You are here

Antibody job failed

2 posts / 0 new
Last post
Antibody job failed
#1

Hello,

I submitted an antibody task to the ROSIE server (job ID 101598) and it failed with the following error:

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: EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPAFGQGTKVEIK
Heavy chain: QLQLQESGPGLVKPSETLSLTCTVSGGSINSSSYYWGWLRQSPGKGLEWIGSFFYTGSTYYNPSLRSRLTISVDTSKNQFSLMLSSVTAADTAVYYCARQSTYYYGSGNYYGWFDRWDQGTLVTVSS
L1 detected: RASQSVSSYLA (11 residues at positions 23 to 33)
L3 detected: QQRSNWPPA ( 9 residues at positions 88 to 96)
L2 detected: DASNRAT (7 residues at positions 49 to 55)
FR_L1:  EIVLTQSPATLSLSPGERATLSC
FR_L2:  WYQQKPGQAPRLLIY
FR_L3:  GIPARFSGSGSGTDFTLTISSLEPEDFAVYYC
FR_L4:  FGQGTKVEIK
L segments:  EIVLTQSPATLSLSPGERATLSC RASQSVSSYLA WYQQKPGQAPRLLIY DASNRAT GIPARFSGSGSGTDFTLTISSLEPEDFAVYYC QQRSNWPPA FGQGTKVEIK
H1 detected: GGSINSSSYYWG (12 residues at positions 25 to 36)
H3 detected: False
ERROR: CDR H3 cannot be recognized !!!  H3 pattern: C[A-Z]{1,33}(W)(G|A|C)[A-Z]{1,2}(Q|S|G|R)

 

Does anybody know why I am getting this error?

 

Thanks,

Lara

Post Situation: 
Fri, 2022-03-25 11:04
larae

For RosettaAntibody to work, it needs to be able to figure out where the CDRs in your antibody are. It does this with sequence-based patterns which represent the conserved motifs which indicate the beginning and end of the CDRs for the vast majority of antibodies.

However, not all antibodies have these patterns. If you have an antibody which does not match this pattern, then you'll have to do something else to let Rosetta know how to model things. The ROSIE online server is set up for the simple cases, and probably will not work for these more complex cases. You may need to install Rosetta locally and run things on your own machines.

Tue, 2022-03-29 15:14
rmoretti