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Mascot 2.1.002 error code list


Mascot is a product from matrixscience.

M00001

(Message number no longer used)

Further help:

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M00002

Accessing outside array: x = [number]

Further help:

Internal program error. Please report this error to Matrix Science, with the data set that caused the error.

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M00003

Error - range less than 0 ([number]) in MAKE_ARRAY.MIN=[number],MAX=[number]

Further help:

Internal program error. Please report this error to Matrix Science, with the data set that caused the error.

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M00004

Could not compile pattern [text]

Further help:

Internal error with the sequence query specified. This message should never be displayed because 'syntax' errors in the user's queries are checked before they are compiled into regular expressions. See the user help text for details of allowed sequence queries and please report this error to Matrix Science, with the data set that caused the error.

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M00005

Error in sequence query - [text]

Further help:

Internal error with the sequence query specified. This message should never be displayed because 'syntax' errors in the user's queries are checked before they are compiled into regular expressions. See the user help text for details of allowed sequence queries and please report this error to Matrix Science, with the data set that caused the error.

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M00006

Error in sequence query - [text]

Further help:

Internal error with the sequence query specified. This message should never be displayed because 'syntax' errors in the user's queries are checked before they are compiled into regular expressions. See the user help text for details of allowed sequence queries and please report this error to Matrix Science, with the data set that caused the error.

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M00007

Too many sequence queries - requested [number requested], max allowed: [number allowed]

Further help:

Reduce the number of seq and comp entries in the search to [number allowed]

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M00008

Value on line [line number] of input file is not an ION intensity: [text entered - should be a number]

Further help:

The wrong file type may have been specified, or there is an error in the formatting of the file. Check the help text for allowed file formats.

Actions:

M00009

Sorry, too many combinations ([number]) - max allowed is [number]

Further help:

The search is too complex - try reducing the number of iterated modifications, or number of peptides specified.

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M00010

(Message number no longer used)

Further help:

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M00011

(Message number no longer used)

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M00012

Can't open [filename] for "[reading/writing]". Error [error message]

Further help:

Check to see if the file specified has been removed, or access to it has been denied.

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M00013

Can't open results file: [filenmame] for "[reading/writing]"

Further help:

The results file (where the search results are stored) cannot be accessed. Check to see if the file specified has been removed, or access to it has been denied.

Actions:

M00014

This script should be referenced with a METHOD of POST.

Further help:

It is only possible to run the cgi script using the POST command. The GET command is not currently supported.

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M00015

(Message number no longer used)

Further help:

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M00016

(Message number no longer used)

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M00017

Sorry, Mascot is not compatible with your browser

Further help:

Mascot will not work with some older browsers. See the 'Browser compatibility' help page. The actuall error is caused by the CONTENT_TYPE environment variable being set to "application/x-www-form-urlencoded"

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M00018

(Message number no longer used)

Further help:

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M00019

(Message number no longer used)

Further help:

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M00020

Sorry, cannot find peptide peak in line [line number] of input file

Further help:

Mascot is looking for a peptide mass, but cannot find it. Possible causes are that the wrong file type has been specified, that the file is corrupt or that the file does not conform to the standards specified in the online user help text.

Actions:

M00021

Invalid units ([units specified]) specified for the "[parameter - e.g. TOL]" parameter

Further help:

This message should not be displayed when using the supplied forms. See the user help text, or the supplied forms, for details of which units (e.g. %, ppm) are allowed for which parameters

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M00022

(Message number no longer used)

Further help:

(Message number no longer used)

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M00023

You specified enzyme [enzyme name] which is not available or no enzyme at all. Choose another.

Further help:

The enzymes that are allowed are specified in the 'enzymes' file. See the section on 'Configuration Files' for details of how to add new cleavage rules to Mascot. If no-enzyme search is desired, please specify 'None'.

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M00024

(Message number no longer used)

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M00025

Internal error in - set to [string]

Further help:

The 'TWO' parameter is no longer used. This must be a very old form or old data set

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M00026

You have not entered any mass data, or the data file does not exist

Further help:

The 'QUE' field is empty, or does not contain any masses. Alternatively, a filename was specified in the file upload box that is empty, or does not exist

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M00027

Sorry, the database ([database name]) is not currently available for searching

Further help:

Only databases listed in mascot.dat can be searched. It is possible that there was an error when the database was 'coming on line'. To check this and to see the status of all databases, look at the status screen (there's a link to it from the home page on the intranet versions). To add a new database, see the 'Sequence Database Setup' chapter.

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M00028

There's an error in your query: Expected a mass value, found [text in query]

Further help:

The search query does not conform to the standards specified in the help text. The first item on any line should be the peptide mass. Check the online help text for details of the allowed formats.

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M00029

There's an error in your SEQ() query - no sequence information!

Further help:

A sequence query, such as just seq() has been entered. Some residues must be added. See the user help text for details

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M00030

Error at line [line number] in your IONS() query. Mass value expected, found [text]

Further help:

There is a problem with the MS-MS data supplied. Possible causes are that the wrong file type has been specified, that the file is corrupt or that the file does not conform to the standards specified in the online user help text.

Actions:

M00031

Max number of ions is [number]. Ignoring ms-ms set starting at line [line number]

Further help:

A very large number of ion masses have been supplied. Try changing the peak detection thresholds in the data acquisition software. Also, check that you are not saving profile data

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M00032

Modification conflict: Both [modification 1] and [modification 2] modify N terminus values. Try setting both as variable modifications

Further help:

If you are not sure which modification to choose, try specifying these modifications as variable rather than fixed modifications.

Actions:

M00033

Modification conflict: Both [modification 1] and [modification 2] modify C terminus values. Try setting both as variable modifications

Further help:

If you are not sure which modification to choose, try specifying these modifications as variable rather than fixed modifications.

Actions:

M00034

Modification conflict: Both [modification 1] and [modification 2] modify the same residue. Try setting both as variable modifications

Further help:

If you are not sure which modification to choose, try specifying these modifications as variable rather than fixed modifications.

Actions:

M00035

There is an error in the modification file: [line with error]

Further help:

Check the allowed format of the mod_file specified in the 'configuration and log files' chapter in the Mascot installation and setup manual

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M00036

(Message number no longer used)

Further help:

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M00037

Error in mascot.dat - database [database name] doesn't have enough parameters

Further help:

Error in mascot.dat - database [database name] doesn't have enough parameters. The chapter 'Sequence Database Setup' has details of each parameter required in the database section.

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M00038

Debug string:[text]

Further help:

Message number used for internal validation by Matrix Science

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M00039

Failed to close file [file name]

Further help:

The file specified failed to close. There is normally no reason for this message to bedisplayed - please inform Matrix Science

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M00040

Invalid ions series ([name of ions series]) value of [value specified] - using default.

Further help:

User choice of ions series is no longer an option. In earlier versions of Mascot, the only allowed values are '1' and '0'

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M00041

Cannot start new database - no test .asc file: '[file name]'

Further help:

Each new database must be tested before being memory mapped. Edit and copy one of the test files in the ../data/test/ directory. See the chapter 'Sequence Database Setup' for more details. Once the file has been supplied, ms-monitor will carry on with the setup and test automatically.Note that from version 1.5 onwards, these files are created automatically

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M00042

Cannot spawn '[program name]' - error code '[detailed error message]'

Further help:

ms-monitor runs nph-mascot.exe for a test search, and sendmail for mailing results and error message. This should never fail unless a file has been removed. If required, contact Matrix Science for further help.

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M00043

Unique ID in the control file is too high

Further help:

(Message number used internally by Matrix Science)

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M00044

Max number of blocks per database is [number] - more were specified for database [name] in mascot.dat file.

Further help:

A maximum of 100 blocks (and threads) can be specified for databases. See the chapter 'Sequence Database Setup' for more details.

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M00045

Num threads for database [name] in config file wrong. Reset to 1

Further help:

The number of threads must be a factor of the number of blocks. See the chapter 'Sequence Database Setup' for more details.

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M00046

Monitor program failed to write to file '[file name]'

Further help:

This is not a fatal error - the file may have been set to read only. Check the file permissions for the specified file

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M00047

Failed to open memory mapped file [file name]. Error: [detailed message]

Further help:

Either the file specified has been removed, there are insufficient access rights to the file or there is insufficient memory in the system to memory map the file. Under Windows NT, this may be caused by the wrong values being present for the NTIUserGroup in the Options section of Mascot.dat. See Chapter 6 for more details.

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M00048

Failed to create memory map for [filename]. Error [detailed message]

Further help:

If there is insufficient memory, try setting the file to be not memory mapped in the mascot.dat file.

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M00049

Failed to create memory map ** for [filename]. Error [detailed message]

Further help:

If there is insufficient memory, try setting the file to be not memory mapped in the mascot.dat file.

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M00050

Failed to map memory handle to a pointer for [filename]. Error [detailed message]

Further help:

This error should never occur - indicates a serious problem. Please contact Matrix Science for further help.

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M00051

Too many searches being run at once

Further help:

There is a limit of 100 simultaneous searches per database. There is also an optional limit in the mascot.dat configuration file to restrict the number of concurrent searches on all databases. The default value for MaxConcurrentSearches is 10. Either increase the value of MaxConcurrentSearches in mascot.dat or wait until some searches have finished before trying to submit more searches.

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M00052

Warning - failed to find old job to delete from list

Further help:

This is not a fatal error message - however, if this occurs often, please contact Matrix Science for further help.

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M00053

Error unmapping file [filename]: ([detailed error message])

Further help:

This should never happen, but does not normally indicate a serious problem.

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M00054

Couldn't get search details from your browser. ([number of bytes read from browser] - [lengthOfData expected])

Further help:

The user pressed cancel in their browser while it was uploading the search details. More specifically, the number of bytes that should have been sent (specified by the environment variable 'CONTENT_LENGTH') could not be read from stdin.

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M00055

No boundary= in CONTENT_TYPE ([actual text])

Further help:

The CONTENT_TYPE environment variable should have a 'boundary=xxx' statement in it. This was missing. This error appears to occur for some interim versions of Internet Explorer 5.01. We recommend that you upgrade the browser

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M00056

First line of input not boundary ([input line]) env=([string])

Further help:

The file uploaded by the browser to the mascot search engine does not have a MIME boundary line.Error often caused when trying to create an automation engine.

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M00057

Expecting a name= in line ([text])

Further help:

Expecting text of the format: -----------------------------16838575810113 Content-Disposition: form-data; name="DB" MSDB with a name statement

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M00058

(Message number no longer used)

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M00059

Too many parameters of form NAME=VAL specified. Ignoring [parameter]

Further help:

The search must be repeating some of the parameters - remove the duplicate parameters.

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M00060

Line too long in query - max length allowed is [number]

Further help:

The line is too long, make it shorter - for example by reducing the number of decimal places in mass values.

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M00061

Invalid value ([text]) specified for the "[text]" parameter

Further help:

See the online help for allowed values for the specified parameter

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M00062

Using the TWO value in a form is rather old-fashioned...

Further help:

This parameter has been replaced by CHARGE

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M00063

Unknown sequence command in line: [text entered]

Further help:

Not a valid sequence command. See the online help for allowed sequence commands

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M00064

You have entered an unknown IONS() flag: ([text entered])

Further help:

Not a valid ions() command. See the online help for allowed ions() commands

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M00065

Failed to open the MAPI DLL

Further help:

Microsoft Windows NT only - failed to open the MAPI Dynamic Link Library. MAPI is probably needs to be installed on this computer.

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M00066

Failed to log into MAPI - error code ([number])

Further help:

Failed to log into MAPI. Error codes:
MAPI_E_FAILURE (2)
- One or more unspecified errors occurred during logon. No session handle was returned.
MAPI_E_INSUFFICIENT_MEMORY (5)
- There was insufficient memory to proceed. No session handle was returned.
MAPI_E_LOGIN_FAILURE (3)
- There was no default logon, and the user failed to log on successfully when the logon dialog box was displayed. No session handle was returned.
MAPI_E_TOO_MANY_SESSIONS (8)
- The user had too many sessions open simultaneously. No session handle was returned.
MAPI_E_USER_ABORT (1)
- The user canceled the logon dialog box. No session handle was returned.

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M00067

Failed to send MAPI message - error code ([number])

Further help:

Failed to send MAPI message. Error Codes:
MAPI_E_AMBIGUOUS_RECIPIENT (21)
- A recipient matched more than one of the recipient descriptor structures and MAPI_DIALOG was not set.
MAPI_E_ATTACHMENT_NOT_FOUND (11)
- The specified attachment was not found.
MAPI_E_ATTACHMENT_OPEN_FAILURE (12)
- The specified attachment could not be opened.
MAPI_E_BAD_RECIPTYPE (15)
- The type of a recipient was not MAPI_TO, MAPI_CC, or MAPI_BCC.
MAPI_E_FAILURE (2)
- One or more unspecified errors occurred.
MAPI_E_INSUFFICIENT_MEMORY (5)
- There was insufficient memory to proceed.
MAPI_E_INVALID_RECIPS (25)
- One or more recipients were invalid or did not resolve to any address.
MAPI_E_LOGIN_FAILURE (3)
- There was no default logon, and the user failed to log on successfully when the logon dialog box was displayed.
MAPI_E_TEXT_TOO_LARGE (18)
- The text in the message was too large.
MAPI_E_TOO_MANY_FILES (9)
- There were too many file attachments.
MAPI_E_TOO_MANY_RECIPIENTS (10)
- There were too many recipients.
MAPI_E_UNKNOWN_RECIPIENT (14)
- A recipient did not appear in the address list.
MAPI_E_USER_ABORT (1)
- The user canceled one of the dialog boxes.

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M00068

Failed to open the MAPI DLL for CMC

Further help:

The Microsoft implementation of CMC is built upon their MAPI implementation, and the MAPI Dynamic Link Library needs to be installed.

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M00069

Failed to log into CMC - error code ([number])

Further help:

Invalid service name or password supplied in the mascot.dat file.

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M00070

Failed to send CMC message - error code ([number])

Further help:

See Microsoft MAPI / CMC documentation for details.

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M00071

Failed to make control file ([file name]) shareable

Further help:

The control file needs to be shared by nph-mascot and ms-monitor. Access rights may not be set up correctly.

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M00072

Corrupted input or incompatible browser

Further help:

The file being uploaded might be a unicode, binary or corrupted file, or your web-browser is incompatible.

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M00073

Failed to lock memory for file [file name]. Error [detailed text]

Further help:

There may be insufficient memory, or insufficient privileges for ms-monitor to lock the memory. If the problem is insufficient memory, try setting the database to be memory mapped but not locked.

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M00074

Locked memory for file [file name]

Further help:

Not an error message - just a comment put into monitor.log

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M00075

Failed to write lastquery.asc file: [file name]

Further help:

Mostly caused by incorrect access rights to the file. Set the file to be writeable by the tasks running nph-mascot.exe from the web server. (typically 'nobody' on Unix systems)

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M00076

Problem with re-searching an old query QUERY([number])

Further help:

Doing a 're-search' of an existing search, the ions masses from an ms-ms data set are loaded from the intermediate file. These masses could not be obtained from the file for some reason. Check the query number in the intermediate file.

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M00077

(Message number no longer used)

Further help:

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M00078

In ref file, expected '[accession number]' to match with '[accession number]' in fasta file

Further help:

The .ref file and the .fasta file are not synchronised or are from different databases. Also, check the parsing rules. See the chapter 'Sequence Database Setup' for more details.

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M00079

-----------------------------------ms-monitor started

Further help:

Not an error message - text put into monitor.log along with the date and time to shown when ms-monitor was started.

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M00080

-----------------------------------ms-monitor stopped

Further help:

Not an error message - text put into monitor.log along with the date and time to shown when ms-monitor was stopped.

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M00081

[database name][sub cluster]-8s[0 or 1] ['state'] to ['state']

Further help:

Not an error message - text put into monitor.log along with the date and time to shown when, for example, a database file was tested.

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M00082

Creating compressed files from [database fasta file]

Further help:

Not an error message - text put into monitor.log to show that compressed files are being created from a database file.

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M00083

Creating compress file [file name]

Further help:

Not an error message - text put into monitor.log to show that a particular compressed files is being created from a database file.

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M00084

Trying to run a test on new database ([database number]), but both are current

Further help:

Should never happen. Please contact Matrix Science.

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M00085

Invalid command line number ([number])

Further help:

Valid command line numbers for nph-mascot are 1,2,3 or 4. See the 'Program Reference' section for details.

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M00086

Problem with intermediate file name handling

Further help:

Error message for Matrix Science public web site only.

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M00087

Running system command: [command string]

Further help:

Not an error message - text put into monitor.log to show that a particular process is being run - for example nph-mascot.exe is run to perform a test search.

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M00088

Invalid command/mass at line [line number] of your query. Line is [text entered]

Further help:

The query does not conform to the required format. The first item on the line should be a mass value. See the online user help for details.

Actions:

M00089

Invalid FORMAT parameter passed from the form ([passed format])

Further help:

The only valid formats are 'Mascot generic', 'Sequest (.DTA)', 'Finnigan (.ASC)', 'Micromass (.PKL), PerSeptive (.PKS), PerSeptive (.PKM), Sciex API III, Bruker reportfile, Bruker (.XML) and mzData (.XML)

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M00090

Invalid SEARCH parameter passed from the form ([parameter])

Further help:

The only valid search parameters are: 'PMF', 'SQ' and 'MIS'

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M00091

BEGIN IONS statement with missing PEPMASS= at line [line number]

Further help:

Every BEGIN IONS in a Mascot File format file must have a corresponding PEPMASS= line. See the online user help for more details.

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M00092

Incorrect .pkl format. Expected 'mass intensity charge' at line [line number]

Further help:

See the online user help for more details of the Micromass PKL file format.

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M00093

Ignoring MS-MS data with parent charge greater than > 8 at line [line number]

Further help:

Currently, Mascot only supports ms-ms data with a charge state of 1, 2, 3, 4, 5, 6, 7 or 8. This data set is ignored, but the search carries on with other data sets. If there are no other data sets, the search is not performed.

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M00094

Using default charge state for MS-MS data set with unknown parent charge state at line [line number]

Further help:

Currently, Mascot only supports ms-ms data with a charge state of 1, 2, 3, 4, 5, 6, 7 or 8 - a number such as -1 has probably been supplied by the mass spectrometer data acquisition software.

Actions:

M00095



Warning: The search page has been updated. Press

Further help:

The formVersion value in the form is not the same as the value in the Mascot.dat file. See the configuration and log file chapter of the Mascot installation and setup manual.

Actions:

M00096

the back button, and force a re-load (refresh) of the page. You may

Further help:

The formVersion value in the form is not the same as the value in the Mascot.dat file. See the configuration and log file chapter of the Mascot installation and setup manual.

Actions:

M00097

have to clear the browser cache or close and re-start the browser

Further help:

The formVersion value in the form is not the same as the value in the Mascot.dat file. See the configuration and log file chapter of the Mascot installation and setup manual.

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M00098

Found '[text entered]' when expecting a number or * in comp() at line [line number] of query: [text entered]

Further help:

The format of the comp() command is incorrect. See the online user help for more details.

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M00099

Missing ')' in comp() at line [line number] of your query: [text entered]

Further help:

The format of the comp() command is incorrect. See the online user help for more details. Each opening bracket must be matched by a closing bracket

Actions:

M00100

Expected a space after ')' at line [line number] of your query: [text entered]

Further help:

The format of the comp() command is incorrect. See the online user help for more details.The commands must be separated by a space

Actions:

M00101

Missing ')' in seq() at line [line number] of your query: [text entered]

Further help:

The format of the seq() command is incorrect. See the online user help for more details.There is probably just a missing closing bracket

Actions:

M00102

Invalid letter before '-' in seq() at line [line number] of your query: [text entered]

Further help:

The format of the seq() command is incorrect. See the online user help for more details.Valid prefixes are 'b-', 'n-', 'y-', 'c-' and '*'

Actions:

M00103

Monitor test search on database [database name] timed out

Further help:

The cause must be investigated. It is possible that the time out specified in mascot.dat is too short. Check the errorlog to see if nph-mascot reported an error. Check to see if the test search is still running. The timeout value in mascot.dat is 'MonitorTestTimeout' in the 'Options' section

Actions:

M00104

This NA sequence is too long - ignoring: [part of sequence]

Further help:

Check that the sequence in the NA file is a valid sequence - there is possibly some corruption in the file, or the database has not been set up correctly in mascot.dat

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M00105

NA sequence 0 residues long found

Further help:

There is a sequence with no residues in the database file.

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M00106

(Message number no longer used)

Further help:

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M00107

Invalid sequence characters in entry for [accession number]. Database path: [database path]

Further help:

Illegal characters in sequence database. Only the first 5 errors are reported. The illegal characters are replaced by X.

Actions:

M00108

Could not initialise thread attributes: [type of attribute]. Error: [error message]

Further help:

Unix only. Under Irix, this can be caused by not setting the 'capabilities' for the executable programs so that they can use system scope (PTHREAD_SCOPE_SYSTEM). This can be corrected by running the command 'chcap CAP_SCHED_MGT+ep *.exe' in the mascot/cgi and mascot/x-cgi directories. You have to be logged in as root for this to work. You can see the capabilites set for a file by using the command 'ls -lP'. If the error still occurs after setting the capabilities, or for any platform other than Irix, please contact Matrix Science for futher help

Actions:

M00109

Could not set stack size for thread

Further help:

Digital Alpha Unix only. Please contact Matrix Science

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M00110

Missing mascot.dat file - cannot continue

Further help:

The file mascot.dat must be present for ms-monitor to run and any searches to run. The file should be in the ../config directory.

Actions:

M00111

Too many peptide masses in your data file. Mascot has a limit of [number] but this system has been configured to have a limit of [number]

Further help:

There is a limit to the number of peptide masses allowed. Are you entering ms-ms data into a pmf form? The maximum number of queries is set by adding a value 'MaxQueries' into the options section of the mascot.dat file. If no value is specified, then the default of 100,000 is used. On the Matrix Science public web site, the limit is 300

Actions:

M00112

Missing END IONS statment at line [line number] of your mascot generic file

Further help:

Each BEGIN IONS must be matched with an END IONS in a mascot generic file.

Actions:

M00113

Error calling getrlimit(RLIMIT_RSS) - error [detailed error message]

Further help:

In order to lock memory, on UNIX systems, the resource limit for memory locking may have to be increased. The user who is running ms-monitor does not have the access rights to call this command, or there is insufficient memory.

Actions:

M00114

Error calling setrlimit(RLIMIT_RSS, [memory requested]) - error [detailed error message]

Further help:

In order to lock memory, on UNIX systems, the resource limit for memory locking may have to be increased. The user who is running ms-monitor does not have the access rights to call this command, or there is insufficient memory.

Actions:

M00115

(Message number no longer used)

Further help:

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M00116

MS/MS tolerance of [value][units] is too large for [number] ion series

Further help:

You need to specify a lower tolerance in order to get a signifcant match.

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M00117

Missing license file: [file name]. Cannot continue

Further help:

A valid licence is required to run mascot. Please contact Matrix Science

Actions:

M00118

Damaged or corrupt mascot license file (checksum 'd')

Further help:

A valid licence is required to run mascot. Please contact Matrix Science

Actions:

M00119

Damaged or corrupt mascot license file (checksum 'l')

Further help:

A valid licence is required to run mascot. Please contact Matrix Science

Actions:

M00120

Your demo license for Mascot expired on [date]. Please contact Matrix Science for a full license

Further help:

A valid licence is required to run mascot. Please contact Matrix Science

Actions:

M00121

Your demo license becomes available on [date]. Please wait until this date or contact Matrix Science

Further help:

A valid licence is required to run mascot. Please contact Matrix Science

Actions:

M00122

Invalid parsing rule syntax in mascot.dat. Expecting RULE_, found [text]

Further help:

Each line in this section of mascot.dat should start with 'RULE_'. See the chapter 'Sequence Database Setup' and the Appendix 'Basic Regular Expressions' for further details.

Actions:

M00123

Parsing rules must have numbers between 1 and [number]: Rule invalid: [text in mascot.dat]

Further help:

Change the number in the PARSE section of mascot.dat to a valid number.

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M00124

Parsing rule [number] in mascot has been defined twice: Second one is: [text in mascot.dat]

Further help:

Each parsing rule must have a unique number.

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M00125

Missing quote in parse rule in mascot.dat: [text in mascot.dat]

Further help:

Parsing rules in the PARSE section of mascot.dat must have quotes () around them. See the chapter 'Sequence Database Setup' and the Appendix 'Basic Regular Expressions' for further details.

Actions:

M00126

Maximimum length of parse string ([limit]) exceeded with: [text in mascot.dat]

Further help:

The parsing rule is too long - try and make it shorter. See the chapter 'Sequence Database Setup' and the Appendix 'Basic Regular Expressions' for further details.

Actions:

M00127

Error compiling the parse rule: [text entered]. Error string: [error message from compiling regular expression]

Further help:

The regular expression does not follow the rules specified in the Appendix 'Basic Regular Expressions'. Also, see the chapter 'Sequence Database Setup' and the for further details.

Actions:

M00128

Only one sub-expression per parse rule allowed. Found [number] in [text entered in mascot.dat]

Further help:

There should only be one 'result' from the regular expression - i.e. only one set of \(... \). See the chapter 'Sequence Database Setup' and the Appendix 'Basic Regular Expressions' for further details.

Actions:

M00129

Could not find description / accession number in [line from fasta database] using rule: [rule in mascot.dat]

Further help:

The regular expression that has been specified in mascot.dat cannot get the description line and accession number from the line shown in the fasta database. See the chapter 'Sequence Database Setup' and the Appendix 'Basic Regular Expressions' for further details.

Actions:

M00130

Warning - accession [[accession]] is too long. Maximal allowed accession length if [number] characters

Further help:

Possibly, you have a malformed fasta file or wrong accession parse rules. Be careful when selecting a parse rule or creating a new one for your fasta database. If you are configuring your custom in-house database try to avoid too long identifiers for the sequences as mascot search engine cannot process them.

Actions:

M00131

In mascot.dat, the database [name] has no [accession / description] rule

Further help:

In the databases section of mascot.dat, a rule number is specified for extracting the description and accession number. There must be a corresponding rule in the PARSE section of mascot.dat, but in this case, that rule is missing

Actions:

M00132

In mascot.dat, the unique ID for database [name] is out of range

Further help:

Choose a smaller, unique number for the database ID

Actions:

M00133

Peptide mass of [entered mass] is too small. The minimum mass allowed is [mass in daltons] . (Or incorrect data format)

Further help:

Only enter masses larger than minimum allowed mass. It is also possible that the data format is wrong - for example you could be entering ms-ms data as PMF, and the ions would then be interpreted as peptides. If the data is in .dta or .pkl format, then there may be unintentional extra blank lines causing each ions value to be recognised as a peptide mass.

Actions:

M00134

Peptide mass of [entered mass] is too big. The maximum mass allowed is [mass in daltons] . (Or incorrect data format)

Further help:

Only enter masses smaller than maximum allowed mass. It is also possible that the data format is wrong - for example you could be entering ms-ms data as PMF, and the ions would then be interpreted as peptides. If the data is in .dta or .pkl format, then there may be unintentional extra blank lines causing each ions value to be recognised as a peptide mass.

Actions:

M00135

Sorry, the modification '[name]' is not available

Further help:

Allowed modifications are specified in config/mod_file - see the chapter 'Configuration and Log Files' for more details.

Actions:

M00136

Too many modifications specified in search. Limit is [number]

Further help:

The number of fixed modifications has been exceeded - choose a lower number of fixed modifications

Actions:

M00137

Too many modifications specified in mod file. Limit is [number]

Further help:

Remove some unwanted modifications from the mod_file in the mascot/config directory. If this limit is a real issue, please contact Matrix Science to have it increased.

Actions:

M00138

Too many variable modifications specified. Limit is [number]

Further help:

For a peptide mass fingerprint, it is rarely sensible to have more than 2 or 3 variable modifications. For MS/MS searches, a very large number of variable modifications can make search times very long. Reduce the number of variable modifications specified

Actions:

M00139

Sorry, a comma (,) is not allowed in a modification name ([modification name])

Further help:

Change the name in 'mod_file' to not include a comma.

Actions:

M00140

(Message number no longer used)

Further help:

Actions:

M00141

Modification [name] in the mod_file contains both residues and terminus

Further help:

Make two modifications - one for the terminus modification, and one for the residue modification(s)

Actions:

M00142

Cannot use [[name]] database - Full text file (.dat or .ref) is missing

Further help:

In mascot.dat, it is specified that there should be a .ref (or .data) file - supply this file, or change mascot.dat.

Actions:

M00143

Error setting/getting security rights for file/memory. Error [number] in [function name]

Further help:

NT Version 4.0 - is service pack 3 or later installed? If it is, then please contact Matrix Science for help.

Actions:

M00144

Failed to get working set size when mapping [file name]. Error: [description]

Further help:

The program does not have access rights to this information - change the access rights of the program that caused the error.

Actions:

M00145

Failed to set working set size when mapping [file name]. Error: [desciption]

Further help:

There may be insufficient memory to map and/or lock this data set. Either add more memory to the computer, or try specifying that it should be mapped, but not locked.

Actions:

M00146

Failed to find information about number of processors available

Further help:

Please report this problem to Matrix Science

Actions:

M00147

Failed to set number of processors to be used. Error: [description]

Further help:

Please report this problem to Matrix Science

Actions:

M00148

ProcessorSet= in mascot.dat specifies unavailable processor - [processor number]

Further help:

The processor specified is not available to the current process. See your system administrator, or specify another processor.

Actions:

M00149

>= [number] processors are named in mascot.dat. Licensed for [number] and [number] available

Further help:

Reduce the number of processors specified in the processors section of mascot.dat

Actions:

M00150

Invalid line starting with ([text in mascot.dat]) in mascot.dat

Further help:

Refer to the documentation about the Processors section of mascot.dat in the 'Configuation & Log Files chapter of the installation and setup manual

Actions:

M00151

Processor [number] specified for database [name] is not in ProcessorSet=

Further help:

Any processor listed for a particular database must also be in the ProcessorSet= line.

Actions:

M00152

There are [number] threads for database '[name]'. Too many processors named

Further help:

The number of threads must match the number of processors for a particular database.

Actions:

M00153

Failed call to sysmp() for multi-processor support. Error: [error message returned by operating system]

Further help:

Refer to your operating system documentation for further information

Actions:

M00154

Too many cron jobs in mascot.dat. The limit is [number]

Further help:

Windows NT Only. There is a limit to the number of 'cron' jobs allowed in mascot.dat - reduce the number to this value.

Actions:

M00155

Invalid * in cron section of mascot.dat. Line is: [text in mascot.dat]

Further help:

Refer to the 'cron' section in chapter 6 of the Mascot Installation and Setup manual for correct syntax.

Actions:

M00156

Invalid character in cron section of mascot.dat. Line is: [text in mascot.dat]

Further help:

Refer to the 'cron' section in chapter 6 of the Mascot Installation and Setup manual for correct syntax.

Actions:

M00157

Expecting number before - in cron section of mascot.dat. Line is: [text in mascot.dat]

Further help:

Refer to the 'cron' section in chapter 6 of the Mascot Installation and Setup manual for correct syntax.

Actions:

M00158

Expecting number before , in cron section of mascot.dat. Line is: [text in mascot.dat]

Further help:

Refer to the 'cron' section in chapter 6 of the Mascot Installation and Setup manual for correct syntax.

Actions:

M00159

Number out of range in cron section of mascot.dat. Line is: [text in mascot.dat]

Further help:

Refer to the 'cron' section in chapter 6 of the Mascot Installation and Setup manual for correct syntax.

Actions:

M00160

Re-setting number of missed cleavage points to maximum of [number]

Further help:

There is a maximum number of missed cleavage points allowed, and this has been exceeded. (This is not possible with the forms supplied by Matrix Science). The value is supplied to nph-mascot using the 'PFA' value.

Actions:

M00161

Invalid character in sequence command: [text entered]

Further help:

See the online user help for allowed sequence command formats

Actions:

M00162

Searching [number] fragment ion peaks at an ions tolerance of [tolerance] against a peptide mass [peptide mass] is not very discriminating. Assuming the tolerance estimate is appropriate, many of the peaks are likely to be noise

Further help:

Reduce tolerances, or improve peak detection parameters in mass spectrometer software.

Actions:

M00163

Missing '[' in your comp() command at line [line number] of your query: [text entered]

Further help:

There must be matching left and right brackets in the query.

Actions:

M00164

Missing ']' in your comp() command at line [line number] of your query: [text entered]

Further help:

There must be matching left and right brackets in the query.

Actions:

M00165

Invalid character '[character]' when expected residue letter(s) in comp() at line [number] of your query: [complete text entered]

Further help:

Expecting a residue letter [A-Z]

Actions:

M00166

Residue '[residue]' is used more than once in comp() at line [number] of your query: [complete text entered]

Further help:

There is no point in putting the same residue more than once in a comp( ) command - this will affect the scoring adversely. See the online user help for allowed comp command formats. Note also that some ambiguous residues (like B or Z) can conflict with different ones (like N, D, E or Q).

Actions:

M00167

Missing comma in PEPTOL() command at line [number] of your query: [text entered]

Further help:

peptol commands must be of the form peptol(value,units) where units can be Da, mmu, % or ppm.

Actions:

M00168

Tolerance <= 0.0 in PEPTOL() command at line [number] of your query: [line entered]

Further help:

peptol commands must be of the form peptol(value,units) where units can be Da, mmu, % or ppm. A tolerance of less than or equal to zero is not allowed

Actions:

M00169

Invalid units in PEPTOL() command at line [number] of your query: [line entered]

Further help:

peptol commands must be of the form peptol(value,units) where units can be Da, mmu, % or ppm.

Actions:

M00170

Failed to create named pipe '[name]'. Error code: [error message from operating system]

Further help:

Internal program error - should never happen - please contact Matrix Science.

Actions:

M00171

Failed to connect to named pipe '[name]'. Error code: [error message from operating system]

Further help:

Internal program error - should never happen - please contact Matrix Science.

Actions:

M00172

Residue '[residue]' not currently allowed in comp() at line [number] of your query: [text entered]

Further help:

Residues J, O, U and X are not currently allowed in comp( ) commands because their meaning is ambiguous.

Actions:

M00173

System error : failed to fork new process ([process name/reason]). Error: [returned by operating system]

Further help:

Unix only. This error indicates an unusual configuration / installation problem. If ms-monitor fails to run, please seek further help. Perhaps the process limit has been exceeded?

Actions:

M00174

Failed to setsid - set process to background yourself. Error: [returned by operating system]

Further help:

This error indicates an unusual configuration / installation problem. Press control 'Z' and then type bg. If ms-monitor fails to run, please seek further help.

Actions:

M00175

Daemon process failed to ignore sighup. Error: [returned by operating system]

Further help:

This error indicates an unusual configuration / installation problem. You should check that ms-monitor continues to run even when the terminal window that started it is closed. If ms-monitor fails to run, please seek further help.

Actions:

M00176

Failed to start service '[service name]'. Error [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details.

Actions:

M00177

Failed to register service handler '[service name]'. Error [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details.

Actions:

M00178

Failed to set NT service status '[service name]'. Error [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details.

Actions:

M00179

Failed to get monitor directory from registry ([name in registry]). Error [returned by operating system]. Re-run setup

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details. If you are very experienced with modifying the Windows NT registry, you could try adding the directory where ms-monitor.exe is installed into the registry entry: HKEY_LOCAL_MACHINE\Software\MatrixScience\Mascot\1.00\MonitorFolder

Actions:

M00180

Failed to change to the directory: [directory name]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details. When the Matrix Science Mascot Service starts, it changes to the mascot\bin directory as defined in the registry. It was unable to change to this directory.

Actions:

M00181

Failed to open service control manager for [service name]. Error: [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details. You may need to be logged into the system as administrator. If this is a cluster installation, and the message is 'Access is denied', check that you have made the MatrixScienceMascotService logon as the Domain Administrator. If the nodes are not part of a Windows domain, then the service should log in as Administrator and the Administrator passwords on the nodes should be the same as the Administrator password on the master. See the 'Cluster Mode' chapter of the Mascot Installation and setup manual for more details

Actions:

M00182

Failed to open service ([service name]). Error: [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details. You may need to be logged into the system as administrator.

Actions:

M00183

Failed to start service ([service name]). Error: [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details. You may need to be logged into the system as administrator. If this is a cluster installation, and the message is 'Access is denied', check that you have made the MatrixScienceMascotService logon as the Domain Administrator. If the nodes are not part of a Windows domain, then the service should log in as Administrator and the Administrator passwords on the nodes should be the same as the Administrator password on the master. See the 'Cluster Mode' chapter of the Mascot Installation and setup manual for more details

Actions:

M00184

Failed to stop service ([service name]). Error: [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details. You may need to be logged into the system as administrator.

Actions:

M00185

Failed to delete service ([service name]). Error: [returned by operating system]

Further help:

Windows NT Only. The MatrixScienceMascotService should not normally be deleted, so this message should not normally be shown.

Actions:

M00186

Failed to get service information ([service name]). Error: [returned by operating system]

Further help:

Windows NT Only. A problem may have occurred during installation. Check the installation logs for details. You may need to be logged into the system as administrator.

Actions:

M00187

Could not create thread. Have you set capabilities? Error: [error text returned by operating system]

Further help:

SGI Only. A program (probably nph-mascot) couldn't run a 'thread'. If the error number is 1, this is probably because it doesn't have the access rights to run the thread. To give nph-mascot.exe the access rights to run the thread, you must enter the command: chcap CAP_SCHED_MGT+ep *.exe in the mascot/cgi, mascot/x-cgi and mascot/bin directories as described in the Unix installation chapter

Actions:

M00188

Failed to set group ownership of file ([file name]). Error: [returned by operating system]

Further help:

Unix only. Unable to set the group ownership of the file, as set by the number in the unixWebUserGroup entry in the Options section of mascot.dat - check that the number in that entry is a valid group ID.

Actions:

M00189

Sockets library not initialised

Further help:

Windows NT version running in cluster mode. Is the Windows sockets library installed?

Actions:

M00190

Could not create socket - Error: [number returned by operating system]

Further help:

Cluster mode only. Unable to create a socket using the 'socket' command. Please report this error to Matrix Science.

Actions:

M00191

About to open socket ([number]) for reading

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00192

About to open socket ([number]) for writing

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00193

About to open socket ([number]) for reading and writing

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00194

Error number: [returned by operating system] trying to get address by hostname for [computer name]

Further help:

Cluster mode only. Indicates some problem with the DNS setup

Actions:

M00195

Error number: [returned by operating system] trying to connect to address: [computer name]

Further help:

Cluster mode only. Indicates some problem with the networking, or possibly the hardware. If the problem persists, please contact Matrix Science for futher advice. Under Windows, it is possible that this message will be shown (with error #10048) without there being a fatal error. Mascot attempts the 'connect' call up to 10 times - reporting this error at each attempt. Therefore, if there are 10 of these messages grouped together, then there is a serious problem, while a single message can simply be treated as a warning

Actions:

M00196

Error number: [returned by operating system] trying to write [number] bytes to socket - wrote [number written]

Further help:

Cluster mode only. Indicates some problem with the networking, or possibly the hardware. If the problem persists, please contact Matrix Science for futher advice

Actions:

M00197

Socket ([number]) is about to be read

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00198

Error number: [returned by operating system] trying to read from socket number [number]. Returned [number returned]

Further help:

Cluster mode only. Indicates some problem with the networking, or possibly the hardware. If the problem persists, please contact Matrix Science for futher advice

Actions:

M00199

Socket ([number]) was just read successfully

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00200

Socket ([number]) just read this text successfully: [text]

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00201

Error number: [returned by operating system] trying to bind to socket

Further help:

Cluster mode only. This can be caused by stopping and restarting the cluster too quickly. Stop ms-monitor.exe, wait for three minutes and try re-starting ms-monitor.exe. If this fails, it indicates some problem with the networking configuration. If the problem persists, please contact Matrix Science for futher advice

Actions:

M00202

Socket ([number]) was just bound successfully

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00203

Error number: [returned by operating system] trying to listen to socket

Further help:

Cluster mode only. Indicates some problem with the networking, or possibly the hardware. If the problem persists, please contact Matrix Science for futher advice

Actions:

M00204

Error number: [returned by operating system] trying to call accept for socket

Further help:

Cluster mode only. Under normal circumstances, this message may be seen occassionally on some unix system with error number 4. Otherwise, this indicates some problem with the networking, or possibly the hardware. If the problem persists, please contact Matrix Science for futher advice

Actions:

M00205

Socket ([number]) was just accepted successfully

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00206

Invalid entry in mascot.dat - Cluster section: [line in mascot.dat]

Further help:

The format of the line specified in mascot.dat is incorrect. See the 'Cluster installation' chapter in the Installation and Setup manual for further information

Actions:

M00207

Socket ([number]) was just closed successfully

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00208

Socket ([number]) was the last socket closed for this app.

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00209

(Message number no longer used)

Further help:

Actions:

M00210

Invalid node number ([number]). Must be in range [low] to [high]

Further help:

Cluster mode only. This error indicates that a cluster node has an invalid 'id'. Possible causes are that more nodes have been setup than there are licenses, or that the license file on thenode is missing or invalid

Actions:

M00211

Invalid cluster command. ([the command send]) was not expected

Further help:

Cluster mode only. This error is set when a cluster node received an invalid command.This could be due to communication problems between the master and the node.

Actions:

M00212

Invalid IPC Lock command: [command string]

Further help:

Trying to lock files for a database into memory, but the cluster node doesn't know about a database with that name. Please contact Matrix Science for further help

Actions:

M00213

Invalid IPC Unlock command: [command string]

Further help:

Trying to lock files for a database into memory, but the cluster node doesn't know about a database with that name. Please contact Matrix Science for further help

Actions:

M00214

Invalid IPC New fasta command: [command string]

Further help:

Trying to let the cluster node know about a new database, but it can't find an entry for thisdatabase in its copy of mascot.dat. Please contact Matrix Science for further help

Actions:

M00215

Invalid response ([response]) to IPC command: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned response was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00216

About to write to socket ([number]) this text: [text]

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00217

Just written to socket ([number]) this text: [text]

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00218

Failed to read the results calculated in one of the threads

Further help:

Cluster mode only. Failed to read the results from one of the nodes. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00219

Failed to get hostname - probably cannot continue

Further help:

Cluster mode only. Unable to find out the name of the computer. Needs this information to determine if it is expecting to run as a master or a node or both. Check that a valid unique computername is specified - see operating system for further information

Actions:

M00220

Invalid IPC Set State command: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00221

Invalid IPC GETSEQ Command: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00222

ms-getseq spawned from cluster node:[[text]]

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00223

Invalid IPC JOBNUMBER Command: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00224

Expecting an environment command - got: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00225

Expecting a job number, but got: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00226

Expecting a number following UPLOADSTART got: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00227

Upload failed - didn't get the NULL terminator!

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00228

Expecting an UPLOADSTART or UPLOADEND command - got: [command]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00229

Sizeof results structure different between platforms [[number]] and [[number]]

Further help:

Although clusters for different platforms are supported, there are some issues with mixed clusters (such as 'Endian' differences) that are not supported. Please contact Matrix Sciencefor further help

Actions:

M00230

nph-mascot spawned from cluster node:[socket [number]]

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00231

From mascot - spawned from socket number [number]

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00232

In nph-mascot - couldn't write OK message to self [socket [number]]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The returned command was invalid. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00233

Socket ([number]) is about to try and read [number] bytes

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00234

Debug IPC [text]

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00235

Cluster master failed to read data from node. Got [number] bytes, asked for [number]

Further help:

Cluster mode only. There are many different commands sent to each of the cluster nodes, and specific responses are expected from each command. The cluster master was unable to read the expected number of bytes. You will need to seek help from Matrix Science, and you may be requested to turn on detailed 'IPC' logging to help track down the cause of the problem.

Actions:

M00236

Invalid protein mass ([mass entered] kDa) entered. Enter a single value between [min] and [max] kDa

Further help:

Enter a valid protein mass in kDa (not Daltons)

Actions:

M00237

A protein segment mass is ignored if there is just one mass value

Further help:

A protein segment mass only makes sense for multiple peptides. see the online help for a description of the segment mass - it is not the mass of the complete intact protein

Actions:

M00238

Sequence with more than [text] residues ignored. (Accession number: [accession])

Further help:

The maximum sequence length is defined in the Options section of mascot.dat - increase the number specifed (MaxSequenceLen). You will then need to rebuild the compressed files. See description for the following message

Actions:

M00239

[number] sequences with more than [number] residues ignored. Longest approx. pnumber]

Further help:

The default maximum length for sequences is 50000, and this means that Mascot will not search against longer sequences. However, this maximum can be changed by adding/changing the MaxSequenceLen xxxxx line in the Options section of mascot.dat. The value needs to be one greater than the value reported in the message. When you have done that, you will need to re-build the compressed files for that database. The easiest way is to stop the mascot service, delete one or more of the compressed files (e.g. db_name.i00), and then re-start the service.

Actions:

M00240

Too many open sockets - cluster job lost

Further help:

Cluster version only. The maximum number of open sockets has been exceeded. Too many jobs running?

Actions:

M00241

Did not find a line starting "Peak Table" at line [line number] of input file

Further help:

See the online help text for the format expected for PerSeptive data files

Actions:

M00242

Did not find a line starting 'Center X' at line [line number] of input file.

Further help:

See the online help text for the format expected for PerSeptive data files

Actions:

M00243

You must specify a precursor mass for [format] format MS-MS Files

Further help:

Some MS/MS data file formats do not contain the precursor mass - please enter one

Actions:

M00244

Did not find a line starting 'STD.Misc' at line [line number] of input file.

Further help:

See the online help text for the format expected for PerSeptive data files

Actions:

M00245

Invalid line [[text in file]] in the file [[file name]]

Further help:

The taxonomy node file needs to be in the format specified in the Taxonomy section of the Mascot installation and setup manual

Actions:

M00246

The taxonomy node file [[file name]] is missing

Further help:

Replace the missing file. It can be downloaded from the NCBI ftp site - see the Taxonomy section of the Mascot installation and setup manual

Actions:

M00247

Invalid entry in mascot.dat - taxonomy section: [text in mascot.dat]

Further help:

See the Taxonomy section of the Mascot installation and setup manual for details of valid formats

Actions:

M00248

Invalid taxonomy name class ([name]) in file [file name]

Further help:

Not a serious error - the NCBI seem to continually add new 'classes' of names - e.g. 'misspelling'

Actions:

M00249

Invalid taxonomy selection. [name selected] is not available

Further help:

The names allowed are specified in the 'taxonomy' file in the mascot/config directory. See the Taxonomy section of the Mascot installation and setup manual for details of how to edit this file.

Actions:

M00250

The parent for taxonomy id: [number] in [file name] conflicts with another file

Further help:

You have set up multiple taxonomy node files, and they have conflicting information about the parentage of the reported taxonomy. Each taxonomy id can only have one parent ID

Actions:

M00251

Taxonomy '[name]' ignored. No taxonomy indexes for this database

Further help:

There is no taxonomy information for this database - the selection is ignored, and all entries in the database will be searched.

Actions:

M00252

[number] sequences ignored because length greater than maximum configured

Further help:

This error is reported to the user for each search on the database. See errors 238 and 239 above

Actions:

M00253

Error in the masses file [filename][error string]: %s

Further help:

See the information in the Installation and setup manual on the format of the masses file

Actions:

M00254

Invalid mass in masses file: [file name]. Minimum allowed is [minimum], maximum [maximum]

Further help:

See the information in the Installation and setup manual on the format of the masses fileand change the mass to be within the limits specified

Actions:

M00255

In taxonomy section of mascot.dat, max prefixes ([number]) exceeded

Further help:

The maximum number of 'PrefixRemoves has been exceeded - reduce the number specified. See the Taxonomy section of the Mascot installation and setup manual for details.

Actions:

M00256

(Message number no longer used)

Further help:

Message numbers divisible by 256 are not used - program error return values would be zero

Actions:

M00257

In taxonomy section of mascot.dat, max no breaks ([number]) exceeded

Further help:

The maximum number of 'NoBreakDescLineIf' has been exceeded - reduce the number specified. See the Taxonomy section of the Mascot installation and setup manual for details.

Actions:

M00258

Too many different taxonomy IDs ([number]) for accession: [accession]

Further help:

The maximum number of taxonomy IDs per database entry has been exceeded. This is very unlikely to be a serious problem, as all the common IDs will have been specified

Actions:

M00259

Uploaded file ([file name]) is a binary file? Mascot only takes text files

Further help:

You should only try and search files with peak lists in text format

Actions:

M00260

Environment variable ([name]) is too long for cluster ([name]).

Further help:

Cluster version only. Internal problem - please contact Matrix Science

Actions:

M00261

Error in line in Options section of mascot.dat - ([text in mascot.dat])

Further help:

Invalid entry. See the configuration and log file chapter of the Mascot installation and setup manual.

Actions:

M00262

Cannot read link '[name]' - error code '[error message from operating system]'

Further help:

Unix only. Trying to find the real name of the database file by following through directory and file name links

Actions:

M00263

Failed to stat '[file name]' - error code '[error message from operating system]'

Further help:

The 'stat' command failed - the detailed error message should describe the cause

Actions:

M00264

Database [name] set to use 'blast' indexes. No index files found

Further help:

If a database is set to use blast indexes, then the index files must be present before the fasta file is made available

Actions:

M00265

Database [name] set to use 'blast' indexes. Cannot create indexes

Further help:

Do not try and use ms-compress to create blast indexes

Actions:

M00266

Trying to socketWriteLargeBlock([number] bytes) - reset to 1 byte

Further help:

Cluster version only. Internal software error. Please inform Matrix Science

Actions:

M00267

Failed to lock file [file name]- error [error message from operating system]

Further help:

The error message from the operating system should describe the cause

Actions:

M00268

In taxonomy section of mascot.dat, max suffixed ([number]) exceeded

Further help:

The maximum number of 'SuffixRemoves has been exceeded - reduce the number specified. See the Taxonomy section of the Mascot installation and setup manual for details.

Actions:

M00269

No database specified - are you using your own search form?

Further help:

Should never happen with forms supplied by Matrix Science. The uploaded mime file must have a 'DB' entry

Actions:

M00270

Browser specifies 0 bytes of data to be uploaded. Please retry

Further help:

It is not clear what causes this error message, but it appears that the user never sees it - the message just appears in the log, and can be safely ignored

Actions:

M00271

Failed to create shared memory block for transferring data

Further help:

Is there sufficient memory available? Try increasing the limits set for shared memory. Please report this error to Matrix Science

Actions:

M00272

Failed to attached to shared memory block for transferring data

Further help:

Is there sufficient memory available? Try increasing the limits set for shared memory. Please report this error to Matrix Science

Actions:

M00273

Failed to remove shared memory [name] for transferring data - error [error message reported by operating system]

Further help:

Is there sufficient memory available? Try increasing the limits set for shared memory. Please report this error to Matrix Science

Actions:

M00274

'[name]' can only be used as a variable modification; setting it to variable

Further help:

This particular modification must be specified as a variable modification and will be converted automatically. There is a number of reasons for the refusal: 1) Wrong modification type (can only be residue or peptide terminus), 2) a peptide neutral loss is specified which can be done only for a variable mod, 3) multiple neutral losses are only for variable modifications.

Actions:

M00275

Mascot is licensed for [number] processors, but this PC has [number] processors

Further help:

Under Linux, it is not easy to restrict the number of processors that is used by Mascot Therefore, the software can only be run on a PC with the same number of processors as the licence

Actions:

M00276

One or more ions have negative masses. These have been ignored

Further help:

The MaxEnt 3 software seems to produce ions that have negative masses - these are ignored

Actions:

M00277

The maximum peptide tolerance for this type of search is [number] [units]

Further help:

Specify a lower tolerance

Actions:

M00278

Did not find a line starting /########... at line [line] of input file

Further help:

The Bruker 'reportfile' format is configurable - however, Mascot only accepts files in the format specified in the online user help

Actions:

M00279

Did not find a line starting 'Peak Mass' at line [line] of input file

Further help:

The Bruker 'reportfile' format is configurable - however, Mascot only accepts files in the format specified in the online user help

Actions:

M00280

You entered a tolerance of [number]. Please enter a value greater than zero

Further help:

All tolerances are plus/minus - please enter a positive value

Actions:

M00281

Failed to read from named pipe '[name]'. Error code: [error message from operating system]

Further help:

Internal error. Please report this error to Matrix Science

Actions:

M00282

Failed to write to named pipe '[name]'. Error code: [error message from operating system]

Further help:

Internal error. Please report this error to Matrix Science

Actions:

M00283

Failed to get info back from ms-lockmem. Continuing...

Further help:

Probably not a serious error. But please report this error to Matrix Science

Actions:

M00284

Debug: [text]

Further help:

Not used in released software

Actions:

M00285

Warning - opening [file name] because cannot mmap control file

Further help:

This is potentially a serious error. Other error messages just before this one should be investigated

Actions:

M00286

Failed to kill process ID: [number]. Cannot open process: Error '[error message from operating system]'

Further help:

A user has tried to kill a job, but this failed - it is possible that the job finished at the same time as the user pressed 'kill'

Actions:

M00287

Killed process ID: [number]ld cleanly

Further help:

A user has tried to kill a job, but this has succeed - information only

Actions:

M00288

Killed process ID: [number]ld

Further help:

A user has tried to kill a job, but this has succeed - information only

Actions:

M00289

Failed to kill process ID: [number]. Error '[error message from operating system]'

Further help:

A user has tried to kill a job, but this failed - it is possible that the job finished at the same time as the user pressed 'kill'

Actions:

M00290

Cluster node asked to kill job [number] - but this job not running

Further help:

A user has tried to kill a job, but this failed - it is possible that the job finished at the same time as the user pressed 'kill'

Actions:

M00291

Cluster node asked to kill job [number] - but this job not found

Further help:

A user has tried to kill a job, but this failed - it is possible that the job finished at the same time as the user pressed 'kill'

Actions:

M00292

Cluster set flag for thread/socket for job [number] to be terminated

Further help:

A user has tried to kill a job - information only

Actions:

M00293

Cluster node aborted thread/socket for job [number]

Further help:

A user has tried to kill a job - this succeeded at this cluster node - information only

Actions:

M00294

Cannot find source file ([file name]) required for cluster node

Further help:

The file specified is missing from the 'cluster' directory

Actions:

M00295

Error trying to set last modification time in file [file name] - error code '[error message from operating system]'

Further help:

Unable to set date time for file. This probably means that updates will occur continually on the cluster node. Report the error number to Matrix Science.

Actions:

M00296

Error [number] trying to read from file [file]

Further help:

Potentially a serious problem - could be a problem on the disk

Actions:

M00297

Error [number] trying to write to file [file]

Further help:

Potentially a serious problem - could be a problem on the disk

Actions:

M00298

Error [number] trying to open file [file]

Further help:

Potentially a serious problem - could be a problem on the disk

Actions:

M00299

Failed to create service ([name]). Error: [error message from operating system]

Further help:

Mascot will not run without the service. The error message should indicate the nature of the problem

Actions:

M00300

[optional sub cluster][state][state] to %s

Further help:

Informational message put into monitor.log

Actions:

M00301

Installed service [name] on computer [computer]

Further help:

Cluster mode setup successfully installed the MascotNodeService on the Mascot Node

Actions:

M00302

Changed service binary file location for service [name] on computer [name]

Further help:

The installation directory for Mascot or a Mascot node has been changed. Information only

Actions:

M00303

Failed to change service ([name]) binary location. Error: [error message from operating system]

Further help:

The installation directory for Mascot or a Mascot node has not been changed successfully. This fault needs to be corrected

Actions:

M00304

Failed to query service ([name]) binary location. Error: [error message from operating system]

Further help:

The error message should detail the reason - probably insufficient access rights?

Actions:

M00305

Failed to open remote registry on ([computer]). Error: [error message from operating system]

Further help:

Cluster mode only. Is the service on the Mascot master being run as Administrator? It cannot be run as Local System Account, because this doesn't have access to other computers

Actions:

M00306

Failed to create registry key on remote computer ([computer]). Error: [error message from operating system]

Further help:

Cluster mode only. Is the service on the Mascot master being run as Administrator? It cannot be run as Local System Account, because this doesn't have access to other computers

Actions:

M00307

Updated registry key [key]\[key]=[value] on remote computer [computer]

Further help:

Cluster version information only - not an error

Actions:

M00308

Successfully updated file: [file name]

Further help:

Cluster version information only - not an error

Actions:

M00309

Successfully updated file: [file name] on computer [computer]

Further help:

Cluster version information only - not an error

Actions:

M00310

Failed to update file: [file name] on computer [computer]

Further help:

Cluster version. You may need to update this file manually if it is not updated automatically later

Actions:

M00311

One or more Mascot cluster nodes have failed - please investigate

Further help:

Check the ms-status screen to see which node has failed, and fix the problem. You will need to restart the service on the master after the problem has been fixed

Actions:

M00312

-----------------------------------Mascot node started

Further help:

Cluster version only - information in monitor.log on the cluster node

Actions:

M00313

-----------------------------------Mascot node stopped

Further help:

Cluster version only - information in monitor.log on the cluster node

Actions:

M00314

Unable to shutdown socket - error number: [number]

Further help:

Problem closing socket. Please report this problem to Matrix Science

Actions:

M00315

Cannot find ip address for computer '[name]'. Enter ip address directly

Further help:

Cluster version only. The Mascot master cannot find the ip address for the node. Either set up name services on the network, or enter the ip address in the cluster section of mascot.dat

Actions:

M00316

There was a crash on [date/time] on cluster node: [computer name]. Please investigate.

Further help:

Cluster version, Windows NT only. An application (possibly not Mascot) crashed on the specified node. You should check the 'Dr. Watson' file on that node

Actions:

M00317

Reboot request on [computer name] computer sent

Further help:

Cluster only. A request to reboot a cluster node has been sent

Actions:

M00318

Reboot request on computer [computer name] failed. Error: [error message from operating system]

Further help:

Cluster only. A request to reboot a cluster node has been sent, but has failed

Actions:

M00319

Error in cluster section of mascot.dat. Block [number] uses invalid node [node]

Further help:

This message not currently used

Actions:

M00320

Error in cluster section of mascot.dat. No node for block [number]

Further help:

This message not currently used

Actions:

M00321

Error in cluster section of mascot.dat. More blocks ([number]) than licenses ([number])

Further help:

This message not currently used

Actions:

M00322

Failed to write temporary file ([file name]) for mail message

Further help:

Mail messages are created using a temp file - the directory for the temp file is set in mascot.dat

Actions:

M00323

The node on port %d at IP address %s has failed to complete the current search

Further help:

This particular search has failed because the specified node has not responded, or has returned an error. Check the ms-status screen to see if the node has failed completely. If the node is running, then check the error log on that node for indications of the cause of the fault

Actions:

M00324

No OS set for cluster node [computer name], and no default available. Chooing NT

Further help:

You should specify an operating system for each node in mascot.dat

Actions:

M00325

Trying to use for cluster at address ip address. No host name.

Further help:

Cluster setup. If you specify a DefaultNodeHomeDirFromMaster, then you must use hostnames rather than just ip addresses in mascot.dat

Actions:

M00326

Two modifications with the name '[name]' in the mod_file

Further help:

Remove one of the entries in the mascot/config/mod_file

Actions:

M00327

The ms-monitor daemon/service is not running, please start it. (Sub Cluster [Sub Cluster number])

Further help:

For Windows NT, start this from the start menu, Programs, mascot, config - Start Mascot Service. For unix, see your sytem administrator. The sub cluster number should be zero except for large clusters.

Actions:

M00328

Another copy of ms-monitor.exe daemon is running - pid [number], file: [filename]

Further help:

Kill the ms-monitor.exe service before re-starting. If it fails to stop with 'kill [pid]', then try kill -KILL [pid]'

Actions:

M00329

Waiting [number] more seconds for searches to end before shut down

Further help:

Informational message put into monitor.log. ms-monitor.exe is trying to shut down (request by kill under Unix, or stop service under NT). ms-monitor will wait 20 seconds for all searches to end, and then it will force a stop

Actions:

M00330

Cluster node [name of computer node] appears to not be initialised. Re-starting ms-monitor.exe

Further help:

The specified node has a service that is running, but doesn't appear to have been initialised. This is probably because the node has been restarted, manually, or the service/daemon has been stopped and re-started. ms-monitor.exe will be 're-started' now

Actions:

M00331

CLUS_MESS_REMOVE_COMP_FILES: [command string]

Further help:

Trying to remove the compressed files from a cluster node, but the parameters seem to be wrong for the command. Please contact Matrix Science for further help

Actions:

M00332

Failed to obtain some/all system information. Error: [error message returned by operating system]

Further help:

Refer to your operating system documentation for further information

Actions:

M00333

Could not create thread. Error: [error text returned by operating system]

Further help:

Unix versions only. A program couldn't run a 'thread'. The error text should help ascertain the cause and rememdy of the problem

Actions:

M00334

Error trying to set setsockoption [socket option to be set] before calling bind for socket: [returned by operating system]

Further help:

Cluster mode only. This indicates some problem with the networking, or possibly the hardware. If this error occurs on it's own, it is not fatal and there should be no performance loss or data loss. If the problem persists, please contact Matrix Science for futher advice

Actions:

M00335

Cluster node '%s' (ip address %s) is not responding to 'ping' - please investigate

Further help:

This node is not responding to basic requests. Please check that it is switched on, and that the ip address and name are correct in nodelist.txt

Actions:

M00336

Invalid IPC Set Stats Info Command: [command string]

Further help:

Trying to let the cluster node know stats for a new database, but the parameters are wrong for this command. Please contact Matrix Science for further help

Actions:

M00337

Cannot bind a thread to processor: [processor number], error: [System error text]

Further help:

The licensing system is trying to bind a process to this thread, but an error has occured

Actions:

M00338

The file [File name] is too large to memory map on this system.

Further help:

The file is larger than 2Gb. The software will continue, but won't lock the file intomemory. Change the setting in mascot.dat so that the database file is not locked.

Actions:

M00339

Requesting more cpus on nodes than there are licences. Request denied

Further help:

If you have more cpus on nodes available than you have licenses, then you will see this message every time the system is started - it can therefore be ignored

Actions:

M00340

Requested node [host name] - [ip address] appears to have gone from list? Was file edited manually?

Further help:

In the node list file, a node was marked as being about to be used. The software thenattempted to start this node, and then mark the status back into the file. However, it couldn'tthen find the node in the file - perhaps it was edited manually? Reliable behaviour cannot now be guaranteed until you restart ms-monitor.exe

Actions:

M00341

Too many nodes in sub cluster [number]. Setting number of nodes to [max nodes allowed]

Further help:

The number of nodes needed to fulfill the number of sub cluster cpus specified in mascot.dat is too high. This value has been now been set to the maximum allowed

Actions:

M00342

Cluster node [name of computer node] cannot be initialised. ms-mascotnode.exe failed to start

Further help:

The specified node has a service that is running, but doesn't appear to have started properly. If it is installed, you could try starting is at a command prompt usingms-mascotnode.exe CLUSTER

Actions:

M00343

No nodes found for sub cluster [sub cluster number]. Will try again in [number of seconds] seconds

Further help:

There are no nodes in the nodelist.txt file that can be used for the specified sub cluster. Add some valid nodes to the nodelist.txt file.

Actions:

M00344

Internal error for database [database]. Last sequence for this node is -1

Further help:

The last sequence for this node is a negative number, indicating some typeof problem with database setup.

Actions:

M00345

isoelectric point (pI) calculation didn't converge in [number] iterations for sequence %s...

Further help:

The code to calculate pI should converge - however this didn't happen evenwith the large number of iterations. The value of pI returned is set to zero

Actions:

M00346

Sub cluster [sub cluster number] is not currently running

Further help:

Trying to run a Mascot search using this sub cluster, but the specified sub cluster is not currently running. Choose another sub cluster

Actions:

M00347

Duplicate entry in nodelist.txt - IP address: [IP address]

Further help:

The duplicate entry in nodelist.txt will be ignored. To prevent the warning from being displayed again, stop ms-monitor.exe and remove the duplicate entry

Actions:

M00348

Failed to create the directory - [Directory]

Further help:

The specified directory could not be created - check access rights

Actions:

M00349

Failed to run the load_node.pl script

Further help:

An error was reported by the load_node script - see the load_node log file

Actions:

M00350

Failed to execute program [Program / script] - error [error message]

Further help:

An error was reported trying to run the named program or script. If the error was a timeout error, then the script was killed

Actions:

M00351

Execute program - return code was [return code] from running [Program / script]

Further help:

The program shown was run successfully - the return code from the program is show

Actions:

M00352

Cannot create the 'pid' file: [File name]. ms-monitor will continue.

Further help:

ms-monitor.exe was unable to create the .pid file in the directory shown. If this is due to access rights, change the location/name of the pid file by adding a line:
MonitorPidFile [pathname]
to the Options section of mascot.dat

Actions:

M00353

Failed to close the Windows socket library : error [error number]

Further help:

Possible errors are:
WSANOTINITIALISED 10093 Should never happen
WSAENETDOWN 10050 A serious error
WSAEINPROGRESS 10036 A blocking Windows Sockets 1.1 call is in progress, or Mascot is still processing a callback function.

Actions:

M00354

ms-monitor.exe (pid = [Process ID]), is not running. It is being re-started.

Further help:

ms-monitor.exe has crashed or been killed. It was restarted

Actions:

M00355

Error trying to recv while closing socket - error number: [number]

Further help:

Problem closing socket. Please report this problem to Matrix Science

Actions:

M00356

[number of bytes] Unexpected bytes received while closing socket - data is [data]

Further help:

Trying to shut a socket, but more data is being sent - not a serious problem.

Actions:

M00357

Error closing socket - error number: [number]

Further help:

Problem closing socket. Please report this problem to Matrix Science

Actions:

M00358

Failed to get volume information for drive '[drive]' - error code '[error message from operating system]'

Further help:

Attempting to get date and time of the file - needs to know filesystem type and has failed to get this information

Actions:

M00359

Failed to set permissions for file ([file name]). Error: [returned by operating system]

Further help:

Unable to modify permissions of the file - check file exists

Actions:

M00360

Error in fragmentation_rules file: [error string]

Further help:

This file should only be modified by an experienced user - please refer to Matrix Science

Actions:

M00361

For searches containing 'comp', there is a peptide mass limit [mass limit (m/z * charge)] Da

Further help:

Please restrict the peptide mass to below that shown, or don't use a comp( ) statement

Actions:

M00362

For test purposes only. Error email should have been sent to: [email address].

Further help:

Make sure email was sent to appropriate email address

Actions:

M00363

The maximum number of searches per user ([number]) has been exceeded. The most complete search is [number]%complete.

Further help:

There is a limit to the number of searches that can be run simultaniously by a single user this is an optional limit in the mascot.dat configuration fileEither increase the value of MaxSearchesPerUser in mascot.dat or wait until some searches have finished before trying to submit more searches.

Actions:

M00364

Message no longer used

Further help:

Actions:

M00365

Too many entries to be searched for an error tolerant search. Max allowed = [number allowed]

Further help:

There is a limit on this system for the number of accession numbers to perform an error tolerant search. A list of accessions must be defined using the ACCESSION= keyword. This limit can be changed by the Mascot administrator - ErrTolMaxAccessions in options section of mascot.dat - if it is set to 0 (the default) then there is no limit

Actions:

M00366

Missing bracket in INTENSITY() command at line [number] of your query: [text entered]

Further help:

intensity commands must be of the form intensity(value)

Actions:

M00367

Socket [number] was connected to address: %s

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00368

Socket [number] was connected to port: %d

Further help:

Cluster mode only. Debugging message entered into IPC log when detailed logging enabled

Actions:

M00369

Too many cpus in sub cluster [number]. Setting number of usable cpus to [max cpus allowed]

Further help:

In mascot.dat, the number of cpus for the sub cluster is too high. This value has been now been set to the maximum allowed

Actions:

M00370

Error unlocking mapping of file [filename]: ([detailed error message])

Further help:

This should never happen, but does not normally indicate a serious problem.

Actions:

M00371

Invalid 'FRAMES' command (expecting list of values 1..6) - supplied value was: [supplied command]. Searching all 6 frames

Further help:

The format should be, for example: 1,2,3 or 1,2,4,6. The text must only contain numbers 1 to 6 and should be comma or space separated

Actions:

M00372

[entered email address] is not a valid email address: Address does not conform to username@hostname.
Refer to the privacy FAQ for further details about email addresses

Further help:

The format should be: username@hostname. A username was not specified

Actions:

M00373

[entered email address] is not a valid email address: Address does not conform to username@hostname.
Refer to the privacy FAQ for further details about email addresses

Further help:

The format should be: username@hostname. A hostname was not specified

Actions:

M00374

[entered email address] is not a valid email address. This email address is on a stop list.
Refer to the privacy FAQ for further details about email addresses

Further help:

The email address specified has been excluded. Please contact Matrix Science to find out why the email address is on the stop list

Actions:

M00375

[entered email address] is not a valid email address. This email address is on a stop list.
Refer to the privacy FAQ for further details about email addresses

Further help:

The email address specified has been excluded. Please contact Matrix Science to find out why the email address is on the stop list

Actions:

M00376

[entered email address] is not a valid email address - User name appears to be invalid.
Refer to the privacy FAQ for further details about email addresses

Further help:

The format should be: username@hostname. The username is not valid

Actions:

M00377

[entered email address] is not a valid email address - host name appears to be invalid.
Refer to the privacy FAQ for further details about email addresses

Further help:

The format should be: username@hostname. The hostname is not valid

Actions:

M00378

[entered email address] is not a valid email address. Email address does not conform to rfc 822
Refer to the privacy FAQ for further details about email addresses

Further help:

The format should be: username@hostname. The email address does not conform to rfc 822

Actions:

M00379

[entered email address] is not a valid email address. Host does not accept email.
Refer to the privacy FAQ for further details about email addresses

Further help:

The format should be: username@hostname. The host does not have an email server (no MX or A record)

Actions:

M00380

You must enter an email address and user name when using the Matrix Science public web site.
Refer to the privacy FAQ for further details about email addresses

Further help:

The format should be: username@hostname. Specify an email address

Actions:

M00381

[advertising]

Further help:

This message used for advertising Mascot on our public web site

Actions:

M00382

The file [filename] cannot be read

Further help:

This message used for advertising Mascot on our public web site

Actions:

M00383

Rebuilding compressed file for database - [.stats file name] is from older version of Mascot

Further help:

Not an error message - just a comment put into monitor.log

Actions:

M00384

Warning: [accession] in database [fasta file name] has a taxonomy id ([taxonomy id]) with a missing link up to 'all species'. Check error M00385 below

Further help:

The file nodes.dmp in the taxonomy directory contains a link to the 'parent' of each species. For example, All Species->Eukaryota->Metazoa-> ...Mammalia->...Homo Sapiens When Mascot creates the compressed files, it checks the taxonomy tree for all sequences. All taxonomy IDs should link to the top of the tree. This one failed, because one of the taxonomy IDs in nodes.dmp is missing. It is fairly common for about 100 entries in the database to have missing taxonomy IDs. If there are more than this, then check that nodes.dmp is up to date. Only five of these errors will be displayed for any fasta file. Error message 385, and also the .stats file will show the total number of sequences with a fault

Actions:

M00385

Warning: There are [number of accessions] ([fasta file name].3f percent) accessions with a missing link up to 'all species' in %s. This warning %s be ignored.

Further help:

See also error number 384, which will be used for the first five of these errors. The file nodes.dmp in the taxonomy directory contains a link to the 'parent' of each species. For example, All Species->Eukaryota->Metazoa-> ...Mammalia->...Homo Sapiens When Mascot creates the compressed files, it checks the taxonomy tree for all sequences. All taxonomy IDs should link to the top of the tree. Multiple entries failed, because one of the taxonomy IDs in nodes.dmp are missing. It is fairly common for about 1 percent of entries in the database to have missing taxonomy IDs. If there are more than this, then check that nodes.dmp is up to date. Only five of these errors will be displayed for any fasta file.

Actions:

M00386

Failed to kill process ID: [number]. Function OpenProcessToken(...) has failed.

Further help:

The process tried to retrieve its security token. It might be needed for getting additional rights.

Actions:

M00387

Failed to kill process ID: [number]. Function LookupPrivilegeValue(...) has failed: Error '[error message from operating system]'

Further help:

The process tried to find a certain privilege value. It might be needed for getting additional security permissions.

Actions:

M00388

Failed to kill process ID: [number]. Cannot adjust token privileges: Error '[error message from operating system]'

Further help:

The process has failed to change its security token. It might be needed for getting additional security permissions.

Actions:

M00389

Cannot read enzyme file. Possibly wrong syntax.

Further help:

Cannot read enzyme file. Possibly wrong syntax. Check allowed keywords, indices etc..

Actions:

M00390

Too many peptide masses in your data file or queries without any ions. Mascot has a limit of [number] for PMF search. Probably wrong type of search or wrong input format.

Further help:

There is a limit to the number of peptide masses allowed in PMF search. Is the user entering ms-ms data into a PMF form? Or selected wrong data file format?

Actions:

M00391

You may have specified the wrong data format. The file extension '[submitted type]' usually corresponds to '[file format type]'

Further help:

Certain file extensions correspond to specific input data file formats. The data submitted might not be parsed correctly.Select another format or sumbit a correct file.

Actions:

M00392

Memory allocation error: [number of bytes]. Memory available: [avail phys]ld / [total phys]ld Mb. Page file: [avail page file]ld / [total page file]ld Mb. Disk: [avail virtual]ld / [total virtual]ld Mb

Further help:

Memory allocation failed. Possible reasons: too large data file, too many threads per process, wrong data format or corrupted data.

Actions:

M00393

Allocated [bytes number] Kb of memory. Memory load: [memory load][total phys], total physical: [avail phys] Kb, available physical: [total page file] Kb, total page file size: [avail page file] Kb, available page file size: [total virtual] Kb, total virtual memory: [avail virtual] Kb, available virtual memory: %d Kb

Further help:

Memory allocation event.

Actions:

M00394

Unknown error occured.

Further help:

Unknown error occured. First, check if there is enough physical memory to run the search. Second, if the input file you submitted was of right format.

Actions:

M00395

Too small peptide masses have been detected [times][limit] times. Only the first %d of them are reported. Are you sure you have choosen the right data format?

Further help:

Look at the description of numerous errors reported before. Only a limited number of similar errors have been reported, a large number of redundant messages might have been suppressed. There might be a wrong data format for the input data.

Actions:

M00396

Too big peptide masses have been detected [times][limit] times. Only the first %d of them are reported. Are you sure you have choosen the right data format?

Further help:

Look at the description of numerous errors reported before. Only a limited number of similar errors have been reported, a large number of redundant messages might have been suppressed. There might be a wrong data format for the input data.

Actions:

M00397

Error occured while processing temporary file [filename].

Further help:

Corrupted or prematurely deleted temporary file makes further processing impossible. Temporary files contain queries data for running search against. Make sure you have enough disk space to run searches with large data-files and don't delete temporary files until they have been processed.

Actions:

M00398

Intermediate file name is missing or empty.

Further help:

One or more queries have been specified for repeated search, but intermediate file name is missing. Program cannot find enough information to start search.

Actions:

M00399

Incompatible TAXID with some other taxonomy rule parameters in taxonomy section of mascot.dat: [text in mascot.dat].

Further help:

Taxonomy rule may not be specified for enabling entry-level taxonomy IDs if database-level taxonomy ID has been specified.

Actions:

M00400

Translation table for gencode ID=[gencode ID] is not available in GENCODE-file.

Further help:

gencode.dmp file doesn't contain a table for the given ID or it has not been read assuming default table with ID=1 whereas a certain sequence belongs to a taxonomy with different gencode ID. Perhaps an invalid database entry or a wrong taxonomy ID.

Actions:

M00401

There is an error in the modification file [mod file name][line with error]: %s

Further help:

Check the allowed format of the mod_file specified in the 'configuration and log files' chapter in the Mascot installation and setup manual

Actions:

M00402

There is an error in the enzymes file [enzyme file name][error string]: %s

Further help:

Check the allowed format of the enzymes file specified in the 'configuration and log files' chapter in the Mascot installation and setup manual

Actions:

M00403

There is an error in a configuration file: [error string returned]

Further help:

An error returned by msparser-lib indicates wrong format or other errors. Consult a manual to make any changes.

Actions:

M00404

There is an error related to the license file: [error string returned]

Further help:

An error returned by msparser indicates problems with the license file. Cannot continue without a valid license.

Actions:

M00405

Error occured when retrieving current CPU configuration: [error string returned]

Further help:

It indicates a problem in underlying OS. Contact MatrixScience to resolve the issue.

Actions:

M00406

Specifying a protein mass disables mixture mode in PMF-search

Further help:

Mascot cannot combine sequences to find protein mixtures if a protein mass limit has been specified.

Actions:

M00407

Error in TAG()/ETAG() command at line [number] of your query: [text entered]

Further help:

tag/etag commands must be of the form tag(value, string, value)

Actions:

M00408

Too many TAG()/ETAG() commands per a query. Maximal number is [number].

Further help:

Mascot cannot process more that a certain number of tag()/etag() commands

Actions:

M00409

Error '[number]' trying to read from file [file]

Further help:

Potentially a serious problem - could be a problem on the disk

Actions:

M00410

Error '[number]' trying to write to file [file]

Further help:

Potentially a serious problem - could be a problem on the disk

Actions:

M00411

Error '[system error]' trying to open file [file]

Further help:

Potentially a serious problem - could even be a problem on the disk

Actions:

M00412

There is an error in a configuration file: [error string returned]

Further help:

An error returned by msparser-lib indicates wrong format or other errors. Consult a manual to make any changes.

Actions:

M00413

Instrument '[instrument name]' cannot be found in fragmentation_rules file

Further help:

Instrument name has to match to one of the entries in fragmentation_rules file. Mascot cannot process queries without it.

Actions:

M00414

Commands ions() and tag()/etag() cannot be used within the same query: line [input file line number]

Further help:

Commands ions() and tag()/etag() are incompatible. Split your query into two similar ones.

Actions:

M00415

Ambiguous resisudes are not allowed in tag/etag() commands: line [input file line number]

Further help:

Residues B, J, O, U, X and Z are not currently supported in tag()/etag() commands.

Actions:

M00416

The etag() command is not allowed with a semi-specific enzyme or without enzyme

Further help:

Usage of etag() command together with semi-specific enzyme or without enzyme specificity makes little sense, because all mass values in the query will be ignored. Try using tag() or seq() commands instead or choose a different enzyme for your search

Actions:

M00417

Node [computer name][error string] returned %s

Further help:

While performing socket communications a cluster node returned an error string to the master.

Actions:

M00418

Cannot compress [[fasta name]] - Taxonomy rules specify that full text file (.dat or .ref) should be used but this file is missing.

Further help:

In the taxonomy rules for this database, the 'FromRefFile' value is set to 1. However, the database rules specify that there is no reference file. If the database is SwissProt, using the database maintenance utility, change the taxonomy from Swiss-prot DAT to Swiss-prot FASTA

Actions:

M00419

Internal configuration error 0x[internal error code]08X. Please contact Matrix Science for support.

Further help:

An internal configuration error happened. Please contact Matrix Science for support.

Actions:

M00420

There is an error in a configuration file: [error string returned]

Further help:

An error returned by msparser-lib indicates wrong format or other errors. Consult a manual to make any changes.

Actions:

M00421

Warning - accession [[accession]] is longer than [number] characters

Further help:

This may not be a problem. However, it might indicate sometime a malformed fasta file or wrong accession parse rules. Be careful when selecting a parse rule or creating a new one for your fasta database. If you are configuring your custom in-house database try to avoid very long identifiers for the sequences as they might increase size of comnpressed files and search result files significantly.

Actions:

M00422

Accession [[accession]] is a duplicate - there is at least one other protein with this accession number

Further help:

If two or more proteins have the same accession string, then Mascot results would be ambiguous. For example, if you were to try view a protein report this protein, Mascot would not know which one to display. This is a fatal error - if you wish to ignore this error, add the database name to the IgnoreDupeAccessions value in the options section of mascot.dat

Actions:

M00423

Cluster node asked to change priority for job [number] - but this job not found

Further help:

A user has tried to change a process priority for a job, but this failed - it is possible that the job finished.

Actions:

M00424

Cluster node asked to pause job [number] - but this job not found

Further help:

A user has tried to pause a job, but this failed - it is possible that the job finished.

Actions:

M00425

Cluster node asked to resume job [number] - but this job not found

Further help:

A user has tried to resume a job, but this failed - it is possible that the job finished.

Actions:

M00426

Job [number] has been killed by an administrator

Further help:

An administrator requested to kill the job. The applications exits.

Actions:

M00427

Using etag() command is not allowed in error-tolerant search

Further help:

Usage of etag() command in error-tolerant search makes little sense. Try deselecting queries with etag() commands before submitting error-tolerant search.

Actions:

M00428

Wrong format for PrecursorCutOut parameter: [string]

Further help:

PrecursorCutOut parameter specifies two numbers delimited by a comma or just one number -1 for default value to take place instead.

Actions:

M00429

There is a missing library for calling 'ping' - cannot start cluster

Further help:

Cannot find either icmp.dll or IPHLPAPI.DLL - or these libraries don't have the required functions. Please contact Matrix Science, giving details with the exact error message from the error log, and the version of Windows that you are using (including service pack)

Actions:

M00430

Missing ion intensity value on line [line number] of input file

Further help:

The wrong file type may have been specified, or there is an error in the formatting of the file. Check the help text for allowed file formats.

Actions:

M00431

Missing ')' in ions() at line [line number] of your query: [text entered]

Further help:

The format of the ions() command is incorrect. See the online user help for more details. Each opening bracket must be matched by a closing bracket

Actions:

M00432

Out of memory - (malloc/calloc/new)

Further help:

The system is very low on memory, or possibly a very large search has been specified. Increase the size of the swap files, put more memory into the system or reduce the size of the searches. It is also possible that there is no virtual address space left - refer to the system administration guides supplied with your computer for details on increasing these limits

Actions:

M00433

Variable modification [modification name] has [number] master neutral losses but only up to [number] is allowed

Further help:

Possibly wrong modification definition or corrupt mod_file

Actions:

M00434

Modification [modification name] has to have at least one master neutral loss or not neutral losses at all

Further help:

Possibly wrong modification definition or corrupt mod_file. Without at least one master neutral loss MS/MS search will not find any significant ions matches

Actions:

M00435

Modification [modification name] definition specifies ambiguous residue

Further help:

Possibly wrong modification definition or corrupt mod_file. All residues must be specified explicitly

Actions:

M00436

Cannot process input xml-file due to error [system id][line number][column][description]: line %d, col %d - %s

Further help:

Corrupt or malformed xml-file. Try to validate it before submitting to Mascot

Actions:

M00437

Wrong format of input xml-file: unxepected or missing element '[element name][line number][column]' at line %d, col %d

Further help:

The xml-file should have a definite structure. You could have submitted a file from non-supported instrument or with a non-standard format. Try to validate it before submitting to Mascot

Actions:

M00438

The input xml-file specifies data for more than one PMF search.

Further help:

You can submit one spectra with a set of PMF-queries at a time or several MS/MS spectra

Actions:

M00439

Error updating session files: [Error from security system]

Further help:

Session files are checked every hour. Any session files that have timed out are removed. Any error performing this is reported here, so this is potentially a serious problem that should be investigated.

Actions:

M00440

You are not logged in. Please login
%s

Further help:

Your session may have timed out, or you may now be denied access to the system. See your system administrator

Actions:

M00441

You are not logged in. Please login
%s

Further help:

Your session may have timed out, or you may now be denied access to the system. See your system administrator

Actions:

M00442

You don't have sufficient priviliges to view this page. Please login as a user with sufficient rights

Further help:

You need to login as a user with more priviliges

Actions:

M00443

Sorry [username][user id][Database name] [%d] - you don't have permission to search the %s database

Further help:

Mascot authentication is enabled, and you don't have permission to search this datbase. See your system administrator

Actions:

M00444

Sorry [username][user id][Database name] [%d] - you don't have permission to perform ms-ms searches

Further help:

Mascot authentication is enabled, and you don't have permission to perform ms-ms searches. See your system administrator

Actions:

M00445

Sorry [username][user id][Database name] [%d] - you don't have permission to perform pmf searches

Further help:

Mascot authentication is enabled, and you don't have permission to perform pmf searches. See your system administrator

Actions:

M00446

Sorry [username][user id][Database name] [%d] - you don't have permission to perform no enzyme ms-ms searches

Further help:

Mascot authentication is enabled, and you don't have permission to perform no enzyme ms-ms searches. Specify an enzyme, or see your system administrator

Actions:

M00447

Sorry [username][user id][Database name] [%d] - you don't have permission to perform no enzyme pmf searches

Further help:

Mascot authentication is enabled, and you don't have permission to perform no enzyme pmf searches. Specify an enzyme, or see your system administrator

Actions:

M00448

Sorry [username][user id][time] [%d] - your search has been terminated because it exceeded the maximum execution time (%ld seconds) allowed

Further help:

Mascot authentication is enabled, and your account has been set to limit the elapsed execution time. Simplify your search, or see your system administrator

Actions:

M00449

Sorry [username][user id][user id used] [%d] - you don't have permission to submit a search as another user id (%d)

Further help:

Mascot authentication is enabled, and you don't have permission to submit a search with a different user id. You need the SECTASK_ALLOWSPOOFOTHERUSER privilige

Actions:

M00450

You don't have sufficient priviliges to change this search. Please login as a user with sufficient rights or

Further help:

You need to login as a user with more priviliges

Actions:

M00451

This method of specifying taxonomy is obsolete

Further help:

Use GI2TAXID for faster and more accurate taxonomy assignment.

Actions:

M00452

ms-searchcontrol is incompatible with the current Mascot version

Further help:

Use GI2TAXID for faster and more accurate taxonomy assignment.

Actions:

M00453

.ref-file is incomplete or invalid for [fasta file name]

Further help:

Error while reading ref-file has happened. Probably, incomplete or invalid file. Try to download it again and restart Mascot

Actions:

M00454

Cannot use taskID [taskID].0f. Perhaps, it is being used by another search

Further help:

Another search with the same taskID has probably started already. It is also possible that a task_id-file cannot be created on the disk. Generate another unique taskID and make sure you have enough disk-space to perform searches.

Actions:

M00455

[number] duplicate accessions (e.g. [example accession][database]) being ignored for database %s

Further help:

Some databases have multiple accessions for for a particular sequence (e.g. MSDB, NCBInr). Mascot stores all the possible accessions, so that old searches are more likely to find a match in the latest version of the database. If there is a 'secondary' accession that is the same as a 'primary'accession (due to an error in the database), this will be removed from the compressed files so that it will not be found when using ms-getseq.exe

Actions:

M00456

Cannot find database '[database]' in the mascot control file

Further help:

Mascot control file has not been updated yet with new database.

Actions: