search

compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
47 stars 19 forks source link

cms file not found error #454

Closed bernt-matthias closed 3 years ago

bernt-matthias commented 3 years ago

Hi @hbarsnes

Just tested the latest PS release (https://github.com/bioconda/bioconda-recipes/pull/28155) with Galaxy and got 

java.io.FileNotFoundException: /tmp/tmpti3s3okg/job_working_directory/000/2/working/PeptideShakerCLI/.PeptideShaker_unzip_temp/searchgui_input_PeptideShaker_temp/data/searchgui_tinyspectra1.cms (No such file or directory)
    at java.base/java.io.RandomAccessFile.open0(Native Method)
    at java.base/java.io.RandomAccessFile.open(RandomAccessFile.java:345)
    at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:259)
    at java.base/java.io.RandomAccessFile.<init>(RandomAccessFile.java:214)
    at com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader.<init>(CmsFileReader.java:91)
    at com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileIterator.<init>(CmsFileIterator.java:43)
    at com.compomics.util.experiment.io.mass_spectrometry.MsFileIterator.getMsFileIterator(MsFileIterator.java:74)
    at com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler.writeCmsFile(MsFileHandler.java:211)
    at com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler.register(MsFileHandler.java:148)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:1038)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:243)
    at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:1389)

in addition to https://github.com/compomics/peptide-shaker/issues/448

The directory .PeptideShaker_unzip_temp does not extist.

command line is:

mkdir output_reports && 
cwd=`pwd` && 
export HOME=$cwd &&  
ln -s '/tmp/tmpti3s3okg/files/1/f/4/dataset_1f4cc036-a677-4525-b78f-7b3675d4939f.dat' searchgui_input.zip &&  
jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   
peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI -gui 0 -temp_folder $cwd/PeptideShakerCLI -use_log_folder 0 -reference 'Galaxy_Experiment_2021042310471619167647' -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par  -out $cwd/peptideshaker_output.psdb  -threads "${GALAXY_SLOTS:-12}"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "galaxyp@umn.edu" -contact_address "galaxyp@umn.edu" -organization_name "University of Minnesota" -organization_email "galaxyp@umn.edu" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
hbarsnes commented 3 years ago

If .PeptideShaker_unzip_temp does not exist, then where is searchgui_input.zip unzipped? Does the PeptideShakerCLI folder exist?

hbarsnes commented 3 years ago

The following command line works fine for me (outside of Galaxy):

java -cp PeptideShaker-2.0.20.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -gui 0 -temp_folder C:\Users\Harald\Desktop\temp1 -use_log_folder 0 -reference Galaxy_Experiment_2021042310471619167647 -identification_files C:\Users\Harald\Desktop\temp2\searchgui_out.zip -out C:\Users\Harald\Desktop\temp1\out\peptideshaker_output.psdb

bernt-matthias commented 3 years ago

If .PeptideShaker_unzip_temp does not exist, then where is searchgui_input.zip unzipped?

I do not know. After PS exits I can not find any unzipped files (in particular not the missing one).

But the output indicates that its unzipped: 

Fri Apr 23 10:47:29 CEST 2021 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Does the PeptideShakerCLI folder exist?

Yes.

hbarsnes commented 3 years ago

Strange. Hopefully @CarlosHorro can take a look at it next week.

CarlosHorro commented 3 years ago

Hi @bernt-matthias ,

I have been able to reproduce it, and, although I have to do some more tests with simpler datasets, it seems to happen when PS uses files generated by SG Galaxy tool instead of the desktop app.

I will tell you more soon...

Greetings, Carlos

hbarsnes commented 3 years ago

@bernt-matthias I've just released new versions of both SearchGUI and PeptideShaker that should solve the problem. (You should only need to update PeptideShaker though.) The problem was that the cms file was outdated and had to be recreated with the new faster compression, but in the process we ended up deleting the old cms file and then trying to refer to again it a couple lines further down. Safety measures have now been out into place so that this cannot happen again.