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[aria-discuss] Errors in output file


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  • From: "Kelly, Mark" <Mark.Kelly AT ucsf.edu>
  • To: Benjamin Bardiaux <bardiaux AT pasteur.fr>, "aria-discuss AT services.cnrs.fr" <aria-discuss AT services.cnrs.fr>
  • Subject: [aria-discuss] Errors in output file
  • Date: Sat, 12 Jun 2021 02:02:35 +0000
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Dear Benjamin,

I’m seeing the errors below in the beginning of my Aria ‘standard out’ —output file. The calculation runs. Is this something I should worry about?

Best,

Mark


USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "sym_type" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "default_shift_error" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "ref_segid" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "proton2_shift_err" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "hetero1_shift_err" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "hetero2_shift_err" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "structural_rules_enabled" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "use_shift_error" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "use_assignments" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "proton1_shift_err" exists, but has never been initialized.
USER ERROR <aria.PeakAssigner.PeakAssignerSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
PeakAssignerSettings: setting "spec_type" exists, but has never been initialized.
USER ERROR <aria.ViolationAnalyser.ViolationAnalyserSettings> File "/Applications/aria2.3.2/src/py/aria/ViolationAnalyser.py", line 96 in __init__
ViolationAnalyserSettings: setting "violation_tolerance" exists, but has never been initialized.
MESSAGE [Project]: Temporary directory has been set to /Users/markkelly/






MESSAGE [Protocol]: ---------------------- Iteration 0 -----------------------

USER ERROR <aria.Calibrator.CalibratorSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
CalibratorSettings: setting "volume_or_intensity" exists, but has never been initialized.
USER ERROR <aria.Calibrator.CalibratorSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
CalibratorSettings: setting "use_bounds" exists, but has never been initialized.
USER ERROR <aria.ViolationAnalyser.ViolationAnalyserSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
ViolationAnalyserSettings: setting "lower_bound_correction" exists, but has never been initialized.
USER ERROR <aria.ViolationAnalyser.ViolationAnalyserSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
ViolationAnalyserSettings: setting "upper_bound_correction" exists, but has never been initialized.
USER ERROR <aria.Network.NetworkSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
NetworkSettings: setting "v_max" exists, but has never been initialized.
USER ERROR <aria.Network.NetworkSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
NetworkSettings: setting "distance_max" exists, but has never been initialized.
USER ERROR <aria.Network.NetworkSettings> File "/Applications/aria2.3.2/src/py/aria/Settings.py", line 728 in update
NetworkSettings: setting "v_min" exists, but has never been initialized.
MESSAGE [Protocol]: Calibrating spectrum "13C HSQC-NOESY"...
MESSAGE [Protocol]: Calibrating spectrum "15N HSQC-NOESY"..


  • [aria-discuss] Errors in output file, Kelly, Mark, 06/12/2021

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