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Changing where temp files are written #1785

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JadeyMac opened this issue Sep 17, 2024 · 5 comments
Closed

Changing where temp files are written #1785

JadeyMac opened this issue Sep 17, 2024 · 5 comments
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@fcyu

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@JadeyMac
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Hi! I have an older computer with minimal local drive space. Everything else runs perfectly fine, but my runs are starting to crash because temp files are not able to be accessed because they are being written on the local drive, which doesn't have enough space. I have deleted everything I can from the local drive, and still don't have enough space for these temp files when I do a big run. Is there a way in the user interface to tell MSFragger/Fragpipe to write the temporary files on my data drive instead?
@fcyu fcyu self-assigned this Sep 17, 2024
@fcyu
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fcyu commented Sep 17, 2024

Yes.

For Windows: #306 (comment)

For Linux: #755 (comment)

Best,

Fengchao

@JadeyMac
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Thank you so much for your response!

I was able to change where temp files are written,but now I'm getting a different issue with the temp file.

Here is the tail end of my log with the error at the bottom. It is now giving an error saying that it can't delete a temp file because it is in use.

Do you have any suggestions?

Thanks!

NFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20.....
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
INFO[13:16:42] Done
Process 'PeptideProphet' finished, exit code: 0
INFO[13:15:10] Executing PeptideProphet v5.0.0
Unknown file type. No file loaded.E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_04/20240717_DCIS_TSH_C3_04_3_Slot1-16_1_3639.mzBIN_calibrated
Unknown file type. No file loaded.E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_04/20240717_DCIS_TSH_C3_04_3_Slot1-16_1_3639.mzBIN_calibrated
file 1: E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_04\20240717_DCIS_TSH_C3_04_3_Slot1-16_1_3639.pepXML
processed altogether 45937 results
INFO: Results written to file: E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_04\interact-20240717_DCIS_TSH_C3_04_3_Slot1-16_1_3639.pep.xml

  • E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_04\interact-20240717_DCIS_TSH_C3_04_3_Slot1-16_1_3639.pep.xml
  • Building Commentz-Walter keyword tree...
  • Searching the tree...
  • Linking duplicate entries...
  • Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0.0
init with X! Tandem nonspecific
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
read in 7028 1+, 24711 2+, 11555 3+, 2366 4+, 277 5+, 0 6+, and 0 7+ spectra.
Found 17321 Decoys, and 28616 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20.....
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
INFO[13:16:46] Done
Process 'PeptideProphet' finished, exit code: 0
INFO[13:15:10] Executing PeptideProphet v5.0.0
Unknown file type. No file loaded.E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01/20240717_DCIS_TSH_C3_01_2_Slot1-12_1_3620.mzBIN_calibrated
Unknown file type. No file loaded.E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01/20240717_DCIS_TSH_C3_01_2_Slot1-12_1_3620.mzBIN_calibrated
file 1: E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01\20240717_DCIS_TSH_C3_01_2_Slot1-12_1_3620.pepXML
processed altogether 46829 results
INFO: Results written to file: E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01\interact-20240717_DCIS_TSH_C3_01_2_Slot1-12_1_3620.pep.xml

  • E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01\interact-20240717_DCIS_TSH_C3_01_2_Slot1-12_1_3620.pep.xml
  • Building Commentz-Walter keyword tree...
  • Searching the tree...
  • Linking duplicate entries...
  • Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0.0
init with X! Tandem nonspecific
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
read in 6501 1+, 24175 2+, 12378 3+, 3160 4+, 615 5+, 0 6+, and 0 7+ spectra.
Found 17544 Decoys, and 29285 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20.....
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
INFO[13:16:50] Done
Process 'PeptideProphet' finished, exit code: 0
INFO[13:15:10] Executing PeptideProphet v5.0.0
Unknown file type. No file loaded.E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01/20240717_DCIS_TSH_C3_01_3_Slot1-12_1_3621.mzBIN_calibrated
Unknown file type. No file loaded.E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01/20240717_DCIS_TSH_C3_01_3_Slot1-12_1_3621.mzBIN_calibrated
file 1: E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01\20240717_DCIS_TSH_C3_01_3_Slot1-12_1_3621.pepXML
processed altogether 46987 results
INFO: Results written to file: E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01\interact-20240717_DCIS_TSH_C3_01_3_Slot1-12_1_3621.pep.xml

  • E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_01\interact-20240717_DCIS_TSH_C3_01_3_Slot1-12_1_3621.pep.xml
  • Building Commentz-Walter keyword tree...
  • Searching the tree...
  • Linking duplicate entries...
  • Printing results...

using Accurate Mass Bins
using PPM mass difference
Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Not using ntt model
Not using nmc model
Using non-parametric distributions
(X! Tandem) (using Tandem's expectation score for modeling)
adding ACCMASS mixture distribution
using search_offsets in ACCMASS mixture distr: 0.0
init with X! Tandem nonspecific
PeptideProphet (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
read in 6583 1+, 24329 2+, 12445 3+, 3034 4+, 596 5+, 0 6+, and 0 7+ spectra.
Found 17610 Decoys, and 29377 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ...
Initialising statistical models ...
Iterations: .........10.........20.....
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 26 iterations
panic: remove E:\TempFiles\277e9256-eaab-45fe-99dd-895a653dc7fa\PeptideProphetParser.exe: Access is denied.

goroutine 1 [running]:
github.com/Nesvilab/philosopher/lib/msg.callLogrus({0xc0024bc0e0, 0x64}, {0xf64557?, 0x1?})
      D:/Projects/philosopher/philosopher/lib/msg/msg.go:327 +0x2ed
github.com/Nesvilab/philosopher/lib/msg.Custom({0x10d1f00?, 0xc0000e4120?}, {0xf64557, 0x5})
      D:/Projects/philosopher/philosopher/lib/msg/msg.go:15 +0x6e
github.com/Nesvilab/philosopher/lib/met.CleanTemp({0xc000020800?, 0x24?})
      D:/Projects/philosopher/philosopher/lib/met/met.go:484 +0x36
github.com/Nesvilab/philosopher/cmd.glob..func12(0x2b756c0?, {0xc000000300, 0x1, 0xc})
      D:/Projects/philosopher/philosopher/cmd/peproph.go:30 +0xe7
github.com/spf13/cobra.(*Command).execute(0x2b756c0, {0xc000000240, 0xc, 0xc})
      D:/Projects/philosopher/philosopher/vendor/github.com/spf13/cobra/command.go:920 +0x847
github.com/spf13/cobra.(*Command).ExecuteC(0x2b76520)
      D:/Projects/philosopher/philosopher/vendor/github.com/spf13/cobra/command.go:1044 +0x3bd
github.com/spf13/cobra.(*Command).Execute(...)
      D:/Projects/philosopher/philosopher/vendor/github.com/spf13/cobra/command.go:968
github.com/Nesvilab/philosopher/cmd.Execute()
      D:/Projects/philosopher/philosopher/cmd/root.go:35 +0x25
main.main()
      D:/Projects/philosopher/philosopher/main.go:23 +0x85
ERRO[13:16:50] remove E:\TempFiles\277e9256-eaab-45fe-99dd-895a653dc7fa\PeptideProphetParser.exe: Access is denied.
Process 'PeptideProphet' finished, exit code: 2
Process returned non-zero exit code, stopping
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
Processing interrupted, stopping PeptideProphet
13:16:50 WARN : Attempt #1 to delete file we need to delete is being used by another process: E:\Users\Taylor\FraggerOut\20240918_DCIS\AA_03\fragpipe-20240717_DCIS_TSH_C3_03_3_Slot1-15_1_3635.pepXML-temp

Cancelling 279 remaining tasks

@fcyu
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fcyu commented Sep 19, 2024

It seems that there was antivirus software or file system issue preventing the files from being deleted. But I think this issue has been fixed in the latest FragPipe, but you are using an old version.

Best,

Fengchao

@JadeyMac
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Is there a way I can fix this issue in version 20? We already published half of the cohort using this version and my PI is adverse to updating.

Is there a reason why we weren't getting this issue before? Does this error occur with specific settings? Can I change antivirus settings? Or do you have any other suggestions I could try?

@fcyu
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fcyu commented Sep 19, 2024

It was due to your computer or operating system, and probably happens at random. You will need to troubleshoot locally.

Best,

Fengchao

@fcyu fcyu closed this as completed Sep 23, 2024
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