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rickhelmus / patRoon

Workflow solutions for mass-spectrometry based non-target analysis.
https://rickhelmus.github.io/patRoon/
GNU General Public License v3.0
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[JOSS Review] BUG: `generatePeakListsMzR` failes with feature groups from KPIC2 #38

Closed hechth closed 2 years ago

hechth commented 2 years ago

After creating the feature groups with KPIC2 I tried generating the peak lists and the method threw a bunch of errors, see the log file below.

Is this related to some parameters missing in the previous function call? Or could it be related to the size of the files/data? Each file is about 700MB, so quite large, and acquired in profile mode and converted without centroiding.

> plists <- patRoon::generateMSPeakListsMzR(groups_kpic2)
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201001_003-QCstd_POS_MU'...
  |================================================================================                                  |  70%2022-01-06T14:26:35.239850Z [rsession-rstudio] ERROR system error 2 (No such file or directory) [path: /home/rstudio/cache.sqlite-journal]; OCCURRED AT time_t rstudio::core::FilePath::getLastWriteTime() const src/cpp/shared_core/FilePath.cpp:1052; LOGGED FROM: time_t rstudio::core::FilePath::getLastWriteTime() const src/cpp/shared_core/FilePath.cpp:1052
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201001_098-QCstd_POS_MU'...
  |========                                                                                                          |   7%2022-01-06T14:28:28.379162Z [rsession-rstudio] ERROR system error 2 (No such file or directory) [path: /home/rstudio/cache.sqlite-journal]; OCCURRED AT uintmax_t rstudio::core::FilePath::getSize() const src/cpp/shared_core/FilePath.cpp:1126
  |==================================================                                                                |  44%2022-01-06T14:29:56.752441Z [rsession-rstudio] ERROR system error 2 (No such file or directory) [path: /home/rstudio/cache.sqlite-journal]; OCCURRED AT time_t rstudio::core::FilePath::getLastWriteTime() const src/cpp/shared_core/FilePath.cpp:1052; LOGGED FROM: time_t rstudio::core::FilePath::getLastWriteTime() const src/cpp/shared_core/FilePath.cpp:1052
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201009_003-QCstd_POS_MU'...
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201009_098-QCstd_POS_MU'...
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201016_003-QCstd_POS_MU'...
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201016_098-QCstd_POS_MU'...
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201021_003-QCstd_POS_MU'...
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201021_098-QCstd_POS_MU'...
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201202_003-QCstd_POS_MU'...
  |==================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201202_098-QCstd_POS_MU'...
  |===================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201209_003-QCstd_POS_MU'...
  |===================================================================================================================| 100%
Loading all MS peak lists for 3821 feature groups in analysis 'Tribrid_201209_090-QCstd_POS_MU'...
  |===================================================================================================================| 100%
Generating averaged peak lists for all feature groups...
  |===================================================================================================================| 100%
There were 50 or more warnings (use warnings() to see the first 50)
rickhelmus commented 2 years ago

Hi @hechth,

I expect that this is related to #36.