Back to Blog
Searchgui searchcli6/10/2023 ![]() ![]() Create a SQLite database for peptide, protein and genomic annotation visualization The output tabular file “Peptides_for_Blast-P_analysis” will contain only those spectra that did not belong to any known proteins. The Query Tabular tool and few test manipulation tools are used to remove spectra that belongs to the reference proteins. The Peptide Shaker’s PSM report is used as an input for the BlastP analysis. Galaxy instance to your local computer in a text file if desired.Ī number of new items will appear in your History, each corresponding to the outputs selected in the PeptideShaker parameters. Used by both SearchGUI and PeptideShaker in the analysis. The “Certificate of Analysis” provides details on all the parameters Param-select “Variable modifications”: Oxidation of M, ITRAQ-4Plex of Y param-select “Fixed Modifications”: Carbamidomethylation of C, ITRAQ-4Plex of K, ITRAQ-4Plex of Ntermini.param-text “Maximum Precursor Isotope” : 1.param-text “Minimum Precursor Isotope” : 0.param-text “Fragment Tolerance (Daltons)”: 0.05 (this is high resolution MS/MS data).param-text “Precursor Ion Tolerance”: 10.param-select “Precursor Ion Tolerance Units”: Parts per million (ppm).param-text “Maximum Missed Cleavages”: 2.For the purpose of this tutorial, X!Tandem we will be Any combination of these programs can be used for Programs that are available in SearchGUI. Please contact the developers.Īt (GraphicsEnvironment.java:207)Īt $SharedOwnerFrame.(SwingUtilities.java:1758)Īt (SwingUtilities.java:1833)Īt (JOptionPane.java:1696)Īt (JOptionPane.java:863)Īt (JOptionPane.java:666)Īt (JOptionPane.java:637)Īt eu.createInputFile(TandemProcessBuilder.java:334)Īt (Thread.The section Search Engine Options contains a selection of sequence database searching Mon Feb 02 07:00: An error occurred while running SearchGUI. No X11 DISPLAY variable was set, but this program performed an operation which requires it. share/isilon/system/local/RESEARCH.LOCAL/proteins/SearchGUI-1.24.0/resources/XTandem/linux_64bit/input_searchGUI.xmlĪt eu.createInputFile(TandemProcessBuilder.java:321)Īt eu.(TandemProcessBuilder.java:280)Īt eu.$SearchWorker.doInBackground(SearchHandler.java:1975) share/isilon/system/local/RESEARCH.LOCAL/proteins/SearchGUI-1.24.0/resources/conf/searchGUI_usermods.xmlĪt java.io.FileOutputStream.open(Native Method)Īt java.io.FileOutputStream.(FileOutputStream.java:213)Īt java.io.FileOutputStream.(FileOutputStream.java:162)Īt java.io.FileWriter.(FileWriter.java:90)Īt .(PTMFactory.java:579)Īt eu.(SearchHandler.java:513)Īt eu.$SearchWorker.doInBackground(SearchHandler.java:1904)Īt $1.call(SwingWorker.java:295)Īt .run(FutureTask.java:266)Īt (SwingWorker.java:334)Īt .runWorker(ThreadPoolExecutor.java:1142)Īt $n(ThreadPoolExecutor.java:617) in MOUSEuniprot.canisoform.12.2014.fasta -dbtype prot ![]() share/isilon/system/local/RESEARCH.LOCAL/proteins/SearchGUI-1.24.0/resources/makeblastdb/linux/linux_64bit/makeblastdb So this way one doesn’t have to deal with IdentificationParametersCLI when the Fasta DB location adjustment is required (on the Parameter file created in GUI view …) SearchGUI.xx.jar eu., basically the same “-db “ switch that I dentificationParametersCLI call has. Time consuming, typing error prone … So wanted to ask you if it isĮasy for you to enable a switch for DB path when calling That solved this but generating Parameter file like this is i more Main Parameter file ( which is not easy to change) Then i noticed that the path to FASTA database file is written in the This parameter file i would use on the linux cluster/ grid. I first aimed to make Parameters file in local linux GUI, and then Maybe i n your tutorial /installation info you could add some installation tips for optimal setup (namely when tools are used on servers, multi users. There are couple of ways to solve this but what do you advise ? So since I'm not member of the root elite i can not write here. rwxrwxr-x 1 root root 6343 Jan 10 01:30 LICENSE.txt Ls -l /share/isilon/system/local/RESEARCH.LOCAL/proteins/SearchGUI-1.24.0/resources/XTandem/linux_64bit/ XTandem/linux_64bit/input_searchGUI.xml (Permission denied). Java HotSpot(TM) 64-Bit Server VM (build 25.31-b07, mixed mode)Ģ) log says …. Java(TM) SE Runtime Environment (build 1.8.0_31-b13) Linux Cluster has java version "1.8.0_31" Log is below and i see different advices on the web forums for it. No X11 DISPLAY variable was set, but this program performed an operation which requires it.” I hope you have advice for the 3 issues i got when running CLI for searchGUI :ġ)error “ Please contact the developers. Last summer I mentioned I'll be testing it on the Local cluster Grid (many servers). Congratulations on the recent article and thank you for the consistent work on these tool.Īfter long time new data is heading our way and I'm back looking into your tools. ![]()
0 Comments
Read More
Leave a Reply. |