Searchgui searchcli6/18/2023 ( 1 : on, 0 : off, default is '0' ) Optional advanced parameters ( 1 : on, 0 : off, default is '0' ) - directag Turn the DirecTag sequencing 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' ) - sage Turn the Sage 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' ) - andromeda Turn the Andromeda 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' ) - comet Turn the Comet 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' ) - msgf Turn the MS - GF 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' ) - myrimatch Turn the MyriMatch search on or off. xtandem Turn the X ! Tandem search on or off. In distributed setups, we recommend keeping a clean copy of SearchGUI, and distribute it to the different workers prior to execution. It is thus important to use a single instance of SearchCLI at a time. Please note that the search engines use indexes and temporary files stored locally in their folders. We recommend redirecting temporary folders and logs when running SearchGUI on the command line. Alternatively, the parameters can be passed directly to SearchCLI by using the command line arguments of the IdentificationParametersCLI. 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. Identification parameters for use in SearchCLI can be provided as a file. 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. 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. PTM Biotinylation of K not found.SearchCLI SearchGUI Command Line Interface Here is the identificationcli QE_0817_10973]$ java -cp $SHAKER_JAR_PATH eu. \Īn error occurred while parsing the variable modifications: However in path.txt, the ptm_configuration path is set well. When I execute IdentificationParametersCLI it returns an error the modification doesnt exist. The variable $_VARIABLE_MODS is set to Biotinylation of K, Biotinylation of N-termini. db $TEMPDIR/db/searchgui_db_concatenated_target_decoy.fasta tide_use_neutral_losses $_TIDE_USE_NEUTRAL_LOSSES xtandem_min_frag_mz $_XTANDEM_MIN_FRAG_MZ ptm_configuration $TEMPDIR/mods/ create parameter file in $TEMPDIR/db/searchgui_db.fasta -decoy > $OUTPUT_DIR/logs/FastaCLI.log 2>
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