Antibody submit script, running with args: {
  "antibody_assemble_exe": "/home/rosie/rosie/rosie.back/data/antibody/antibody_assemble_CDRs.static.linuxgccrelease", 
  "antibody_model_cdr_h3_exe": "/home/rosie/rosie/rosie.back/data/antibody/antibody_model_CDR_H3.static.linuxgccrelease", 
  "antibody_root": "/home/rosie/rosie/rosie.back/data/antibody", 
  "blast": "/home/rosie/prefix/blast+/bin/blastp", 
  "daemon_id": "GrayLab.Jazz", 
  "data": "/home/rosie/rosie/rosie.back/data", 
  "debug": false, 
  "here": "/home/rosie/rosie/rosie.back", 
  "profit": "profit", 
  "rosetta_database": "/home/rosie/rosie/rosie.back/data/antibody/rosetta_database", 
  "scripts": "/home/rosie/rosie/rosie.back/data/antibody/scripts", 
  "working_dir": "/home/rosie/rosie/rosie.back/Jobs/Job_01280/"
}
Antibody job input json: {
  "model_h3_loop": true
}
Running Antibody script...
 /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody.py --light-chain input/light_chain.fasta --heavy-chain input/heavy_chain.fasta --blast /home/rosie/prefix/blast+/bin/blastp --blast-database /home/rosie/rosie/rosie.back/data/antibody/scripts/blast_database --antibody-database /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database --profit profit --prefix=output/  --antibody-assemble /home/rosie/rosie/rosie.back/data/antibody/antibody_assemble_CDRs.static.linuxgccrelease --rosetta-database /home/rosie/rosie/rosie.back/data/antibody/rosetta_database
Rosetta Antibody script [Python, version 2.0]. Starting...
Prefix: output/
antibody_assemble: /home/rosie/rosie/rosie.back/data/antibody/antibody_assemble_CDRs.static.linuxgccrelease
Blast database: /home/rosie/rosie/rosie.back/data/antibody/scripts/blast_database
Antibody database: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database

Light chain: 'ENVLTQSPAIMSASPGEKVTMTCRASSSVSSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYSGYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE'
Heavy chain: 'AVQLEQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKERFAFSLETSASAAYLQINNLKNEDTATYFCARDYYGSTYPYYAMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG'

Running blast as: /home/rosie/prefix/blast+/bin/blastp
With datbase in:/home/rosie/rosie/rosie.back/data/antibody/scripts/blast_database
The template for FRL is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1eo8_chothia.pdb
The template for FRH is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb2adf_chothia.pdb
The template for light is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1v7m_chothia.pdb
The template for heavy is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb3ojd_chothia.pdb
The template for L1 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1ors_chothia.pdb
The template for L2 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb3oz9_chothia.pdb
The template for L3 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb2b2x_chothia.pdb
The template for H1 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb4d9q_chothia.pdb
The template for H2 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1a4j_chothia.pdb
The template for H3 is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb2qhr_chothia.pdb
The template for light_heavy is derived from: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database/pdb1uwx_chothia.pdb

Running antibody_assemble as: /home/rosie/rosie/rosie.back/data/antibody/antibody_assemble_CDRs.static.linuxgccrelease
With rosetta_datbase in:/home/rosie/rosie/rosie.back/data/antibody/rosetta_database

Prepare hfr.pdb