Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • primerpro PRIMER3IN no records created

    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

    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
    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.

  • #2
    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.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-27-2024, 06:37 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X