[Bio-Linux] msatfinder pipeline fails to find primers

[Jeremy Shearman]

I recently tried msatfinder in bio-linux7 to compare it to misa that a colleague used. Msatfinder seemed to find all the same microsatellite sequences but on my system completely failed to produce primers with the message "No valid primers found for ..." printed to the terminal. I know there are valid primers because misa found them (but I don't know what versions of things) and when I took the fasta sequence from the msatfinder FASTA output folder, web based primer3 found several primer pairs.

To troubleshoot I took a random sequence from human chr1
(http://www.ncbi.nlm.nih.gov/nuccore/NC_000001.10?report=fasta&from=3556583&to=3665309) and ran msatfinder on it.

Here is the final microsat results from the terminal dump:
Found (taaa)5 msat at 104492:
FT   repeat_region   104492..104511
FT                   /label={taaa}5
FT                   /note="(taaa)5"
FT                   /note="Coding:  0"
FT                   /note="Gene:      N/A"
FT                   /note="Product: N/A"
FT                   /note="Protein: N/A"
Opening output file 224589800_3556583-3665309.msat_tab
Writing MINE file 224589800_3556583-3665309.104492.taaa.5.db
Opening fasta FILE Fasta/224589800_3556583-3665309.104492.taaa.5.fasta
Determining PCR primers.
Outfile: Primers/224589800_3556583-3665309.104492.taaa.5.primers.txt
Running command: /usr/bin/eprimer3 -sequence Primers/224589800_3556583-3665309.104492.taaa.5.temp -outfile Primers/224589800_3556583-3665309.104492.taaa.5.primers.txt -target 298,320 -primer
Unlinking file: Primers/224589800_3556583-3665309.104492.taaa.5.temp
No valid primers found for 224589800_3556583-3665309
-----


A total of 1 files surveyed
Hs_chr_1_3556583-3665309
Msatfinder finished!

When I then went to the FASTA file (224589800_3556583-3665309.104492.taaa.5.fasta) primer3 on the web gave primers.

I turned on debugging info in the msatfinder.rc file which caused the temp file in the primers folder to not get deleted, running eprimer3 with that file gives this error:

Error: Missing SEQUENCE tag

Anyone know what the problem is?

Cheers
Jeremy

Jeremy Shearman, PhD
à¨àÃÍÁÕè àªÕÂÃìáÁ¹
National Centre for Genetic Engineering and Biotechnology, NSTDA
113 Thailand Science Park, Phahonyothin Road, Klong1, Klong Luang, Pathumthani 12120
Ph: +66 2564 6700 ext. 3234       fax: +66 2564 6584

ReasearcherID: F-1618-2010
http://www.researcherid.com/rid/F-1618-2010
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