Error Interface analyser

[Anonymous]

Hi people,

I’m trying to use the interfaceAnalyzer, but this error is showing.

This is the script I run

obs. I don’t know why the output score doesn’t make.

-out:levels all:warning core.init:info protocols.jd2.JobDistributor:info

-s all_0001Giro_90.pdb

-nstruct 10000

-partners P_A

-dock_pert 3 8

-spin false

-ex1

-ex2aro

-use_input_sc

-ignore_unrecognized_res

-ignore_zero_occupancy false

-out:file:silent_struct_type binary

-out:file:silent all_0001Giro_90.out

-overwrite

-score:docking_interface_score 1

This is the script and the error

 

 ~/rosetta_bin_linux_2017.08.59291_bundle/main/source/bin/InterfaceAnalyzer.static.linuxgccrelease -in:file:silent all_0001Giro_90.out -out:file:silent_struct_type binary -ignore_unrecognized_res -ignore_zero_occupancy false -interface P_A -out:file:score_only interface.sc -compute_packstat -score:weights talaris2014.wts

core.init: Rosetta version unknown:3bdcad6272fdb86400b86da9e5673f3fa62656ec 2017-02-18 05:03:14 -0500 from /home/benchmark/release/rosetta/git/release/rosetta.binary.linux.release.git

core.init: command: /home/verena/rosetta_bin_linux_2017.08.59291_bundle/main/source/bin/InterfaceAnalyzer.static.linuxgccrelease -in:file:silent all_0001Giro_90.out -out:file:silent_struct_type binary -ignore_unrecognized_res -ignore_zero_occupancy false -interface P_A -out:file:score_only interface.sc -compute_packstat -score:weights talaris2014.wts

core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-415492664 seed_offset=0 real_seed=-415492664

core.init.random: RandomGenerator:init: Normal mode, seed=-415492664 RG_type=mt19937

core.init: Resolved executable path: /home/verena/rosetta_bin_linux_2017.08.59291_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/static/InterfaceAnalyzer.static.linuxgccrelease

core.init: Looking for database based on location of executable: /home/verena/rosetta_bin_linux_2017.08.59291_bundle/main/database/

core.io.silent.SilentFileData: Reading all structures from all_0001Giro_90.out

core.io.silent: ERROR: trying to index off the end of the secstruct array, idx is 1267 secstruct_.size() is 1266

Error: ERROR: Exception caught by JobDistributor while trying to fill the input jobs with JobInputter of type type ‘SilentFile’

Error: failure to read decoy all_0001Giro_90_08551 from silent-file all_0001Giro_90.out

Error: 

ERROR:: Exit from: src/protocols/jd2/JobDistributor.cc line: 1135

[0x1383de8]

[0x533dbcf]

[0xce355a]

[0x33b8cc1]

[0x33b949f]

[0x33bd562]

[0x344f990]

[0x33be456]

[0x33bda20]

[0x410c4c]

[0x5826694]

[0xabfb9d]

caught exception 

[ERROR] EXCN_utility_exit has been thrown from: src/protocols/jd2/JobDistributor.cc line: 1135

 

Thanks

Tips????

[Anonymous]

This has nothing to do with Interface Analyzer – all Rosetta modes will fail.  Your silent file is corrupt.

What went in to the silent file?  When I’ve had this secstruct array error before, it was because I accidentally embedded poses of different lengths into the same silent file (which apparently you can’t do).  I assume the first command line is the docking command you used to create the silent file (which looks fine to me), except that overwrite and silent files don’t go together.

Look at the decoy all_0001Giro_90_08551 , which is the one with the error.  Is it cut off in some way?  Can you just delete it from the file manually and see if the rest of the file is ok?  Is there more than one copy of the decoy due to -overwrite?

[Anonymous]

This has nothing to do with Interface Analyzer – all Rosetta modes will fail.  Your silent file is corrupt.

What went in to the silent file?  When I’ve had this secstruct array error before, it was because I accidentally embedded poses of different lengths into the same silent file (which apparently you can’t do).  I assume the first command line is the docking command you used to create the silent file (which looks fine to me), except that overwrite and silent files don’t go together.

Look at the decoy all_0001Giro_90_08551 , which is the one with the error.  Is it cut off in some way?  Can you just delete it from the file manually and see if the rest of the file is ok?  Is there more than one copy of the decoy due to -overwrite?

[Anonymous]

This has nothing to do with Interface Analyzer – all Rosetta modes will fail.  Your silent file is corrupt.

What went in to the silent file?  When I’ve had this secstruct array error before, it was because I accidentally embedded poses of different lengths into the same silent file (which apparently you can’t do).  I assume the first command line is the docking command you used to create the silent file (which looks fine to me), except that overwrite and silent files don’t go together.

Look at the decoy all_0001Giro_90_08551 , which is the one with the error.  Is it cut off in some way?  Can you just delete it from the file manually and see if the rest of the file is ok?  Is there more than one copy of the decoy due to -overwrite?

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