INPUT PROBLEM: Missing SEQUENCE tag -- error designing primers for repeats

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What steps will reproduce the problem?
1. any of My fasta file
2. the test fasta file that comes with msat commander
3.

I am running the latest version of msatcommander on Linux, Ubuntu 11.10. the 
program successfully finds the repeat regions and exports results to the search 
results output file.csv, but the primer 3 folder has just empty text files.  
All of the sequences that are in the search output are named as text files, but 
they are empty and say "input problem missing sequence tag".

Any ideas? I unpacked and tested the primer 3 libraries with the test script 
(passed all tests) and put the primer 3 core in the top of the msatcommander 
directory. No other errors were reported. 

Thanks,
Louis

Original issue reported on code.google.com by louis.pl...@gmail.com on 6 Feb 2012 at 10:34

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Louis,

can you tell me which version of msatcommander you are using and also which 
version of primer3 you are using?  If i know that, then i can begin to figure 
out what the issue might be...

Also, please ensure that msatcommander.conf is set correctly to provide the 
locations of the primer3_core binary and the other files required by primer3.  
the defaults are:

[paths]
primer3 = "./primer3_long"
primer3_config = "./primer3_config"
mispriming_library = "misprime_lib_weight"

Original comment by brant.fa...@gmail.com on 6 Feb 2012 at 11:43

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Hello,
I'm using msatcommander-0.8.2 and primer3-2-3-4 on Ubuntu 12.04. I have the 
same problem as above.
Where can I find the referred "same other files"?:
[paths]
primer3 = "./primer3_long"
primer3_config = "./primer3_config"
mispriming_library = "misprime_lib_weight"

Original comment by raul.ll...@gmail.com on 18 Dec 2012 at 2:13

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raul,

are you using the standard primer3?  try to build the primer3 here:

https://github.com/faircloth-lab/mod-primer3/ 
(https://github.com/faircloth-lab/mod-primer3/tree/long/src)

and then input the paths to this binary (which should compile to "primer3_long) 
in the configuration file.  my guess is that you're using the standard primer3, 
which does not allow for the design of longer, tagged primers.

alternatively, in libprimer3, you can edit the source to set:

#define MAX_PRIMER_LENGTH 55
#define MAX_NN_TM_LENGTH 55

and recompile primer3.  however, i don't recommend this because it can 
potentially cause problems when you use primer3 on its own.

-b

Original comment by brant.fa...@gmail.com on 18 Dec 2012 at 2:30

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Hi again;

thanks for the advise. I deleted my Primer3 version and compiled the modified 
version that you send me, without failure. However, I can't find the 
msatcommander.conf (or any other configuration file) for adding he paths. 
Should I change something inside the msatcommander.py file (as adding the 
paths) there?

Many many thanks!
Raúl

Original comment by raul.ll...@gmail.com on 19 Dec 2012 at 8:48

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I'm getting the above error and I've done the mentioned steps with out a 
resolution. Any other suggestions?

Original comment by ianmisne...@aim.com on 17 Jun 2013 at 5:26

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Are you sure that the paths to the modified version of primer3 are correct?  
Also, what operating system are you using and which version of msatcommander?

Original comment by brant.fa...@gmail.com on 17 Jun 2013 at 5:28