protocols.jd2.JobDistributor: [ ERROR ]

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    • April 11, 2019 at 4:30 pm #3114
      Anonymous

        Hi I met the error “protocols.jd2.JobDistributor: [ ERROR ] ” when I run antibody_designer of RAbD, that I tried to use 3ogo.pdb (renumbered with PyIgClassify), which is a nanobody-antigen complex structure, as input.

        Has anyone come across the same error before?

        My command was:

        /home/cltam/Desktop/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/antibody_designer.static.linuxgccrelease -s 3ogoOut.pdb -primary_cdrs H3 -graft_design_cdrs H3 -seq_design_cdrs H1 H2 -allow_omega_mismatches_for_north_clusters

        Thanks in advance!

         

      • April 11, 2019 at 4:33 pm #14655
        Anonymous

          Hey Johnny!

           

          Can you include the full output here?  I’ve never seen an error like this before. 

        • April 11, 2019 at 4:40 pm #14656
          Anonymous

            Make sure to include the -nstruct option.

            • April 13, 2019 at 2:01 pm #14657
              Anonymous

                I used the following command:

                /home/cltam/Desktop/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/antibody_designer.static.linuxgccrelease -s both-prepwizarded_remove-ACE-NMA.pdb -primary_cdrs H3 -graft_design_cdrs H3 -seq_design_cdrs H1 H2 -allow_omega_mismatches_for_north_clusters -nstruct 10

                Which gave me the following error message with highlight (other than as shown, no other errors appeared):

                …

                antibody.AntibodyInfo: Setting up CDR Cluster for H1

                protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT

                antibody.AntibodyInfo: Setting up CDR Cluster for H2

                protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTTTT

                antibody.AntibodyInfo: Setting up CDR Cluster for H3

                protocols.antibody.cluster.CDRClusterMatcher: Length: 15 Omega: TTTTTTTTCTTTTTT

                protocols.antibody.clusters.CDRClusterSet: Adding cacheable cluster data to pose

                protocols.antibody.NativeAntibodySeq: Setting full pose sequence

                protocols.jd2.JobDistributor: [ ERROR ] 

                [ERROR] Exception caught by JobDistributor for job both-prepwizarded_remove-ACE-NMA_0001

                File: src/protocols/antibody/AntibodyInfo.cc:1117

                L1 start resnum not found in pose: 24 L  

                Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB. 

                This could also mean missing density in the cdr loop.  Loop modeling applications can be used to fill missing residues 

                protocols.jd2.JobDistributor: [ ERROR ] 

                protocols.jd2.JobDistributor: [ WARNING ] both-prepwizarded_remove-ACE-NMA_0001 reported that its input was bad and will not retry

                protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: both-prepwizarded_remove-ACE-NMA_0001

                protocols.jd2.JobDistributor: no more batches to process… 

                protocols.jd2.JobDistributor: 10 jobs considered, 1 jobs attempted in 2 seconds

                Error: [ ERROR ] ERROR: Exception caught by antibody_design application:

                File: src/protocols/jd2/JobDistributor.cc:329

                1 jobs failed; check output for error messages

                 

                Although I have already used schrodinger prepwizard to fill loops for both my antibody (already renumbered with PyIgClassify) and antigen, I still got the same error message.

                Do you have any idea what happened?

                Thank you!

            • April 15, 2019 at 5:56 pm #14658
              Anonymous

                Hey Johnny,

                Can you send me an email with the inputs?  I’ll try this locally and try to see what the problem is . Can you also try with these options?   I use these for most of my work in Rosetta:

                -ignore_unrecognized_res

                -ignore_zero_occupancy false

                -load_PDB_components false

                 

                Thanks,

                -Jared

              • April 16, 2019 at 4:15 pm #14662
                Anonymous

                  This has been fixed in a branch and will be available in the next weekly release of Rosetta. 

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