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:
I think I am getting anomalous (no records created) output from PRIMER3IN because it says:
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.
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
Copyright (c) 1996,1997,1998,1999,2000,2001,2004
Whitehead Institute for Biomedical Research. All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. Redistributions of
source code must also reproduce this information in the source code itself.
2. If the program is modified, redistributions must include a notice
(in the same places as above) indicating that the redistributed program is
not identical to the version distributed by Whitehead Institute.
3. All advertising materials mentioning features or use of this
software must display the following acknowledgment:
This product includes software developed by the
Whitehead Institute for Biomedical Research.
4. The name of the Whitehead Institute may not be used to endorse or
promote products derived from this software without specific prior written
permission.
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.
Code available at
http://fokker.wi.mit.edu/primer3/.
THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
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
============
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
Copyright (c) 1996,1997,1998,1999,2000,2001,2004
Whitehead Institute for Biomedical Research. All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. Redistributions of
source code must also reproduce this information in the source code itself.
2. If the program is modified, redistributions must include a notice
(in the same places as above) indicating that the redistributed program is
not identical to the version distributed by Whitehead Institute.
3. All advertising materials mentioning features or use of this
software must display the following acknowledgment:
This product includes software developed by the
Whitehead Institute for Biomedical Research.
4. The name of the Whitehead Institute may not be used to endorse or
promote products derived from this software without specific prior written
permission.
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.
Code available at
http://fokker.wi.mit.edu/primer3/.
THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND ANY
EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
SUCH DAMAGE.
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
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
Use of uninitialized value $count in concatenation (.) or string at C:\primerpro
/script/p3in.pl line 34, <SRC> chunk 52142.
records created.
DONE
I am using primerpro for windows. My OS is Windows 7 64-bit.
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