We were trying to use MASCOT on CPAS, all the required information, i.e. Mascot server, user name and password were entered correctly, and then we tested using the given test option in CPAS. CPAS did not gave any error. I went to pipeline and setup a directory of data. I clicked on Process and Upload Data. That gave me a button to do "Mascot Peptide Search." I clicked on that. That took me to a "Search MS2 Data page". I entered the protocols specification, the search engine field said "Mascot" and the Sequence Databases said the name of the databases on the Mascot server. I selected "NCBInr" which is the NR database on the mascot server. The mascot XML field was left with the default parameters. I pressed search and following error was given:
That gives me an error:"Sequence database 'NCBInr' is not found in local FASTA root."
How can i fix this error, CPAS should not be looking for local FASTA file.
For the sake of it, i downloaded FASTA file on my local driver. I set the path for the FASTA root, when i reached to "Search MS2 Data page", i entered the required information but i was not able to see the local FASTA File, i am not able to run MASCOT. All the database options that are shown reside on the remote server.
I am using MASCOT version 2.1.
Please help.
Following error was shown
21 Feb 2007 16:41:55,717 INFO : Mascot search for 7MIX_STD_110802_1.mzXML
21 Feb 2007 16:41:55,717 INFO : =======================================
21 Feb 2007 16:41:55,785 INFO : MzXML2Search output
21 Feb 2007 16:41:55,785 INFO : =======================================
21 Feb 2007 16:41:55,938 INFO : running: MzXML2Search -mgf 7MIX_STD_110802_1.mzXML
21 Feb 2007 16:41:55,966 INFO :
21 Feb 2007 16:41:55,967 INFO : MzXML2Search - Mascot Generic Format
21 Feb 2007 16:41:55,967 INFO :
21 Feb 2007 16:41:55,967 INFO : Reading 7MIX_STD_110802_1.mzXML
21 Feb 2007 16:41:55,967 INFO : Getting the index offset
21 Feb 2007 16:41:55,967 INFO : Reading the index
21 Feb 2007 16:41:56,751 INFO : scan: 1 000% 2 000% 3 000% 4 000% 5 000% 6 000% 7 000% 8 000% 9 000% 10 000% 11 000% 12 000% 13 000% 14 000% 15 000% 16 000% 17 000% 18 000% 19 000% 20 000% 21 000% 22 000% 23 000% 24 000% 25 000% 26 000% 27 000% 28 000% 29 000% 30 000% 31 000% 32 000% 33 000% 34 000% 35 000% 36 000% 37 000% 38 000% 39 000% 40 000% 41 000% 42 000% 43 000% 44 000% 45 000% 46 000% 47 000% 48 000% 49 000% 50 000% 51 000% 52 000% 53 000% 54 000% 55 000% 56 000% 57 000% 58 000% 59 000% 60 000% 61 000% 62 000% 63 000% 64 000% 65 000% 66 000% 67 000% 68 000% 69 000% 70 000% 71 000% 72 001% 73 001% 74 . .
. . .
099% 7126 099% 7127 099% 7128 099% 7129 099% 7130 099% 7131 099% 7132 099% 7133 099% 7134 099% 7135 099% 7136 099% 7137 099% 7138 099% 7139 099% 7140 099% 7141 099% 7142 099% 7143 099% 7144 099% 7145 099% 7146 099% 7147 099% 7148 099% 7149 099% 7150 099% 7151 099% 7152 099% 7153 099% 7154 099% 7155 099% 7156 099% 7157 099% 7158 099% 7159 099% 7160 099% 7161 100%
21 Feb 2007 16:41:56,756 INFO : Done.
21 Feb 2007 16:41:56,756 INFO :
21 Feb 2007 16:41:56,756 INFO : mascot client output
21 Feb 2007 16:41:56,756 INFO : =======================================
21 Feb 2007 16:41:56,757 INFO : Creating Mascot session...
21 Feb 2007 16:41:57,056 INFO : Creating Mascot search task...
21 Feb 2007 16:41:57,273 INFO : Submitting search to Mascot server...
21 Feb 2007 16:42:09,386 INFO : Mascot search task status: query upload completed
21 Feb 2007 16:42:39,657 INFO : Mascot search task status error: (26)
21 Feb 2007 16:42:39,657 INFO : Mascot search status: error=26

21 Feb 2007 16:42:39,898 INFO : Mascot session ended.
21 Feb 2007 16:42:39,918 ERROR: Failed running Mascot.