( 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 $_TIDE_USE_NEUTRAL_LOSSES ms_amanda_instrument "'$_MS_AMANDA_INSTRUMENT'" xtandem_min_frag_mz $_XTANDEM_MIN_FRAG_MZ
ptm_configuration $TEMPDIR/mods/ create parameter file in $TEMPDIR/db/searchgui_db.fasta -decoy > $OUTPUT_DIR/logs/FastaCLI.log 2>&1 PWIZ_PATH=/nfs3_ib/ip32/home/xroucou_group/apps_centos7/pwiz_release-3_0_8789 build db SHAKER_JAR_PATH=$TEMPDIR/softwares/PeptideShaker-1.16.38/PeptideShaker-1.16.38.jar SEARCHGUI_JAR_PATH=$TEMPDIR/softwares/SearchGUI-3.3.13/SearchGUI-3.3.13.jar Here is the context:Ĭp -r /nfs3_ib/ip32/home/xroucou_group/analysis/test/pej_newmodif/programs/SearchGUI-3.3.13/ $TEMPDIR/softwares/Ĭp -r /nfs3_ib/ip32/home/xroucou_group/analysis/test/pej_newmodif/programs/PeptideShaker-1.16.38/ $TEMPDIR/softwares/Ĭp /nfs3_ib/ip32/home/xroucou_group/apps/compomics/clean_install/ptmFactory-4.12.14.json $TEMPDIR/mods/ I am trying to load new PTM on centos7 cluster as discussed in this thread but cant seem to get this done right. Importing PSMs from ch_15Feb2018_HEK293-TMT0_undCHARGE_2_ Or even better, any help on getting a custom modification into SearchCLI (ideally without having to use the GUI) and having it work correctly if it is not listed in psi-mod? I looked in the PeptideShaker log, and there isn't actually anything written there about this error. However, when I go to run PeptideShaker I get hit with the error shown below. I made sure the file paths were correct in the file before using it. Although this modification has an accession in unimod (739), it does not have a name there. The modification is for the TMT zero reagent.
Searchgui searchcli how to#
After looking around at ModificationsCLI a bit, I wasn't able to figure out how to work it correctly, so I ended up making a custom modification in the SearchGUI interface on Windows and porting the parameters file over to the CentOS server where I usually run these programs. I am running into some difficulties when handling custom modifications in SearchCLU and PeptideShakerCLI.
0 kommentar(er)
