MISA : Issue with misa

[Wkutti]

Hello..

I am new to this field. I was using MISA combined with primer3 for generating markers. For testing the tool I used the sequence of 'SOPF01000005.1', which is downloaded from ncbi. I used the follwing command to genrate the '.misa' file. It worked fine and I got the 'SOPF01000005.fasta.misa' and 'SOPF01000005.fasta.statistics' as output file, which contains valid data.

perl misa.pl "SOPF01000005.fasta"

Now from the above 'SOPF01000005.fasta.misa'. I tried to generate the 'SOPF01000005.fasta.p3in' file using the following command. The file is generated but it has 0 record in it.

perl p3_in.pl "SOPF01000005.fasta.misa"

Can anybody help me in this matter.

Some content of SOPF01000005.fasta.misa
-----------------------------------------------------------
ID SSR nr. SSR type SSR size start end
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 1 p1 (T)10 10 77 86
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 2 p1 (A)10 10 814 823
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 3 p2 (TC)11 22 1034 1055
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 4 c (T)10c(A)11 22 1304 1325
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 5 p2 (AC)9 18 1881 1898
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 6 p3 (TCC)5 15 3195 3209
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 7 c (T)12gatgaa(T)10 28 4259 4286
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 8 p1 (A)11 11 8990 9000
SOPF01000005.1_Hypericum_perforatum_isolate_OBUPD-D1_Hpctg8,_whole_genome_shotgun_sequence 9 c (A)10gaaacaaagaacaagatt(A)12 40 9207 9246

Some content of SOPF01000005.fasta.statistics
----------------------------------------------------------------


Specifications
==============

Sequence source file: "SOPF01000005.fasta"

Definement of microsatellites (unit size / minimum number of repeats):
(1/10) (2/6) (3/5) (4/5) (5/5) (6/5)

Maximal number of bases interrupting 2 SSRs in a compound microsatellite: 100



RESULTS OF MICROSATELLITE SEARCH
================================

Total number of sequences examined: 1
Total size of examined sequences (bp): 251776
Total number of identified SSRs: 113
Number of SSR containing sequences: 1
Number of sequences containing more than 1 SSR: 1
Number of SSRs present in compound formation: 13