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How to fix this error when launching texindy in windows using TeXstudio editor?

I noticed that recently, when I launch texindy using the shortkey in TeXstudio F12 it throws an error:

Process started: texindy.exe

usage: texindy.pl [-V?h] [-qv] [-iglr] [-d magic] [-o outfile.ind] [-t log] \ [-L lang] [-C codepage] [-M module] [-I input] [idx0 idx1 ...] GNU-STYLE LONG OPTIONS FOR SHORT OPTIONS: -V / --version -? / -h / --help -q / --quiet -v / --verbose -i / --stdin -g / --german -l / --letter-ordering -r / --no-ranges -d / --debug (multiple times) (supported: script, keep_tmpfiles, markup, level=n) -o / --out-file -t / --log-file -L / --language -C / --codepage -M / --module (multiple times) -I / --input-markup (supported: latex, omega) C:\texlive\2013\bin\win32\runscript.tlu:650: command failed with exit code 1: perl.exe c:/texlive/2013/texmf-dist/scripts/xindy/texindy.pl

Process exited with error(s)  

Below is a screenshot of texindy configuration in TeXstudio:
enter image description here

When I use arara to compile there is no problem with xindy, here is the arara code:

% arara: xelatex: { shell: true }
% arara: makeglossaries
% arara: biber
% arara: xelatex: { shell: true }   
% arara: xelatex: { shell: true } 

This is an excerpt from arara log file.txt regarding xindy:

added glossary type 'main' (glg,gls,glo)
xindy  -L english -C utf8 -I xindy -M "phdmain" -t "phdmain.glg" -o "phdmain.gls" "phdmain.glo"
Opening logfile "phdmain.glg" (done)
Reading indexstyle...
Loading module "iaheC42kMp"...
Loading module "lang/english/utf8-lang.xdy"...
Loading module "lang/english/utf8.xdy"...
Finished loading module "lang/english/utf8.xdy".
Finished loading module "lang/english/utf8-lang.xdy".
Loading module "phdmain.xdy"...
Loading module "tex.xdy"...
Finished loading module "tex.xdy".
Finished loading module "phdmain.xdy".
Finished loading module "iaheC42kMp".
Finished reading indexstyle.
Finalizing indexstyle... (done)

This is an excerpt from the running messages while compiling the document successfully using arara:

Status: SUCCESS

Running MakeGlossaries...

makeglossaries version 2.07 (2013-06-17)
added glossary type 'main' (glg,gls,glo)
xindy  -L english -C utf8 -I xindy -M "phdmain" -t "phdmain.glg" -o "phdmain.gls" "phdmain.glo"

Opening logfile "phdmain.glg" (done)
Reading indexstyle...
Loading module "iaheC42kMp"...
Loading module "lang/english/utf8-lang.xdy"...
Loading module "lang/english/utf8.xdy"...
Finished loading module "lang/english/utf8.xdy".
Finished loading module "lang/english/utf8-lang.xdy".
Loading module "phdmain.xdy"...
Loading module "tex.xdy"...
Finished loading module "tex.xdy".
Finished loading module "phdmain.xdy".
Finished loading module "iaheC42kMp".
Finished reading indexstyle.
Finalizing indexstyle... (done)

Reading raw-index "oxOB1i9YoU"...
Finished reading raw-index.

Processing index... [10%] [20%] [30%] [40%] [50%] [60%] [70%] [80%] [90%] [100%]
Finished processing index.

But as I said when I invoke xindy alone it throws the error mentioned in the beginning of the question.

So what am I missing here? how to fix this error?

Note:
TeXstudio version: 2.6.4
Xindy version: 2.4
Distribution TexLive2013