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.
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
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.)
-rt_obs_pred_file Path to the file where to write the observed and predicted RT values for each PSM.
(Existing file will be overwritten.)
-peaks_intensities_file
Path to the file where to write the observed and predicted peaks intensities for
each PSM. (Existing file will be overwritten.)
-psm_ids_for_peaks_export
Path to the file which includes the IDs of the PSMs for which the peaks of the
predicted and observed spectra will be exported.
-percolator_benchmark_results
Path to the file containing Percolator results for each PSM.
(Existing file will be overwritten.)
-psm_identifiers_file Path to the file where to write the existing identifiers for each PSM.
(Existing file will be overwritten.)
-percolator_cache Enable the caching of Percolator features (1: true, 0: false, default is '0').
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
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'.
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'.
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.
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.