PeptideShakerCLI

PeptideShaker Command Line Interface

PeptideShaker provides several command line interfaces that can be used to process MS identification files produced by search and de novo engines and output results in various formats.

  • A) PeptideShakerCLI - creates a PeptideShaker project
  • B) ReportCLI - exports identification results from a PeptideShaker project as text file
  • C) FollowUpCLI - export files for follow up analysis from a PeptideShaker project
  • D) MzidCLI - export an mzIdentML file from a PeptideShaker project
  • E) StirredCLI - export an mzIdentML file from a set of MS identification files produced by search and de novo engines
  • F) PathSettingsCLI - set the paths to use
  • G) General - general command line help

Note that ReportCLI, FollowUpCLI, MzidCLI and PathSettingsCLI options can also be appended directly to PeptideShakerCLI command lines.

All command line options have the same overall structure and only differ in the features and parameters available.

Identification parameters can be provided as a file. Identification parameter files are in the json format and can be created in the graphical user interface, using the IdentificationParametersCLI, or using third party tools. Alternatively, the parameters can be passed directly to PeptideShakerCLI by using the command line arguments of the IdentificationParametersCLI.

Temporary folders used in the processing can be set via PathSettingsCLI. It is recommended to use a single instance of PeptideShakerCLI at a time. In distributed setups, we recommend keeping a clean copy of PeptideShaker, and distribute it to the different nodes prior to execution.


A - PeptideShakerCLI

Standard command line

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI [parameters]

Mandatory parameters

-reference                 The reference/name for the project.

-fasta_file (*)            The complete path to the FASTA file.

-identification_files      Identification files in a comma separated list, as compressed zip file, 
                           or an entire folder. 
                           Example: "/myFolder/file1.omx,/myFolder/file1.mzid,/myFolder/file1.t.xml".

-spectrum_files (*)        The spectrum files (mgf or mzML format) in a comma separated list or an 
                           entire folder. Example: "/myFolder/file1.mzml,/myFolder/file2.mzml".

-id_params (*)             The identification parameters file (.par). 
                           Generated using the GUI or via IdentificationParametersCLI.
                           Example: "/myFolder/search_parameters.par". 
                           Alternatively, IdentificationParametersCLI parameters can be passed directly.

(*) Not mandatory if these files are part of a zip file input with the identification files.

Optional output parameters

-out                       PeptideShaker output file (.psdb). If the file already exists 
                           it will be silently overwritten. Example: "/myFolder/ps_output.psdb".

-zip                       Exports the entire project as a zip file in the file specified.

-output_mgf                When using zipped output, exports mgf file(s) out of the zip file 
                           into the same folder in addition. 0: no, 1: yes, default is '0'.

Optional processing parameters

-project_type              The type of project (0: psm, 1: peptide, 2: protein).

-threads                   The number of threads to use. Defaults to the number of available CPUs.

-gui                       Use a dialog to display the progress (1: true, 0: false, default is '0').

PeptideShakerCLI Example

PeptideShakerCLI example where X, Y and Z have to be replaced by the actual version of PeptideShaker and my folder by the folder containing the desired files:

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI 
-reference myReference -fasta_file "/myFolder/my_data.fasta"
-identification_files "/myFolder" -spectrum_files "/myFolder" 
-id_params "/myFolder/my_search_params.par" 
-out "/myFolder/myCpsFile.psdb"

Note that for readability the command is here split over multiple lines. When used the command should of course be a single line.

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B - ReportCLI

Standard command line

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.ReportCLI [parameters]

Mandatory parameters

-in                        PeptideShaker project (.psdb or zip file)

-out_reports               Output folder for report files. (Existing files will be overwritten.)

Optional report options

-reports                   Comma separated list of types of report to export. 
                           0: Certificate of Analysis, 
                           1: Default Hierarchical Report, 
                           2: Default PSM Phosphorylation Report, 
                           3: Default PSM Report, 
                           4: Default PSM Report with non-validated matches, 
                           5: Default Peptide Phosphorylation Report, 
                           6: Default Peptide Report, 
                           7: Default Peptide Report with non-validated matches, 
                           8: Default Protein Phosphorylation Report, 
                           9: Default Protein Report, 
                           10: Default Protein Report with non-validated matches, 
                           11: Extended PSM Report, 
                           12-n: Your own custom reports.

-report_prefix             Prefix added to the report file name.

-documentation             Comma separated list of types of report documentation to export. 
                           0: Certificate of Analysis, 
                           1: Default Hierarchical Report, 
                           2: Default PSM Phosphorylation Report, 
                           3: Default PSM Report, 
                           4: Default PSM Report with non-validated matches, 
                           5: Default Peptide Phosphorylation Report, 
                           6: Default Peptide Report, 
                           7: Default Peptide Report with non-validated matches, 
                           8: Default Protein Phosphorylation Report, 
                           9: Default Protein Report, 
                           10: Default Protein Report with non-validated matches, 
                           11: Extended PSM Report, 
                           12-n: Your own custom reports.
                           
-gzip                      Indicates whether the report should be compressed.
                           0: no, 1: yes, default is 0.

To add custom reports see Export > Identification Features > Reports in PeptideShaker.

ReportCLI Example

ReportCLI example where X, Y and Z have to be replaced by the actual version of PeptideShaker:

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.ReportCLI 
-in "/myFolder/myCpsFile.psdb" -out_reports "/myFolder" -reports "0, 3" -report_prefix "my_" -gzip 0

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C - FollowUpCLI

Standard command line

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.FollowUpCLI [parameters]

Mandatory parameters

-in                        PeptideShaker project (.psdb or zip file)

Optional recalibration parameters

-recalibration_folder      Output folder for the recalibrated files. (Existing files will be overwritten.)

-recalibration_mode        Recalibration type. 
                           0: precursor and fragment ions (default), 
                           1: precursor only, 
                           2: fragment ions only.

Optional spectrum export parameters

-spectrum_folder           Output folder for the spectra. (Existing files will be overwritten.)

-psm_type                  Type of PSMs. 
                           0: Spectra of Non-Validated PSMs (default),  
                           1: Spectra of Non-Validated Peptides, 
                           2: Spectra of Non-Validated Proteins, 
                           3: Spectra of Validated PSMs, 
                           4: Spectra of Validated PSMs of Validated Peptides, 
                           5: Spectra of validated PSMs of Validated Peptides of Validated Proteins.

Optional Progenesis export parameters

-progenesis_file           Output file for identification results in Progenesis LC-MS compatible format. 
                           (Existing files will be overwritten.)

-progenesis_type           Type of hits to export to Progenesis. 
                           0: Validated PSMs of Validated Peptides of Validated Proteins.
                           1: Validated PSMs of Validated Peptides, 
                           2: Validated PSMs,
                           3: Validated PSMs containing confidently localized PTMs.

-progenesis_ptms           Comma separated list of PTMs to include in reports of Type 3.

Optional protein accessions export parameters

-accessions_file           Output file to export the protein accessions in text format. 
                           (Existing files will be overwritten.)

-accessions_type           When exporting accessions, select a category of proteins. 
                           0: Main Accession of Validated Protein Groups (default),
                           1: All Accessions of Validated Protein Groups, 
                           2: Non-Validated Accessions.

Optional protein sequences (in FASTA format) export parameters

-sequences_file            File where to export the protein details in fasta format. 
                           (Existing files will be overwritten.)

-sequences_type            When exporting protein details, select a category of proteins. 
                           0: Main Accession of Validated Protein Groups (default), 
                           1: All Accessions of Validated Protein Groups, 
                           2: Non-Validated Accessions.

Optional inclusion list generation parameters

-inclusion_list_file       Output file for an inclusion list of validated hits. 
                           (Existing files will be overwritten.)

-inclusion_list_format     Format for the inclusion list. 
                           0: Thermo (default), 
                           1: ABI, 
                           2: Bruker, 
                           3: MassLynx.

-inclusion_list_peptide_filters     
                           Peptide filters for the inclusion list export (comma separated). 
                           0: Miscleaved Peptides, 
                           1: Reactive Peptides, 
                           2: Degenerated Peptides.

-inclusion_list_protein_filters     
                           Protein inference filters for the inclusion list export (comma separated). 
                           1: Related Proteins, 
                           2: Related and Unrelated Proteins, 
                           3: Unrelated Proteins.

-inclusion_list_rt_window  Retention time window for the inclusion list export (in seconds).

Optional proteoforms parameters

-proteoforms_file      Output file for the proteoforms. (Existing file will be overwritten.)

Optional DeeplLC parameters

-deeplc_file           Path to the file where to write DeepLC peptide files. If the PeptideShaker project 
                       was built using multiple MS files, one file per MS file will be exported. 
                       (Should end with .gz. Existing file will be overwritten.)

Optional MS2PIP parameters

-ms2pip_file           Path to the file where to write ms2pip peptide files. If the PeptideShaker project 
                       was built using multiple MS files, one file will be exported for all. 
                       (Should end with .gz. Existing file will be overwritten.)

-ms2pip_models         Comma separated list of models to write a config file for. Default: CID,HCD.

Optional Percolator parameters

-precolator_rt_file    Path to the file containing the RT predictions to include in the percolator 
                       training file.

-precolator_fragmentation_file         
                       Path to the file containing the fragmentation predictions to include in the 
                       percolator training file.

-precolator_file       Path to the file where to write the percolator training file. DeepLC and ms2pip 
                       files can be provided using the respective options. 
                       (Should end with .gz. Existing file will be overwritten.)

FollowUpCLI Example

FollowUpCLI example where X, Y and Z have to be replaced by the actual version of PeptideShaker and my folder by the folder containing the desired files:

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.FollowUpCLI -in "/myFolder/myCpsFile.psdb" -spectrum_folder "/myFolder" -psm_type 0

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D - MzidCLI

Standard command line

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.MzidCLI [parameters]

Mandatory parameters

-in                        PeptideShaker project (.psdb or zip file)

-output_file               Output file.

-contact_first_name        Contact first name.

-contact_last_name         Contact last name.

-contact_email             Contact e-mail.

-contact_address           Contact address.

-organization_name         Organization name.

-organization_email        Organization e-mail.

-organization_address      Organization address.

Optional parameters:

-gzip                      Indicates whether the mzIdentML file should be compressed.
                           0: no, 1: yes, default is 0.

-contact_url               Contact URL.

-organization_url          Organization URL.   

-include_sequences         Include the protein sequences. 
                           1: true, 0: false, default is '0'.

-mzid_version              The version of the mzIdentML scheme to use. 
                           0: v1.1, 1: v1.2, default is '0'.

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E - StirredCLI

Standard command line

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.StirredCLI [parameters]

Mandatory parameters


-i/--input                 Identification files in a comma separated list, as compressed zip file, 
                           or an entire folder. 
                           Example: "/myFolder/file1.omx,/myFolder/file1.mzid,/myFolder/file1.t.xml".

-o/--output                The folder where to write the results..

-f/--fasta (*)             The complete path to the FASTA file.

-s/--spectrum (*)          The spectrum files (mgf or mzML format) in a comma separated list or an 
                           entire folder. Example: "/myFolder/file1.mzml,/myFolder/file2.mzml".

-p/--id_params (*)         The identification parameters file (.par). 
                           Generated using the GUI or via IdentificationParametersCLI.
                           Example: "/myFolder/search_parameters.par". 
                           Alternatively, IdentificationParametersCLI parameters can be passed directly.

(*) Not mandatory if these files are part of a zip file input with the identification files.

Optional parameters:

-cfn/--contactFirstName    The first name of the contact to annotate in the mzIdentML file. 
                           Default: 'Unknown'.

-cln/--contactLastName     The last name of the contact to annotate in the mzIdentML file. 
                           Default: 'Unknown'.

-ca/--contactAddress       The address of the contact to annotate in the mzIdentML file.
                           Default: 'Unknown'.

-ce/--contactEmail         The email of the contact to annotate in the mzIdentML file.
                           Default: 'Unknown'.

-con/--contactOrgName      The name of the organization of the contact to annotate in the mzIdentML file.
                           Default: 'Unknown'.

-coa/--contactOrgAddress   The address of the organization of the contact to annotate in the mzIdentML file.
                           Default: 'Unknown'.

-coe/--contactOrgEmail     The email of the organization of the contact to annotate in the mzIdentML file.
                           Default: 'Unknown'.

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F - PathSettingsCLI

Standard command line

java -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PathSettingsCLI [parameters]

Generic temporary folder

-temp_folder               A folder for temporary file storage. Use only if 
                           you encounter problems with the default configuration.

-log                       Folder where the log files are written.

-use_log_folder            Use the log folder. 0: write logs and errors to standard output, 
                           1: use the log folder. Default: 1.

Specific path setting

-peptideshaker_matches_directory    
                           Folder where identification matches are temporarily 
                           saved to reduce the memory footprint.

-peptideshaker_user_preferences     
                           Folder containing the PeptideShaker user preferences file.

-peptideshaker_exports     Folder containing the user custom exports file.

-utilities_user_preferences         
                           Folder containing the compomics utilities user preferences file.

-ptm_configuration         Folder containing the PTM user preferences file.

-fasta_indexes             Folder containing the indexes of the protein sequences databases.

-gene_mapping              Folder containing the gene mapping files.

-pride_annotation          Folder containing the PRIDE annotation preferences.

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G - General

Comma Separated Lists

When using comma separated lists as input please pay attention to the quotes required. Surround the full content of the option in quotes and not the individual items:

-spectrum_files "/../file_1.mgf,/../file_2.mgf"

Absolute Paths

In general it is recommended to use absolute paths. Its is recommended to avoid spaces and special characters in paths.

Memory Settings

Remember that big datasets require more than the default memory provided to the Java virtual machine, so for larger dataset please increase the maximum memory setting. Example, for a maximum of 2 GB of memory:

java -Xmx2048M -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI [parameters]

See also: JavaTroubleShooting.

Threads and I/O

For most commands, you can set the number of variants to process in parallel using the command line options. Note, however, that if the performance on your setup is limited by the I/O, this will not have much of an effect. If this is the case please make sure that PeptideShaker has direct and rapid access to the files (i.e. not accessing them through a network). IO is dramatically improved using SSD discs.

Some tasks are parallelized at a deeper level using all available resources. You can override the number of threads used by default using the -Djava.util.concurrent.ForkJoinPool.common.parallelism argument.

Example with 32 threads:

java -Djava.util.concurrent.ForkJoinPool.common.parallelism=32 -cp PeptideShaker-X.Y.Z.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI [parameters]

Opening PeptideShaker Projects

To open a PeptideShaker project (cps file or zipped cps file) from the command line (for display in PeptideShaker) use the following command:

java -jar PeptideShaker-X.Y.Z.jar -cps "/myFolder/myCpsFile.psdb"

To open a zipped PeptideShaker project via a URL from the command line (for display in PeptideShaker) use the following command:

java -jar PeptideShaker-X.Y.Z.jar -zipUrl "http://my_url/PS.zip" -zipUrlFolder "/my_folder/"

Opening a PX Accession for Reshaking

To open a PX accession directly in the Reshake mode use:

java -jar PeptideShaker-X.Y.Z.jar -pxAccession "yourPxAccesion"

To open private data use:

java -jar PeptideShaker-X.Y.Z.jar -pxAccession "yourPxAccesion" -pxAccessionPrivate

Help

If you experience any problems with the command line or have any suggestion please contact us via the PeptideShaker issue tracker.

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