Mega2 produces these additional output files, containing further details of the current run. These files are either stored in a special directory described below, or tagged with the date and time of the run, if Mega2 terminated abnormally in the very early stages of its execution, e.g. if you ran Mega2 at 2:30 pm on June 15, 2004, then you may end up with a files named MEGA2.LOG.2004-6-15-14-30, MEGA2.ERR.2004-6-15-14-30 etc.
The summary file directory (also referred to as the run-directory), contains the summary files created by Mega2, along with html-versions of these files. This directory is created within the output folder specified in the input menu, and identified by the date and time of the run. For example, in the previous example, if Mega2 ran without problems, you should see a directory named 2004-6-15-14-30.
In addition to the sate and time of the last run and input file names,
this file is a copy of Mega2's screen output including summary statistics
on the input pedigrees and locus data, the analysis option name, what loci
were selected for reordering, pedigree statistics after locus selection,
and finally, what output files were produced.
It may also contain other important messages such as families and
individuals excluded from analysis, breaking or re-connection of loops
in inbred pedigrees, individuals whose genotypes were zeroed out, etc. If
there were any warnings or error messages, they are written into this file
in addition to the MEGA2.ERROR file.
Note that the backup copy MEGA2.LOG.old is no longer created.
This file contains all the error and warning messages produced during
a single run of Mega2. These messages include problems encountered with
the input files, such as inconsistent or invalid phenotype/genotype data
(Mendelian inconsistencies, markers named in the locus file but missing
from the map file and vice-versa etc.), and if there are problems with
creating and writing new files, directories during the execution.
For a detailed list of errors and warnings, see the
trouble shooting section . It is
a good idea to examine this file carefully and consult the
Trouble-shooting documentation, if Mega2 terminates abnormally. We have
made all efforts to make the error and warning messages as informative
as possible, in order to help the user debug her data. We always
appreciate feedback and suggestions for improvement in this area.
This is a default batch file created every time Mega2 is run in the interactive mode. See the section on Running Mega2 in Batch Mode for details on the format and contents.
This file contains a list of input and output pedigree and person
identifiers. It relates each input pedigree record to its corresponding
output pedigree record. Since, several of the output formats within
Mega2 require reordering individuals, or re-assigning pedigree and
person ids, it is difficult for the user to match up the output against
the input. Therefore, it was felt necessary to create a mapping between
input and output pedigree data. From the key file, the user can
idenitfy loops that were broken up or re-connected, or which nuclear
pedigrees were created from an extended pedigree. In the case of PAP,
for instance, where individuals are assigned completely new IDs,
the key file should help greatly.
Here is an example MEGA2.KEYS
file.
---------------------
Fri Oct 11 13:15:05 2002
Input file names
locus file: datain.ex
pedigree file: pedin.ex1
map file: map.ex
omit file: omit.ex
Untyped pedigree option: Include all pedigrees whether typed or not
---------------------
INPUT OUTPUT
Pedigree Person Ped: Per: Loop id Pedigree Person
1 1 1 1 1 1
1 2 1 2 1 2
1 3 1 3 1 3
1 4 1 4 1 4
1 5 1 5 1 5
1 6 1 6 1 6
1 7 1 7 1 7
1 8 1 8 1 8
1 9 1 9 1 9
1 10 1 10 1 10
1 11 1 11 1 11
2 1 2 1 2 1
2 2 2 2 2 2
2 3 2 3 2 3
2 4 2 4 2 4
2 5 2 5 2 5
2 6 2 6 2 6
2 7 2 7 2 7
2 8 2 8 2 2 8
2 11 2 8 2 2 8
2 9 2 9 2 9
2 10 2 10 2 10
This file is created if the user selects random-genotyping error generation in the input menu. Details on this file can be found in the Mistyping section .
This file contains a list of recoded marker loci with the original allele names, recoded identifiers, allele frequencies, the type of individuals counted for the purpose of estimating allele frequencies, and total number of alleles counted for each allele and each marker. Given below is an excerpt for a recode summary file.
---------------------
Wed Apr 7 13:21:43 2004
Input file names
locus file: names.02
pedigree file: pedin.02
map file: map.02
Untyped pedigree option: Include all pedigrees whether typed or not
Allele frequency computed from:
Genotyped founders or a randomly chosen individual.
---------------------
Recoded loci:
---------------------
Marker 2: d2s131 has 3 alleles typed at 8 people
Allele Code Frequency Count
1 1 0.25000 4
2 2 0.43750 7
3 3 0.31250 5
Marker 3: d2s165 has 3 alleles typed at 10 people
Allele Code Frequency Count
1 1 0.35000 7
2 2 0.35000 7
3 3 0.30000 6
Marker 4: d2s177 has 4 alleles typed at 10 people
Allele Code Frequency Count
1 1 0.30000 6
2 2 0.25000 5
3 3 0.25000 5
4 4 0.20000 4
At the start of the execution, existing error, log, key, and recode summary
files are moved into MEGA2.ERR.old, MEGA2.LOG.old, MEGA2.KEYS.old and
MEGA2.RECODE.old respectively.
The MEGA2.LOG and MEGA2.KEYS files are created each time Mega2 is executed.
The batch file MEGA2.BATCH is created only if Mega2 is run in the interactive
mode. In this case the existing batch file is backed up into MEGA2.BATCH.old.
MEGA2.ERR is created only if there are warnings and messages for the current run.
MEGA2.SIM is created only in the error simulation mode. The existing MEGA2.SIM file
is renamed into MEGA2.SIM.old.
MEGA2.RECODE is created only if a names file is used instead of a linkage-format
locus data file.
This file along with three other html files (MEGA2links.html, MEGA2outputfiles.html, and MEGA2file.html) contains links to the relevant summary files, input and output files for easy reference. Please note this uses frames. In addition, the input and output files are all text files, but may not be recognized as such by the browser, unless its settings are modified. The run summary files point to links which are html-versions of the text-format summaries, and should display correcly.