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statisticalbiotechnology / maracluster

Matthew The's implementation of MaRaCluster
Apache License 2.0
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Running batch on ProteoWizard converted mzML files resulting in unsupported file format error, in converting to .dat step; #27

Closed pareamit closed 10 months ago

pareamit commented 1 year ago 
maracluster batch -b mzml_list.txt --output-folder test_maracluster_output/
MaRaCluster version 1.04.0, Build Date Nov 20 2022 09:30:42
Copyright (c) 2015-19 Matthew The. All rights reserved.
Written by Matthew The (matthewt@kth.se) in the
School of Biotechnology at the Royal Institute of Technology in Stockholm.
Issued command:
maracluster batch -b mzml_list.txt --output-folder test_maracluster_output/
Started Mon Mar  6 16:40:30 2023
 on amit-biodisco-0
Converting input files to .dat binary format
  Processing mzml_data/file_1.mzML (100%).
  Processing mzml_data/file_2.mzML (50%).
terminate called after throwing an instance of 'std::runtime_error'
  what():  [MSDataFile::readFile()] Unsupported file format.
Aborted
MatthewThe commented 1 year ago

Thank you for reporting this problem. Would it be possible to share one of the converted mzML files?

pareamit commented 1 year ago

Thank you for reporting this problem. Would it be possible to share one of the converted mzML files?

We were able to hunt down the issue with the file breaking_file.zip, the files are empty and don't have any spectra.