error 'mega2log2html.pl' may not be installed

[Jessica Perez Alquicira]

Hi, I am using mega2 for getting the structure format files from ped, however I got several errors including: "WARNING: The program 'mega2log2html.pl' may not be installed on your system." I already run ./installl.sh  What are the suggestions to solve this problem?

Thanks!!

                default [MARKERS]

After selecting traits and covariates

1 trait locus 

      1 Affection status locus: 

                default

Done checking locus integrity.

Checking pedigree integrity...

ERROR: Pedigree Sample1: member 1 has unknown sex (0)

ERROR: Pedigree Sample2: member 1 has unknown sex (0)

ERROR: Pedigree Sample3: member 1 has unknown sex (0)

ERROR: Pedigree Sample4: member 1 has unknown sex (0)

ERROR: Pedigree Sample5: member 1 has unknown sex (0)

ERROR: Pedigree Sample6: member 1 has unknown sex (0)

ERROR: Pedigree Sample7: member 1 has unknown sex (0)

ERROR: Pedigree Sample8: member 1 has unknown sex (0)

ERROR: Pedigree Sample9: member 1 has unknown sex (0)

ERROR: Pedigree Sample10: member 1 has unknown sex (0)

ERROR: Pedigree Sample11: member 1 has unknown sex (0)

ERROR: Pedigree Sample12: member 1 has unknown sex (0)

Done checking pedigree integrity.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Fatal errors in pedigree file PLINK11junomis30depth25qual.ped.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

===========================================================

Run parameters stored in batch file 2015-7-01-15-11/MEGA2.BATCH

See run summaries in directory 2015-7-01-15-11 

   MEGA2.LOG, MEGA2.RECODE, MEGA2.ERR

sh: mega2log2html.pl: command not found

WARNING: Execution of the shell failed for 'mega2log2html.pl'.

WARNING: No 'MEGA2*.html' files will have been created.

WARNING: Unable to create html-formatted run summary.

WARNING: The program 'mega2log2html.pl' may not be installed on your system.

WARNING: Run 'install.sh scripts' to install it.

===========================================================

input_check.cpp:612 Mega2 terminated. Error "DATA_INCONSISTENCY" (#6).

[Dan Weeks]

 We see that you were having problems using Mega2.

Your post shows two problems.  The first was reported as:  “Checking pedigree integrity...

ERROR: Pedigree Sample1: member 1 has unknown sex (0)

…"

Mega2 is requiring that the members’ sex be specified.  This failure leads to the error which terminates Mega2 at which time additional errors are noticed.  To handle the first error, you could use the PLINK option to generate/guess the member sex (—impute-sex) if that makes sense for your data (e.g., if you have typed enough markers so as to be able to accurately estimate gender).  PLINK —impute-sex will generate a new ped file that can be used with Mega2 that will contain non zero sex entries.

The second problem you report 

sh: mega2log2html.pl: command not found

means that Mega2 was not installed completely on your system - in fact, it is likely that Perl is not installed on your system.  What platform are you running on?  Where is PERL installed?  and Where did you install the Mega2 tools when you ran the ./install.sh.