_POS_UMETAB404_Blank_02.mzML -f=2 -e
2023-11-20 15:00:12 INFO Started parsing data/raw/20231113_Ac-C18_POS_UMETAB404_Blank_02.raw
2023-11-20 15:00:13 INFO Processing 4114 MS scans
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

2023-11-20 15:00:22 ERROR An unexpected error occured:
2023-11-20 15:00:22 ERROR System.ObjectDisposedException: Cannot access a disposed object.
Object name: 'Stream has been closed'.
  at System.IO.FileStream.Write (System.Byte[] array, System.Int32 offset, System.Int32 count) [0x00010] in <12b418a7818c4ca0893feeaaf67f1e7f>:0
  at System.Security.Cryptography.CryptoStream.FlushFinalBlock () [0x00077] in <12b418a7818c4ca0893feeaaf67f1e7f>:0
  at System.Security.Cryptography.CryptoStream.Dispose (System.Boolean disposing) [0x00011] in <12b418a7818c4ca0893feeaaf67f1e7f>:0
  at System.IO.Stream.Close () [0x00000] in <12b418a7818c4ca0893feeaaf67f1e7f>:0
  at ThermoRawFileParser.Writer.MzMlSpectrumWriter.Write (ThermoFisher.CommonCore.Data.Interfaces.IRawDataPlus rawFile, System.Int32 firstScanNumber, System.Int32 lastScanNumber) [0x011b3] in <0f1e74e6c948465884a8f57636fcb120>:0
  at ThermoRawFileParser.RawFileParser.ProcessFile (ThermoRawFileParser.ParseInput parseInput) [0x00177] in <0f1e74e6c948465884a8f57636fcb120>:0
  at ThermoRawFileParser.RawFileParser.Parse (ThermoRawFileParser.ParseInput parseInput) [0x001a6] in <0f1e74e6c948465884a8f57636fcb120>:0
  at ThermoRawFileParser.MainClass.RegularParametersParsing (System.String[] args) [0x00919] in <0f1e74e6c948465884a8f57636fcb120>:0

Standard error: Process 'mono' did not finish successfully (exit code: ). Please check the log.

Any ideas?

drboothtj avatar Nov 20 '23 14:11 drboothtj