SearchCLI
SearchGUI Command Line Interface
The command line interface to SearchGUI, referred to as SearchCLI, makes it possible to run all search engines and de novo algorithms supported by SearchGUI using a single command line.
SearchCLI searches spectrum files according to search parameters using X! Tandem, MyriMatch, MS Amanda, MS-GF+, OMSSA, Comet, Tide, Andromeda, MetaMorpheus, Sage, Novor and DirecTag.
Identification parameters for use in SearchCLI 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 SearchCLI by using the command line arguments of the IdentificationParametersCLI.
We recommend redirecting temporary folders and logs when running SearchGUI on the command line. Please note that the search engines use indexes and temporary files stored locally in their folders. It is thus important to use a single instance of SearchCLI at a time. In distributed setups, we recommend keeping a clean copy of SearchGUI, and distribute it to the different workers prior to execution.
General command line
java -cp SearchGUI-X.Y.Z.jar eu.isas.searchgui.cmd.SearchCLI [parameters]
Mandatory parameters
-spectrum_files Spectrum files (mgf or mzml), comma separated list or an entire folder.
Example: "c:\file1.mgf, c:\file2.mzml".
-fasta_file The complete path to the FASTA file.
-output_folder The output folder, example: "c:\output_folder".
-id_params The identification parameters file (.par).
Generated using the GUI or via IdentificationParametersCLI.
Example: "c:\search_parameters.par".
Alternatively, IdentificationParametersCLI parameters can be passed directly.
Optional common parameters
-xtandem Turn the X!Tandem search on or off.
(1: on, 0: off, default is '0')
-myrimatch Turn the MyriMatch search on or off.
(1: on, 0: off, default is '0')
-ms_amanda Turn the MS Amanda search on or off.
(1: on, 0: off, default is '0')
-msgf Turn the MS-GF+ search on or off.
(1: on, 0: off, default is '0')
-omssa Turn the OMSSA search on or off.
(1: on, 0: off, default is '0')
-comet Turn the Comet search on or off.
(1: on, 0: off, default is '0')
-tide Turn the Tide search on or off.
(1: on, 0: off, default is '0')
-andromeda Turn the Andromeda search on or off.
(1: on, 0: off, default is '0')
-meta_morpheus Turn the MetaMorpheus search on or off.
(1: on, 0: off, default is '0')
-sage Turn the Sage search on or off.
(1: on, 0: off, default is '0')
-novor Turn the Novor sequencing on or off.
(1: on, 0: off, default is '0')
-directag Turn the DirecTag sequencing on or off.
(1: on, 0: off, default is '0')
Optional advanced parameters
-xtandem_folder The folder where X!Tandem is installed, defaults
to the provided version for the given OS.
-myrimatch_folder The folder where MyriMatch is installed, defaults
to the provided version for the given OS.
-ms_amanda_folder The folder where MS Amanda is installed, defaults
to the provided version for the given OS.
-msgf_folder The folder where MS-GF+ is installed.
-omssa_folder The folder where OMSSA is installed, defaults
to the provided version for the given OS.
-comet_folder The folder where Comet is installed, defaults
to the provided version for the given OS.
-tide_folder The folder where Tide is installed, defaults
to the provided version for the given OS.
-tide_index_file The file where the Tide index should be stored.
If this option is provided and the index is found,
the creation of the index will be skipped. If this
option is not provided, the index will always be
created and stored either in the Tide or the temp
folder.
-andromeda_folder The folder where Andromeda is installed, defaults
to the provided version for the given OS.
-meta_morpheus_folder The folder where MetaMorpheus is installed, defaults
to the provided version for the given OS.
-sage_folder The folder where Sage is installed, defaults
to the provided version for the given OS.
-novor_folder The folder where Novor is installed, defaults
to the provided version for the given OS.
-directag_folder The folder where DirecTag is installed, defaults
to the provided version for the given OS.
-makeblastdb_folder The folder where makeblastdb is installed, defaults
to the provided version for the given OS.
-mgf_check_size Turn the mgf size check on or off.
0: off, 1: on, default is '0'.
-mgf_splitting The maximum mgf file size in MB before
splitting an mgf. Default is '1000'.
(See also MGF Splitting below.)
-mgf_spectrum_count The maximum number of spectra per mgf file
when splitting. Default is '25000'.
-correct_titles Correct for duplicate spectrum titles.
(0: no correction, 1: rename spectra,
2: delete spectra, default is '1').
-missing_titles Add missing spectrum titles. (From v1.19.0)
(0: no correction, 1: add missing spectrum titles, default is '0').
-threads The number of threads to use for the processing.
Default is the number of cores available.
-ref_mass Reference mass for the conversion of the fragment ion tolerance
from ppm to Dalton. Default is '2000'.
Optional output compression parameters
-output_default_name Optional output default name, default is 'searchgui_out'.
-output_gzip Gzip result files (0: no, 1: yes, default is '1').
-output_option Optional result file compression:
0: Single zip file,
1: One zip file per mgf,
2: One zip file per algorithm,
3: No zipping,
default is '0'.
-output_data Include mgf and FASTA in the zipped output
(0: no, 1: yes, default is '0').
-output_date Include date in zipped output name
(0: no, 1: yes, default is '0').
-rename_xtandem Turn the renaming of the X! Tandem files on/off.
0: off, 1: on, default is '1'.
-target_decoy_tag The tag added after adding decoy sequences to a FASTA file.
Default is '_concatenated_target_decoy'.
PathSettingsCLI
Standard command line
java -cp SearchGUI-X.Y.Z.jar eu.isas.searchgui.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
-search_engine_temp Folder where search engine temporary files are stored.
(Note: does not work for Andromeda!)
-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.
Comma Separated List
When using comma separated lists as input for the mgf files please pay attention to the quotes required. Surround the full content of the option in quotes and not the individual items:
-spectrum_files "C:\..\file_1.mgf, C:\..\file_2.mgf"
MGF Splitting
If the provided MGF files become too big it can result in memory issues for the search engines, e.g., OMSSA often struggles with files bigger than 1GB. SearchGUI therefore provides an option to split the MGF files. This option should only be used if you are experiencing memory issues with the search engines, as it is always best to search the complete MGF files in a single search. However, if a tool such as PeptideShaker is used to combine the search results afterwards, the effects of the splitting should be minimal.
The list of MGF files used in the search (after splitting) is always listed in the file output_folder\searchGUI_input.txt. Please refer to this file when forwarding the SearchGUI search results to PeptideShaker.
Examples
Here is an example for Windows using a search parameters file. X, Y and Z have to be replaced by the actual version of SearchGUI and my folder by the folder containing the desired files:
java -cp SearchGUI-X.Y.Z.jar eu.isas.searchgui.cmd.SearchCLI
-spectrum_files "C:/my_folder"
-output_folder "C:/my_folder/output"
-id_params "C:/my_folder/SearchGUI.parameters"
Note that for readability the commands are here split over multiple lines. When used the commands should of course be single lines.
FASTA File Handling
SearchGUI also has a separate FastaCLI command line for manipulating FASTA files.
General command line
java -cp SearchGUI-X.Y.Z.jar eu.isas.searchgui.cmd.FastaCLI [parameters]
Mandatory parameters
-in The FASTA file.
Optional parameters
-decoy Create a concatenated target/decoy database.
-decoy_suffix Target decoy suffix, defaults to _concatenated_target_decoy.fasta.
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.
The PathSettingsCLI options can also be used directly as options to FastaCLI.
Help
If you experience any problems with the command line or have any suggestion please contact us via the SearchGUI issue tracker.