9. Error Messages

Errors are reported with a unique three digit identification number, a brief description, and, if applicable, the place of error that gives the line and the column position in the input data file. If MEGA is not installed from the master diskette(s) (i.e., copied from someone else's computer), only the error numbers may be displayed, you must request MEGA from the authors to obtain the master diskette(s).

Abnormal program termination

If memory is insufficient to run the MEGA program, this error will occur. Please see error number 001. If the problem persists, contact the authors.

001 RAM memory is exhausted

IBM personal computers run under the DOS operating system that allows only 640KB of RAM. DOS, other device drivers, and the MEGA program occupy much of this memory, and a small amount of memory is left for use during analysis. Look at the lower-right comer of your screen. If you think that the amount of memory shown there is enough, try the same command again. If the same message appears again and the amount of memory indicated is less than 200KB, try some of the following remedies.

1 . If you have a version of DOS earlier than 5.0, upgrade it to DOS 5.0. Load DOS in high memory area to free extra 100KB memory. Details for loading DOS to high memory area are found in most of the DOS reference manuals.

2. Memory resident programs such as virus scanners and DOS clocks use a large amount of RAM memory. Removing these programs will give you additional memory (30-50KB). The procedure to remove such memory resident programs is described in the DOS reference manual.

3. Device drivers for printing, networking, etc., take up some RAM memory, and computers running network software do not have much free RAM. You may free some memory by removing such programs.

002 Specified input data file is not found

Check the spellings of the input file name. If it is correct, then check that you are in the correct working directory. If not, use the File I Change Dir command to go to the appropriate directory.

003 Unexpected end of input data file

While reading input data file, more information was expected to follow, but the input file suddenly ended. Examine the contents of the data file with the File I Browse command and check the file. Does your input file contain non-ASCII characters?

004 Temporary file could not be created

MEGA creates many intermediate files to protect the original data. Make sure that your hard disk has at least 1MB of free space to store these files. If not, clean up your hard disk to free at least 1MB.

005 Numbers fall outside the valid range

All integer and real numbers entered in MEGA must be inside the pre-defined range for a particular option. If you have reasons to believe that some of these bounds are not justified, write to us about the reasons so that the range can be modified.

006 Invalid value

An invalid character or number has been entered.

007 User terminated the process

This message informs that the user terminated the process.

011 "TITLE" is not found in input data file

Check if your data file contains keyword "Title" on the second line. All input data files must include the Title keyword on the second line following the mega format specifier, #mega. (Read chapter 2 for more information.)

012 First OTU label must have preceding # sign

In MEGA, every OTU label should be prefixed with # sign. Check the beginning of the first OTU label. (Read chapter 2 for examples of input file.)

013 OTU label did not end

A blank space, tab, or a new-line should separate the OTU label and the sequence. Also, make sure that only one OTU label is written on any line.

014 Only one sequence is detected

Only one sequence is found in the input file. It may be because of the # sign missing in the second OTU label or because of the absence of a blank, a tab, or a newline. If you have only one sequence to analyze and you are interested in using Data|Data Presentation utilities, then simply duplicate the sequence in the input data file.

015 Invalid character encountered in data file

A character that is neither a valid nucleotide base (or amino acid residue) nor a special character for missing, identical, and alignment gap symbols is present. Examine the character at the place of error indicated. (For more information, consult chapter 2.)

016 No identical-site symbol is permitted in the first sequence

The first sequence should not contain any identical-site symbols because this symbol is used in the following sequences and is resolved in reference to the homologous site in the first sequence.

017 Last sequence seems incomplete

In the input data file all the sequences must be aligned and of equal length. Check if the last sequence in the file is of a different length.

018 Sequences are of unequal lengths

In the input data file, all the sequences must be aligned such that they are of equal length. Check the sequence data at the place of error.

019 Chosen data type is not implemented

Please consult the authors with appropriate information given in chapter 1.

020 Symbols for missing-information-, gap- and identical-site are not unique

Missing-information, gap, and identical sites symbols must be unique.

021 End of comment is missing

Comments are written like quotations within a pair of double quotes (e.g., "this is a comment"). Check if a double quote (") is missing.

022 Incomplete sequence encountered

All sequences must be of equal length in the input data file. Check data close to the place of error specified.

023 Vertical tabs are not permitted

Remove all vertical tabs from your data file.

024 Corresponding OTU labels must be identical in different data blocks

In interleaved sequences, all the OTUs must be presented in every block in the same order and with the same OTU labels. Check the OTU labels and their order in the input data file.

025 The number of OTUs is different in different blocks of interleaved sequences

In interleaved sequences, all the OTUs must be present in every block in the same order (see example in chapter 2). Note that blocks of interleaved data must be separated by at least one blank line and that the sequence data for different OTUs must be present on consecutive lines without any blank lines between them in every block.

026 One of the distance values read is invalid

The distance values in the input file must be positive or 0. The presence of negative values and other non-numeric character will result in errors. Do not use the scientific format for real numbers (1.24E2, etc.).

027 Input data must contain at least two OTUs

MEGA is designed for comparing different OTUs. So, there must be at least two entities for comparison. If you have only one sequence to analyze and you are interested in using Data|Data Presentation utilities, simply duplicate the sequence in the input data file.

028 New data file cannot be activated

Please report it to the authors with all the relevant information (chapter 1).

029 #mega format specifier missing

The very first line in the data file must contain #mega format specifier. This identifier is required to indicate that the data file is prepared for MEGA.

030 Data file contains too many OTUs

This error message can appear because of several reasons. First, the upper limit of the number of OTUs that can be read by MEGA is 500, so the data file should not contain more than 500 OTUs. If the sequence data in the file is in the interleaved format and MEGA attempt to read the data file using the noninterleaved option, this error may occur. Also, if your data file has no blank line between the blocks of interleaved sequences, this error will occur.

031 Error occurred during distance calculation

Please report this error to the authors with the information requested in chapter 1.

032 No distance type is selected, so distances cannot be calculated

Distance calculation is a two step process first, a distance calculation method is selected, and then the Distances|Compute Distances command is invoked. For reconstructing phylogenies, select a distance estimation method, select a tree-building method, and call the Phylogeny|Make Tree(s) or Phylogeny|Bootstrap command.

033 Failure in estimating distances

Distances are calculated under a model that provides distance estimation formula. Most formulas are only applicable for a certain range of observed difference. For instance, if the proportion (p) of nucleotide differences between two sequences >=0.75, the argument in the log term of Jukes-Cantor's distance becomes <=0, and the distance estimate is no longer obtainable. In MEGA, such invalid distances are shown with an '*'.

After computation of distances, the tree-building process is aborted. In this case, you may use the Distance|Compute Distances command and output distances to a file to identify OTUs that produce invalid distances. Remove these OTUs from the data set with the Data|Select OTUs command.

034 Program lost some important information required for internal use

Please report to the authors with appropriate information.

035 Stop codon(s) encountered in protein-coding sequences

Coding sequence should not contain any stop codons. This error may be caused by the use of an incorrect genetic code table. Select the appropriate genetic code table with the Distance|Genetic Code Table command and examine the sequence data with the Data|Data Presentation command in translation mode.

041 Phylogenetic trees cannot be reconstructed

Please consult the authors.

042 Less than 3 OTUs detected during phylogenetic reconstruction

Phylogenetic reconstruction is meaningless for a data set with only two OTUs.

043 No bootstrap replications specified

The message is obvious.

044 Bootstrap test is not available for the specified tree building method

MEGA does not provide the bootstrap test for the MP method.

045 None of the bootstrap replications produced valid results

This means that your data set is not appropriate for a bootstrap test.

051 No site/codon in data subset

Inspect the current data subset using the Data|Data Presentation command. Use the Data|Select Sites/Codons command to include desired data to the current data subset for analysis.

052 No OTU found in the currently active data set

Somehow all the OTUs from the data subset have been deleted. Use the Data|Select OTUs command to include some OTUs.

053 An error occurred during preparation of data for analysis

This error usually occurs due to the shortage of memory to store the data. Please refer to error number 001.

054 Protein-coding or noncoding mode are not specified

Please report this error to the authors.

055 No parsimony informative sites found in the sequence data

In the current data set none of the sites is informative for constructing an MP tree.

056 The data contain just one site (codon)

It is not possible to conduct bootstrap test if there is only one data site (codon).

057 Number of parsimony informative sites are less than number of OTUs

MEGA does not attempt to build a parsimony tree if the number of parsimony informative sites are less than the number of OTUs, because it is impossible to resolve the phylogeny in this case and many MP trees exist. Choose only representative OTUs, and delete others.

061 Device drivers may be missing

For printing phylogenetic trees on printers or for previewing them in graphic environment on the screen, MEGA comes with its own device drivers. This message indicates that it failed to find them in the appropriate directory. If you copied MEGA from someone else's computer, or if MEGA is not installed properly from the master diskette(s), this problem may arise. Please re-install MEGA from master diskette(s) properly. If the problem persists, contact the authors.

062 Tree drawing initialization error
063 Tree drawing error

Before a phylogenetic tree is drawn for previewing and printing, it is drafted in the vector format on an intermediate file. Apparently this file could not be initialized in the present case. Please report the error to the authors. Also see error number 081.

064 Trees cannot be previewed since there is no graphics capability

The user-interface is implemented in text-mode, but the tree image can be previewed before printing if some graphic capability is available. The EGA, VGA, and Hercules monitors are supported for this purpose.

071 Tree drawing file is missing

Before a phylogenetic tree is drawn for previewing and printing, it is drafted in the vector format on an intermediate file. This message indicates that this file has been lost. Try to use the print command again. If this does not help, report the error to the authors.

072 Printer cannot be opened for printing

Printers are usually connected to computers through PRN, LPT1, LPT2 or LPT3 ports. MEGA uses PRN to send data to the printers. Somehow this PRN port could not be opened for printing. Check printer connections.

073 I/O read error during tree printing

074 I/O write error during tree printing

075 Temporary file error

No free space on the disk. Please refer to error numbers 004 and 081.

076 Drawing file is corrupted

Before a phylogenetic tree is drawn for previewing and printing, it is drafted in the vector format on an intermediate file. Apparently this file has been corrupted. Try to use the print command again. If this does not help, report the error to the authors.

077 Unknown error occurred
078 Unknown error occurred
079 Unknown error occurred

The cause of the error is unknown, but the errors are detected by one of the error checking routines. You may see error number 081. If the problem persists, please contact the authors.

080 Drawing file error

Refer to error number 076.

081 Out of memory during tree drawing

Not enough memory is available for drawing the tree. Tree printing routines require at least 120KB (and more) of memory for drawing and printing. Look at the lower right corner of your screen. If the amount of memory available is less than 120KB, refer to the error number 001.

082 Cannot write to the printer

This is an input/output error. Use a different printer to print the phylogenetic tree. Also, report this error to the authors.

083 Device drivers are corrupted

For printing phylogenetic trees on various kinds of printers and previewing them in graphic environment, MEGA comes with many device drivers. This message indicates that the desired device driver has been corrupted. This problem can be solved by reinstalling MEGA to the computer using the master diskettes.

084 Printing aborted by the user

The Esc key was pressed to abort tree printing.

085 Bad drawing file

See error number 076.

086 Tree cannot be output in PCX format

The PCX file format is for storing the tree in a file that may be modified in the PC PaintBrush (Microsoft Windows) program afterwards. An input-output error occurred while writing this file. Please report your finding to the authors.

087 EPS output function failed

The EPS output is used to create a PostScript file or to send a PostScript file to a PostScript printer for printing. An input-output error occurred during this process. Please report your finding to the authors.

088 Polygon can not be drawn due to insufficient memory

089 Graphics mode cannot be initialized

Please report it to the authors.

090 Specified device driver is missing

091 Desired font file is missing

To remove this error, reinstall MEGA from the master diskette(s). If the problem persists, contact the authors.

092 Printer is either off line or paper is out

The printer is not responding to the program. Please check the connections.

093 Font file seems to be corrupted

To remove this error, reinstall MEGA from the master diskette(s). If the problem persists, contact the authors.