fragment_picker problem

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    • December 18, 2012 at 9:15 am #1488
      Anonymous

        Hi,
        I’m trying to run fragmet_picker on my sequence using this commnad:

        /home/advas/tools/rosetta3.4/rosetta_source/bin/fragment_picker.linuxgccrelease -database /home/advas/tools/rosetta3.4/rosetta_database -in::file::vall /home/advas/tools/rosetta3.4/rosetta_tools/fragment_tools/vall.jul19.2011 -in::file::fasta 2anna.fasta -frags::ss_pred 2anna.psipred_ss2 predA -frags::scoring::config simple.wghts -frags::bounded_protocol -frags::frag_sizes 9 3 -frags::n_candidates 200 -frags::n_frags 200 -out::file::frag_prefix frags -frags::describe_fragments frags.fsc

        my sequence is
        >2anna
        VDKKKYLWILSTLWPATPMIGIWLANETGWGIFYGLVLLVWYGALPLLDAMFGEDFNNPPEEVVPKLEKERYYRVLTYLTVPMHYAALIVSAWWVGTQPMSWLEIGALALSLGIVNGLALNTGHELGHKKETFDRWMAKIVLAVVGYGHFFIEHNKGHHRDVAVWSFDNEILQPMIITVILYAVLLALFGPKMLVFLPIQMAFGWWQLTSANYIEHYGLLRQKME

        after changing the fasta file so the sequence will be in one line I got rosetta to read the whole sequence
        but then after it creates the fragment scoring scheme I get this error:

        ERROR: pos <= total_residue_
        ERROR:: Exit from: src/core/fragment/SecondaryStructure.hh line: 93

        Can anyone help?

        Thanks,
        Adva

      • December 18, 2012 at 5:28 pm #8249
        Anonymous

          How many residues are in your FASTA file?

          How many residues are in your SS prediction files?

        • December 23, 2012 at 11:52 am #8262
          Anonymous

            after trying lots of ways to solve the problem, I think there are few important things anyone should know before running fragment_picker:
            1. The fasta file should contain lines with maximum length of 50 amino acids (similar to the fasta file you get in Robetta’s output). It will read 1 long line of sequence but it won’t match the ss2 file.
            2. The ss2 file should be downloaded from psipred server. The file from Robetta’s results was not recognised!
            3. You must give a reference PDB structure. yes, even if you use fragment_picker for ab-initio…. because you dont have any template to work with… I used raptorX because it gave fast results. Rosetta will use it only for the RMSD column of the results, not for picking or scoring fragments so don’t worry.

            good luck!

          • December 4, 2013 at 4:12 pm #9544
            Anonymous

              I’ve been trying to run fragment_picker, and since it didn’t work with the fasta file and the ss2 file I took the ss scores out of the quota file. Now I get the following error:
              ERROR: pos <= profile_.size()
              ERROR:: Exit from: src/core/sequence/SequenceProfile.cc line: 319
              Can anyone help?
              Thanks,
              Sabine

            • December 19, 2012 at 7:53 am #8252
              Anonymous

                225 in both. no errors when reading the sequence…

              • December 19, 2012 at 7:19 pm #8256
                Anonymous

                  I’d check your SS prediction file – make sure that in addition to having only 225 residues, the residue numbers for each entry also doesn’t exceed 225. (The residues should be sequentially numbered starting from 1, rather than any sort of non-zero origin “pdb” numbering.)

                  The other suggestion is to compile in debug mode, and re-run the program. Often there’s some safety check triggered in the debug mode which makes tracking down the problem easier.

                • December 20, 2012 at 9:25 am #8257
                  Anonymous

                    Residue numbers start from 1. no problem with the fasta or ss2 files.
                    here is what I get:

                    advas@adva:~/projects/anna/fragment_picker$ core.init: Mini-Rosetta version unknown from unknown
                    core.init: command: /home/advas/tools/rosetta3.4/rosetta_source/bin/fragment_picker.linuxgccrelease -database /home/advas/tools/rosetta3.4/rosetta_database -in::file::vall /home/advas/tools/rosetta3.4/rosetta_tools/fragment_tools/vall.jul19.2011 -in::file::fasta 4annA.fasta -frags::ss_pred 4annA.psipred_ss2 predA -frags::scoring::config simple.wghts -frags::bounded_protocol -frags::frag_sizes 9 3 -frags::n_candidates 200 -frags::n_frags 200 -out::file::frag_prefix frags -frags::describe_fragments frags.fsc
                    core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1486397136 seed_offset=0 real_seed=1486397136
                    core.init.random: RandomGenerator:init: Normal mode, seed=1486397136 RG_type=mt19937
                    protocols.frag_picker.FragmentPicker: reading a query sequence from: 4annA.fasta
                    protocols.frag_picker.FragmentPicker: picking fragments for query sequence: VDKKKYLWILSTLWPATPMIGIWLANETGWGIFYGLVLLVWYGALPLLDAMFGEDFNNPPEEVVPKLEKERYYRVLTYLTVPMHYAALIVSAWWVGTQPMSWLEIGALALSLGIVNGLALNTGHELGHKKETFDRWMAKIVLAVVGYGHFFIEHNKGHHRDVAVWSFDNEILQPMIITVILYAVLLALFGPKMLVFLPIQMAFGWWQLTSANYIEHYGLLRQKMED
                    protocols.frag_picker.VallProvider: vallChunksFromLibrary
                    protocols.frag_picker.VallProvider: Reading Vall library from /home/advas/tools/rosetta3.4/rosetta_tools/fragment_tools/vall.jul19.2011 … startline: 1 endline: 0
                    protocols.frag_picker.VallProvider: … done. Read 4126307 lines. Time elapsed: 45 seconds.
                    protocols.frag_picker.VallProvider: Total chunks: 25463
                    protocols.frag_picker.VallProvider: Largest chunk: 1264 aa
                    core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6225 residue types
                    protocols.frag_picker.FragmentPicker: Will pick fragments of size:9 3
                    protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_WP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_WP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_WP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_TP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_TP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_TP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_LP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_LP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_LP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_NP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_NP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_NP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_PP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_PP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_PP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_VP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_VP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_VP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_VP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_VP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_QP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_QP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_QP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_QP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_QP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_QP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_GP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_GP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_GP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_LP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_LP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_LP.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_F.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_H.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
                    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts

                    ERROR: query_prediction->total_residue() == query_len_
                    ERROR:: Exit from: src/protocols/frag_picker/scores/SecondarySimilarity.cc line: 132

                    What is LP , QP , GP ? why does rosetta read two amino acids together?

                  • December 20, 2012 at 10:55 am #8258
                    Anonymous

                      I also tried to run the debug mode using gdb.
                      the error is not that informative to me…

                      ERROR: query_prediction->total_residue() == query_len_
                      ERROR:: Exit from: src/protocols/frag_picker/scores/SecondarySimilarity.cc line: 132
                      fragment_picker.default.linuxgccdebug: src/utility/exit.cc:155: void utility::exit(const string&, int, const string&, int): Assertion `false’ failed.

                      Program received signal SIGABRT, Aborted.
                      0x00002aaaace5c425 in raise () from /lib/x86_64-linux-gnu/libc.so.6

                    • December 20, 2012 at 3:35 pm #8260
                      Anonymous

                        To your first question: You may notice that all the doubled types end in proline. The Ramachandran table is notably different near proline; this represents the use of a tweaked table for pre-proline positions.

                        To your second question: This narrows it down to the SecondarySimilarity class, but it’s still clearly a length mismatch – two arguments are coming in to the class where one thing says “length X” and one thing says “length Y”. You can try turning off SecondarySimilarity in your simple.wghts weights file; this may dodge the problem (but will probably result in inferior fragments).

                      • December 4, 2013 at 3:28 pm #9542
                        Anonymous

                          I have the same error message as you described. I’ve tried to reformat the fasta file the way you describe it, but still can’t make it work. Could you please elaborate exactly how you formatted your fasta file so it worked? I have the same amount of residues in each file and created my ss2 file using psipred. In the output I can see that my sequence is read correctly, but in the end I either get the query_len error or just a segmentation fault. Hope you can give me some advise!

                        • December 4, 2013 at 4:15 pm #9545
                          Anonymous

                            Hi sabine,

                            If you’re willing to post your commandline and input files, as attachments to the forum (rename them with a .txt extension), I can try tracking down the issue locally.

                          • December 4, 2013 at 4:56 pm #9546
                            Anonymous

                              Hi,
                              thanks for taking a look at the problem. Attached are my input files (fasta and ss2), quota, weight file etc and my command line input. Please let me know if you need anything else!
                              Thanks,
                              Sabine

                            • December 5, 2013 at 6:50 pm #9548
                              Anonymous

                                Unfortunately, I can’t seem to reproduce the error you’re seeing — I get a segmentation fault instead. ;( I think I tracked down the issue, though. You’ve got several things going on here.

                                The first is that you’re trying to use the SecondarySimilarity scorer for psipred, sam, and porter, but are only giving the secondary structure predictions for psipred. Remove the sam and porter lines from the quota_scores.wghts file to fix this.

                                The other issue is that you’re using the ProfileScoreL1 scorer, but you aren’t giving a PSSM profile with the -in::file::pssm flag. Remove the ProfileScoreL1 from your quota_scores.wghts file.

                                Removing those 5 lines from the quota_scores.wghts file and re-running results in the run going to completion with rosetta3.4

                                The fact that you don’t get a decent error message is certainly a bug, and I’ll try to get those corrected for future releases.

                              • December 9, 2013 at 6:56 pm #9566
                                Anonymous

                                  Thank you for the clarification. It’s running fine now.

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