Please change localize_delta_mass to 0.

[johnpleid]

Hi to everybody
I get this error
Checking database...
It is a closed search while localize_delta_mass = 1. Please change localize_delta_mass to 0.

But i can't findin which tab is: localize_delta_mass to 0.

someone can help me?
thanx
Giovanni

[anesvi]

It is in MSFragger tab. But you should not see this message unless you you start changing default parameters and do something wrong. Please use one of the default workflows before changing things.

[fcyu]

It's called "localize mass shift (LOS)" in the MSFragger tab. But, yeah, don't change the parameters that you are not sure what they are.

Best,

Fengchao

[johnpleid]

thank you it worked. I get the results, but now I tried to add quantification activating "run ms1 quant" and separating all the runs and separating the runs replicates while before were merged, and now the analysis stop at level of "'PhilosopherFilter"
I add the log file of the run if someone can help. Thanx
log_2024-09-27_09-57-17.txt

[fcyu]

There are 0 IDs with probability > 0.05. Please double check your sample or settings.

Best,

Fengchao

[johnpleid]

strange because without quantification on it worked

[fcyu]

Can you share the log file?

Thanks,

Fengchao

[johnpleid]

it is in my previous post

[fcyu]

Your precious post said that that it didn't work

I get the results, but now I tried to add quantification activating "run ms1 quant" and separating all the runs and separating the runs replicates while before were merged, and now the analysis stop at level of "'PhilosopherFilter"
I add the log file of the run if someone can help. Thanx
log_2024-09-27_09-57-17.txt

But now you said

strange because without quantification on it worked

Thus, I asked for the log file corresponding to the "worked" one just to make sure that it really worked or you made any other mistakes.

Best,

Fengchao

[johnpleid]

log_2024-09-23_10-18-58.txt
Ah i haven't understood you want the good one...here is the log when worked

[fcyu]

Thanks for sharing the log file. The difference is that in the failed one, you assigned each mzML file to a separated experiment group, but in the success one, you just assigned three groups and each group has multiple mzML files.

LCMS files:
  Experiment/Group: BSC_1
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_BSC180.mzML	DDA
  Experiment/Group: BSC_2
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_BSC182.mzML	DDA
  Experiment/Group: BSC_3
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_BSC183.mzML	DDA
  Experiment/Group: ECC_1
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC106.mzML	DDA
  Experiment/Group: ECC_2
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC108.mzML	DDA
  Experiment/Group: ECC_3
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC109.mzML	DDA
  Experiment/Group: ECC_4
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC117.mzML	DDA
  Experiment/Group: ECC_5
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC118.mzML	DDA
  Experiment/Group: PC_1
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC203.mzML	DDA
  Experiment/Group: PC_2
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC205.mzML	DDA
  Experiment/Group: PC_3
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC206.mzML	DDA
  Experiment/Group: PC_4
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC207.mzML	DDA
  Experiment/Group: PC_5
  - D:\Data\gio\leila\20190514_QE7_nLC7_MEM_COLLAB_PC193.mzML	DDA
  Experiment/Group: PC_6
  - D:\Data\gio\leila\20190514_QE7_nLC7_MEM_COLLAB_PC195.mzML	DDA

LCMS files:
  Experiment/Group: BSC
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_BSC180.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_BSC182.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_BSC183.mzML	DDA
  Experiment/Group: ECC
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC106.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC108.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC109.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC117.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_ECC118.mzML	DDA
  Experiment/Group: PC
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC203.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC205.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC206.mzML	DDA
  - D:\Data\gio\leila\20190411_QE7_nLC3_MEM_COLLAB_PC207.mzML	DDA
  - D:\Data\gio\leila\20190514_QE7_nLC7_MEM_COLLAB_PC193.mzML	DDA
  - D:\Data\gio\leila\20190514_QE7_nLC7_MEM_COLLAB_PC195.mzML	DDA

The first file 20190411_QE7_nLC3_MEM_COLLAB_BSC180.mzML happened to have no IDs. When you assigned it to its own experiment group, the Philosopher filter command crashed. When you assigned it and other files in one group, the Philosopher filter command didn't crash because other files have non-zero IDs.

Best,

Fengchao

[johnpleid]

thank you i try to relunch the analysis without the empty run...however it is unconfortable that for a no good LC MS run it stop en entire procedure

[fcyu]

Can you share the log file?

[johnpleid]

It crashed also removing the no Ids file
log_2024-09-30_06-10-07.txt

[fcyu]

There are more than one file with no IDs. If you want to maintain the experiment group assignment that each file in a separated group, you should remove all of them.

Or, you could change the experiment groups to the one used in one of your log log_2024-09-23_10-18-58.txt

Best,

Fengchao

[johnpleid]

ok thank you