primerpro PRIMER3IN no records created

[cdseq]

I am trying to run primerpro v-1.0 but no records were created for the following file:

1. *.fasta.results.primerblast
2. *.fasta.results.csv

In the above files, only headers were created. File size is only 1kb for each file.

I tried it with the example.fasta (file included when downloaded) and I got the expected results. The error that I am receiving is:

PRIMER3IN
============

Preparing input for primer3
Use of uninitialized value $count in concatenation (.) or string at C:\primerpro
/script/p3in.pl line 34, <SRC> chunk 52142.

records created.
DONE

PRIMER3
=============

Running Primer3

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4. The name of the Whitehead Institute may not be used to endorse or
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We also request that use of this software be cited in publications as

Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users
and for biologist programmers." In S. Krawetz and S. Misener, eds.
Bioinformatics Methods and Protocols in the series Methods in
Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386.
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USAGE: C:\primerpro/primer3/primer3 [-format_output] [-2x_compat] [-strict_tags]

This is primer3 (primer3 release 1.0)
Input must be provided on standard input.
For example:
$ primer3_core < my_input_file
Can't spawn "cmd.exe": Inappropriate I/O control operation at C:\primerpro\prime
rpro.pl line 121, <PARAM> line 78.
DONE

PRIMER3OUT
=============

Formating primer3 outputUse of uninitialized value $count in concatenation (.) o
r string at C:\primerpro/script/p3out.pl line 76.

Primer modelling was successful for sequences.
Use of uninitialized value $count_failed in concatenation (.) or string at C:\pr
imerpro/script/p3out.pl line 77.
Primer modelling failed for sequences.
DONE

I think I am getting anomalous (no records created) output from PRIMER3IN because it says:

Preparing input for primer3
Use of uninitialized value $count in concatenation (.) or string at C:\primerpro
/script/p3in.pl line 34, <SRC> chunk 52142.

records created.
DONE

I have no idea how to solve this problem. Any help will be very much appreciated.

I am using primerpro for windows. My OS is Windows 7 64-bit.

[Sythe]

I had this problem when running the unix version of primerpro v1.0 on command line.
Have you tried changing the supplied version of PRIMER3 to version 1.1.3? In versions of PRIMER3 +2.0, there was a change in how input tags for sequences were handled (I think they changed the SEQUENCE tag to SEQUENCE_TEMPLATE in the later versions). I also needed to swap out blast for version 2.2.23 in order to create *.primerblast files.

Try making these changes and modifying the config.txt file to point to updated versions.