Binary silent Output file reading problem

[Anonymous]

Hi,all:

I have run an ab initio relax with binary silent output and encountered a reading problem from the outputfile.

The input looks like:
/rosetta_source/bin/AbinitioRelax.linuxiccrelease @flag

The flags are
-database /rosettatorun/rosetta_database
-in:file:fasta sec2.fasta
-in:file:frag3 ../../aat000_03_05.200_v1_3
-in:file:frag9 ../../aat000_09_05.200_v1_3
-abinitio:relax -relax:fast
-abinitio:increase_cycles 10
-abinitio::rg_reweight 0.5
-abinitio::rsd_wt_helix 0.5
-abinitio::rsd_wt_loop 0.5
-use_filters true
-psipred_ss2 ../../sec2.psipass2
-out:file:silent sec_2_1.out
-out:file:silent_struct_type binary
-nstruct 50
-seed_offset 10

It was disrupted and generated 40+ structures. (similar job for another 20 runs)

When I tried to combine these results by using:
/rosetta_source/bin/score_jd2.linuxiccrelease (or combine_silent.linuxiccrelease) @flag
the flags are:
-database /rosettatorun/rosetta_database
-in:file:silent sec_2_1.out
-in:file:silent_struct_type binary
-in:file:fullatom
-out:file:silent test.out
-out:file:fullatom
-out:file:silent_struct_type binary
-silent_read_through_errors
-overwrite

It gives me an Error which could not be passed without “-silent_read_through_errors” option:

core.io.silent: Reading all structures from sec_2_1.out
core.io.silent: ERROR: trying to index off the end of the secstruct array, idx is 353 secstruct_.size() is 352
core.io.silent: Finished reading 46 structures from sec_2_1.out
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9019 residue types
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue …
core.io.silent: [ WARNING ] (in residue 3 natoms_pose=19atm_seqpos 3 natoms_struct=11)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue …
core.io.silent: [ WARNING ] (in residue 4 natoms_pose=19atm_seqpos 4 natoms_struct=24)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue …
core.io.silent: [ WARNING ] (in residue 5 natoms_pose=19atm_seqpos 5 natoms_struct=15)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue …
core.io.silent: [ WARNING ] (in residue 8 natoms_pose=15atm_seqpos 8 natoms_struct=19)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue …
core.io.silent: [ WARNING ] (in residue 9 natoms_pose=11atm_seqpos 9 natoms_struct=24)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue …
core.io.silent: [ WARNING ] (in residue 10 natoms_pose=24atm_seqpos 10 natoms_struct=7)
core.io.silent: [ WARNING ] Number of atoms in pose and silent file disagree! Attempting to continue …
core.io.silent: [ WARNING ] (in residue 11 natoms_pose=19atm_seqpos 11 natoms_struct=10)

I am confused with such index-off-one problem. Did someone encountered similar situation before?

Thanks a lot!

Weilin

[Anonymous]

Solved.
After I print out “tag” in BinaryProteinSilentStruct.cc, I found a corrupt block in the middle of the binary file not at the end.

[Author]

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