Antibody prediction with ROSIE failed

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    • August 3, 2017 at 6:45 am #2709
      Anonymous

        Dear all,

        I submitted the sequeces for the variable regions of the heavy and light chains of a antibody to ROSIE in order to predict the 3d structures. However when the job finished there seemed no structure output. The following is the output message: 


        
Antibody script failed with message: Rosetta Antibody script [Python, version 2.0]. Starting...
        
Could not find output/details/... creating it...
        
Output prefix: output/
        
Blast database: /home/rosie/rosie/rosie.back/data/antibody/scripts/blast_database
        
Antibody database: /home/rosie/rosie/rosie.back/data/antibody/scripts/antibody_database
        
rosetta_bin: /home/rosie/rosie/rosie.back/data/antibody/bin  [platform: static.linuxgccrelease]
        
rosetta_database: /home/rosie/rosie/rosie.back/data/antibody/rosetta_database
        
Using full antibody database (no homolog exclusion)
        
Idealize: False
        
Relax: True
        

        
Light chain: DVVMTQSPSFLSASVGDRVTITCRASQDITINLNWFQHKPGKAPKRLIYVASRLERGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQYNNYPLTFGPGTKLDIKRTV
        
Heavy chain: EVQLVQSGGGLVQPGGSMRLSCEASGLSLSDYFMHWVRQAQGKGLEWIGLIQTKAFTYKTEYPAAVKGRFTISRDDSKNTLYLQMSSLKPEDTALYYCIAVTPDFYYWGQGVLVTVSS
        
L1 detected: RASQDITINLN (11 residues at positions 23 to 33)
        
L3 detected: QQYNNYPLT ( 9 residues at positions 88 to 96)
        
L2 detected: VASRLER (7 residues at positions 49 to 55)
        
FR_L1:  DVVMTQSPSFLSASVGDRVTITC
        
FR_L2:  WFQHKPGKAPKRLIY
        
FR_L3:  GVPSRFSGSGSGTEFTLTISSLQPEDFATYYC
        
FR_L4:  FGPGTKLDIKRT
        
L segments:  DVVMTQSPSFLSASVGDRVTITC RASQDITINLN WFQHKPGKAPKRLIY VASRLER GVPSRFSGSGSGTEFTLTISSLQPEDFATYYC QQYNNYPLT FGPGTKLDIKRT
        
H1 detected: GLSLSDYFMH (10 residues at positions 25 to 34)
        
H3 detected: VTPDFYY (7 residues at positions 100 to 106)
        
H2 detected: LIQTKAFTYKTEYPAAVKG (19 residues at positions 49 to 67)
        
FR_H1:  EVQLVQSGGGLVQPGGSMRLSCEAS
        
FR_H2:  WVRQAQGKGLEWIG
        
FR_H3:  RFTISRDDSKNTLYLQMSSLKPEDTALYYCIA
        
FR_H4:  WGQGVLVTVSS
        
H segments:  EVQLVQSGGGLVQPGGSMRLSCEAS GLSLSDYFMH WVRQAQGKGLEWIG LIQTKAFTYKTEYPAAVKG RFTISRDDSKNTLYLQMSSLKPEDTALYYCIA VTPDFYY WGQGVLVTVSS
        

        
Running /home/rosie/prefix/blast+/bin/blastp
        
I: Queryname=FRL
        
I: Found 600 blast results (limit 600)
        
Could not find output/details/filters/... creating it...
        

        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
FRL template: pdb1dql_chothia.pdb
        
I: Queryname=FRH
        
I: Found 600 blast results (limit 600)
        

        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
FRH template: pdb3eot_chothia.pdb
        
I: Queryname=light
        
I: Found 600 blast results (limit 600)
        

        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
light template: pdb3uc0_chothia.pdb
        
I: Queryname=heavy
        
I: Found 600 blast results (limit 600)
        

        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
heavy template: pdb1ad0_chothia.pdb
        
I: Queryname=L1
        
I: Found 342 blast results (limit 600)
        

        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
L1 template: pdb1ikf_chothia.pdb
        
I: Queryname=L2
        
I: Found 70 blast results (limit 600)
        

        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
L2 template: pdb1ai1_chothia.pdb
        
I: Queryname=L3
        
I: Found 170 blast results (limit 600)
        

        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
L3 template: pdb2cmr_chothia.pdb
        
I: Queryname=H1
        
I: Found 22 blast results (limit 600)
        

        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
H1 template: pdb1uj3_chothia.pdb
        
I: Queryname=H2
        
I: Found 58 blast results (limit 600)
        

        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
H2 template: pdb2bmk_chothia.pdb
        
I: Queryname=H3
        
I: Found 0 blast results (limit 600)
        

        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        

        
WARNING: No template avaliable for H3 after filtering! Using a random template of the same length as the query
        

        
H3 template: pdb2xkn_chothia.pdb
        
I: Queryname=light_heavy
        
I: Found 600 blast results (limit 600)
        

        
light_heavy template: pdb1dql_chothia.pdb
        
light_heavy template: pdb1dee_chothia.pdb
        
light_heavy template: pdb1hez_chothia.pdb
        
light_heavy template: pdb2wuc_chothia.pdb
        
light_heavy template: pdb3eo9_chothia.pdb
        
light_heavy template: pdb3bn9_chothia.pdb
        
light_heavy template: pdb3k2u_chothia.pdb
        
light_heavy template: pdb3skj_chothia.pdb
        
light_heavy template: pdb1dfb_chothia.pdb
        
light_heavy template: pdb1jpt_chothia.pdb
        

        
Running ProFit...
        
profit < output/details/profit-H.in > output/details/profit-H.out sh: /bin/profit: Permission denied

         

        Could anyone tell me why the job failed?  And how at the end Running ProFit got  “Permission denied” error?

        Best regards

        Yeping Sun

      • August 3, 2017 at 6:50 pm #13645
        Anonymous

          Thank you for letting us know! This looks like a server error, could you please tell me the job number so we can troubleshoot it?

        • August 4, 2017 at 2:16 am #13646
          Anonymous

            The job number is 33960

          • May 8, 2019 at 11:10 pm #14703
            Anonymous

              Hi Sergey,

              I just ran into the very same problem with job no 69652 .  Has anybody placed an additional installation of profit into /bin ?

              Cheers,

              Steffen

            • May 9, 2019 at 3:15 pm #14704
              Anonymous

                This shold be fixed now. Could you please try to re-submit your jobs?

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