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-s parameter fails to convert scan data

See original GitHub issue

Hi, the -s parameter introduced after the discussion in #99 does not work in the latest version 1.3.4. (I have not tested previous releases so I don’t know if it worked in the past and got broken at some point)

A simple test: I use a 15MB .raw file called a.raw. After running ThermoRawFileParser.exe -i a.raw I get a complete mzML file a.mzML with comparable size (~10 MB). When I run ThermoRawFileParser.exe -s -i a.raw > a.mzML the output file is tiny (~3 KB) and contains only the mzML header but no scan data.

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:5 (2 by maintainers)

github_iconTop GitHub Comments

caeteracommented, May 18, 2021

Hi Tomas, thank you for reporting. The cause of the error is likely because since 1.3.3 the default output format is indexed mzML, it is not possible to index piped output and thus TRFP crashes (I am actually surprised it does not spit any error or exception it does not throw any error since the logging is silenced in piped output). In future, -s should imply regular mzML, as quick work around, please, try using -f=1 (regular mzML)

caeteracommented, May 16, 2022

Closed in 410ff006b2592f95c7227af2418e281b3a79a35a. STDOUT (-s) always forces plain mzML instead of indexed mzML

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