The following options have been set but have not yet been used

Hi guys...

I'm using the Basic Homology Modeling, and received this massage on the final of the execution.

protocols.jd2.JobDistributor: WARNING: The following options have been set, but have not yet been used:
        -in:file:frag3 3rvyCH1_03_05.200_v1_3
        -in:file:frag9 3rvyCH1_09_05.200_v1_3
        -in:file:psipred_ss2 3rvyCH1.ss2
        -loops:frag_files  3rvyCH1_09_05.200_v1_3 3rvyCH1_03_05.200_v1_3 none
        -out:output 
        -out:pdb 

Here is my script

/home/jrcf/rosetta/main/source/bin/minirosetta.linuxgccrelease \
-run:protocol threading \
-in:file:alignment 3rvyCH13rvy.aln \
-cm:aln_format general \
-frag3 3rvyCH1_03_05.200_v1_3 \
-frag9 3rvyCH1_09_05.200_v1_3 \
-in:file:fasta 3rvyCH1.fasta \
-in:file:fullatom \
-loops:frag_sizes 9 3 1 \
-loops:frag_files 3rvyCH1_09_05.200_v1_3 3rvyCH1_03_05.200_v1_3 none \
-in:file:psipred_ss2 3rvyCH1.ss2 \
-in:file:fullatom \
-nstruct 1 \
-in:file:template_pdb 3rvy.pdb \
-database /home/jrcf/rosetta/main/database \
-loops:extended \
-loops:build_initial \
-loops:remodel quick_ccd \
-loops:refine refine_ccd \
-random_grow_loops_by 4 \
-select_best_loop_from 1 \
-out:file:fullatom \
-out:output \
-out:file:scorefile threaded_model.fasc \
-run:constant_seed \
-run:jran 1111111 \
-ignore_unrecognized_res \
-overwrite \
-out:pdb \
-out:path /home/jrcf/fragmentfile/3rvyCH1/pdb/

Someone can tell me why this message appears ? really not form the necessary files?

Thank's everyone.