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kevinkovalchik / RawTools

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.
Apache License 2.0
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Error with quantification flags #47

Open chrishuges opened 5 years ago

chrishuges commented 5 years ago

Describe the bug Processing some data files for quantification with TMT. If I use the flags -quxmR -r TMT11, it will throw an error that -q and -r are mutually dependent. If I use -q and -r alone, the program will execute correctly. If I try to stack anything with -q, it won't work and will throw the same error. If I do -q -r TMT11 -uxmR, it will also work fine.

Description of raw file Standard DDA file.

Command line arguments This differs, but generally using the -q and -r flags.

Command line output

bash-4.2$ mono /projects/ptx_analysis/chughes/software/RawTools/rawtools202/RawTools.exe -f ./20190706_BMBP_SS_Sorensen_PDX-Renata_F01_016.raw -quxmR -r TMT11 -o ./                            
ERROR: The following arguments are mutually depent: -q, -r.

Screenshots Screen Shot 2019-09-12 at 1 34 12 PM

Desktop & RawTools information:

kevinkovalchik commented 5 years ago

Okay, that sounds like it should be pretty easy to fix. You are using v2.0.2?

Kevin

On Thu, Sep 12, 2019, 4:37 PM Christopher Hughes, notifications@github.com wrote:

Describe the bug Processing some data files for quantification with TMT. If I use the flags -quxmR -r TMT11, it will throw an error that -q and -r are mutually dependent. If I use -q and -r alone, the program will execute correctly. If I try to stack anything with -q, it won't work and will throw the same error. If I do -q -r TMT11 -uxmR, it will also work fine.

Description of raw file Standard DDA file.

Command line arguments This differs, but generally using the -q and -r flags.

Command line output

bash-4.2$ mono /projects/ptx_analysis/chughes/software/RawTools/rawtools202/RawTools.exe -f ./20190706_BMBP_SS_Sorensen_PDX-Renata_F01_016.raw -quxmR -r TMT11 -o ./ ERROR: The following arguments are mutually depent: -q, -r.

Screenshots [image: Screen Shot 2019-09-12 at 1 34 12 PM] https://user-images.githubusercontent.com/9595225/64818974-18bc0f80-d562-11e9-9cd3-801398344b31.png

Desktop & RawTools information:

  • OS: CentOS 7
  • RawTools version: 2.0.2

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