RepeatModeler Error

[fahmida]

Hi,

I've properly installed RepeatModeler and all the required libraries and external programs. It seems it can create the database, however in the second stage RepeatModeler is generating the error as shown below.

I've checked the fasta input file and the database created. Both are ok(as I checked 'blast' is working fine with the database)

1)
BuildDatabase -name sample -engine ncbi sample.fa
-------
Building database sample:
Adding sample.fasta to database
Number of sequences (bp) added to database: 28319 ( 247822612 bp )
--------
2)
RepeatModeler -database sample

----
.....
.....
Error: Unrecognized format specification: '%i'
Error: Unrecognized format specification: '%i'
Error: Unrecognized format specification: '%i'
RepeatModeler Version open-1.0.7
================================
Search Engine = ncbi
Database = sample
Database sample does not contain any sequences!
-----


Any help or suggestions?

[poxley]

I know this answer comes too late for fahmida, but for any future answer seekers:

The error is due to RepeatModeler sending the wrong input into blastdbcmd. It looks at the blastdbcmd version, and if it is not 2.2.23+, it asks for the output format '%i' instead of '%t'. If your version of blastdbcmd is 2.2.25+ however, it doesn't understand this format, and issues the error (probably because at the time of coding 2.2.23 was the only version with the new format?)

My solution was to change the code in RepeatModeler so that it looked for version 2.2.25+ (my version) instead of 2.2.23+. This seems to have correctly solved the issue.

[fahmida]

Cheers poxley, got it sorterd.

[Lventur]

Dear fahmida, may I ask how did you get it sorted? I am stuck with the program constantly giving this to me as output:

RepeatModeler Round # 1
========================
Searching for Repeats
-- Sampling from the database...
- Gathering up to 40000000 bp
- Final Sample Size = 0 bp ( 0 non ambiguous )
- Num Contigs Represented = 0
-- Running RepeatScout on the sequences...
Can't take log of 0 at /opt/RepeatModeler/RepeatModeler-debug line 1098.

I have already corrected the "version" issue, and tried with different input files (genome files, sequences retrieved directly from GenBank such as the elephant.fa used in the example, etc.)