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Antibody prediction with ROSIE failed

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Antibody prediction with ROSIE failed
#1

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

Post Situation: 
Wed, 2017-08-02 23:45
Sunyp_IM

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?

Thu, 2017-08-03 11:50
Sergey

The job number is 33960

Thu, 2017-08-03 19:16
Sunyp_IM