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

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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

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.

Post Situation: 
Fri, 2015-10-09 10:48

This message appears to tell you that some of the options you specified weren't ever used by Rosetta. This either means that you specified extra options that weren't needed for the protocol, or that the protocol you think you're running isn't actually working the way you expect it. In either case, you should take a look at things and make sure that everything is working the way you expect it to.

I'm not sure why you're getting this message. It could be that there is some error with the run, such that you never get to the point where the options are needed. Or you might not be processing any files, in which case the protocol never uses any of the options. Are there other messages that get printed out before/after the unused option message? Are you getting any structure output at all?

Mon, 2015-10-12 14:16

Hi Rmoretti.

I'm using the script demo located in /rosetta/demos/public/homology_modeling_threading_basic 

You get no message or previous warning, just the normal information when you run the program. the output is also correct.
That left me with fear if the script assembly is correct or if I'm putting flags unnecessary.

Fri, 2015-10-16 10:57