0000301: seg fault at fragment picker

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Date Submitted

Last Update

0000301

Rosetta

[All Projects] Crash

public

2013-09-06 09:42

2013-09-06 09:45

Reporter

kimdn

Assigned To

Priority

high

Severity

crash

Reproducibility

always

Status

new

Resolution

open

Platform

x86

Linux

OS Version

Ubuntu

Product Version

Trunk

Fixed in Version

Summary

0000301: seg fault at fragment picker

Description

With
# score name priority wght max_allowed extras
RamaScore 400 2.0 - predA
SecondarySimilarity 350 1.0 - predA
FragmentCrmsd 450 1.0 1

it dumped core.

It seems that at least 3mers are produced (while 9mers are not produced).
I attach all input/output files (crmsd_has_1_wt_and_1_max_seg_fault.zip).

I copy report at additional information.

Steps To Reproduce

fragment_picker.linuxgccrelease @best-frags.flags @ trunk version id 55681

http://test.rosettacommons.org/revs?revs_tgp_no=2&revs_tgp_limit=31 [^]

Additional Information

kimdn@contador:~/scr/run/fragment_picker/native/1ten/frag_picker/BestFragmentsProtocol/w_manually_checked_ss/crmsd_be_highest_prio_value/crmsd_has_1_wt_and_1_max$ source run_example
core.init: Rosetta version 7db9a2230de5363b620fe9f992085c8077653ab5 2013-08-26 13:00:07 -0400 from kimdn@152.19.81.197:~/rosetta/main
core.init: command: fragment_picker.linuxgccrelease @best-frags.flags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=607751371 seed_offset=0 real_seed=607751371
core.init.random: RandomGenerator:init: Normal mode, seed=607751371 RG_type=mt19937
protocols.frag_picker.FragmentPicker: reading a query sequence from: input_files/seq_in_fasta
protocols.frag_picker.FragmentPicker: picking fragments for query sequence: LDAPSQIEVKDVTDTTALITWFKPLAEIDGIELTYGIKDVPGDRTTIDLTEDENQYSIGNLKPDTEYEVSLISRRGDMSSNPAKETFTT
protocols.frag_picker.VallProvider: vallChunksFromLibrary
protocols.frag_picker.VallProvider: Reading Vall library from /home/kimdn/rosetta/tools/fragment_tools/vall.apr24.2008.extended.gz ... startline: 1 endline: 0
protocols.frag_picker.VallProvider: ... done. Read 2330105 lines. Time elapsed: 21 seconds.
protocols.frag_picker.VallProvider: Total chunks: 13717
protocols.frag_picker.VallProvider: Largest chunk: 1264 aa
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types
protocols.frag_picker.FragmentPicker: Will pick fragments of size:3 9
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_AP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_W.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_KP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_VP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_KP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_I.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_M.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_NP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_F.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
protocols.frag_picker.scores.FragmentCrmsd: Reference structure to score fragments by crmsd loaded from: input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 2 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASP
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 6 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 8 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: GLU
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 10 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 23 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 38 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 44 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 54 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 55 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 60 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 62 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 74 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 4 atoms at position 75 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 81 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: ASN
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 84 in file input_files/1ten_chain_A_res-renum_starting_w_2L_res-renum.pdb. Best match rsd_type: LYS
core.pack.task: Packer task: initialize from command line()
protocols.frag_picker.FragmentPicker: Picking 200 fragments based on 10000 candidates
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme for the selection step
protocols.frag_picker.FragmentPicker: Collector for fragment size: 3 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Collector for fragment size: 9 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Fragment scoring scheme used:
-----------------------------------------
id fragment score method name weight
  1 FragmentCrmsd 1
  2 RamaScore 2
  3 SecondarySimilarity 1
-----------------------------------------

protocols.frag_picker.FragmentPicker:
fragment_picker: After setup; size of a query is: 89
fragment_picker: Picking candidates
fragment_picker: Running bounded protocol
protocols.frag_picker.FragmentPicker: pick fragments using bounded protocol...
protocols.frag_picker.FragmentPicker: Picking candidates...
protocols.frag_picker.FragmentPicker: 0% done at 1aoc
protocols.frag_picker.FragmentPicker: 1% done at 1baz
protocols.frag_picker.FragmentPicker: 2% done at 1c3m
protocols.frag_picker.FragmentPicker: 3% done at 1cyo
protocols.frag_picker.FragmentPicker: 4% done at 1dm5
protocols.frag_picker.FragmentPicker: 5% done at 1e8c
protocols.frag_picker.FragmentPicker: 6% done at 1eq2
protocols.frag_picker.FragmentPicker: 7% done at 1f6b
protocols.frag_picker.FragmentPicker: 8% done at 1fs0
protocols.frag_picker.FragmentPicker: 9% done at 1g7s
protocols.frag_picker.FragmentPicker: 10% done at 1gtt
protocols.frag_picker.FragmentPicker: 11% done at 1h7c
protocols.frag_picker.FragmentPicker: 12% done at 1hxs
protocols.frag_picker.FragmentPicker: 13% done at 1iir
protocols.frag_picker.FragmentPicker: 14% done at 1j2j
protocols.frag_picker.FragmentPicker: 15% done at 1jh6
protocols.frag_picker.FragmentPicker: 16% done at 1jwi
protocols.frag_picker.FragmentPicker: 17% done at 1kcg
protocols.frag_picker.FragmentPicker: 18% done at 1kxo
protocols.frag_picker.FragmentPicker: 19% done at 1ll2
protocols.frag_picker.FragmentPicker: 20% done at 1m40
protocols.frag_picker.FragmentPicker: 21% done at 1ml9
protocols.frag_picker.FragmentPicker: 22% done at 1n4x
protocols.frag_picker.FragmentPicker: 23% done at 1nkr
protocols.frag_picker.FragmentPicker: 24% done at 1nyk
protocols.frag_picker.FragmentPicker: 25% done at 1ocs
protocols.frag_picker.FragmentPicker: 26% done at 1orf
protocols.frag_picker.FragmentPicker: 27% done at 1p9r
protocols.frag_picker.FragmentPicker: 28% done at 1psq
protocols.frag_picker.FragmentPicker: 29% done at 1q7s
protocols.frag_picker.FragmentPicker: 30% done at 1qop
protocols.frag_picker.FragmentPicker: 31% done at 1r5m
protocols.frag_picker.FragmentPicker: 32% done at 1rp3
protocols.frag_picker.FragmentPicker: 33% done at 1s3z
protocols.frag_picker.FragmentPicker: 34% done at 1six
protocols.frag_picker.FragmentPicker: 35% done at 1t0h
protocols.frag_picker.FragmentPicker: 36% done at 1tdh
protocols.frag_picker.FragmentPicker: 37% done at 1tuv
protocols.frag_picker.FragmentPicker: 38% done at 1u6l
protocols.frag_picker.FragmentPicker: 39% done at 1uli
protocols.frag_picker.FragmentPicker: 40% done at 1uxo
protocols.frag_picker.FragmentPicker: 41% done at 1v9m
protocols.frag_picker.FragmentPicker: 42% done at 1vim
protocols.frag_picker.FragmentPicker: 43% done at 1vpv
protocols.frag_picker.FragmentPicker: 44% done at 1w2w
protocols.frag_picker.FragmentPicker: 45% done at 1wfx
protocols.frag_picker.FragmentPicker: 46% done at 1wui
protocols.frag_picker.FragmentPicker: 47% done at 1x8h
protocols.frag_picker.FragmentPicker: 48% done at 1xkp
protocols.frag_picker.FragmentPicker: 49% done at 1xxg
protocols.frag_picker.FragmentPicker: 50% done at 1yar
protocols.frag_picker.FragmentPicker: 51% done at 1ym3
protocols.frag_picker.FragmentPicker: 52% done at 1yz7
protocols.frag_picker.FragmentPicker: 53% done at 1zd1
protocols.frag_picker.FragmentPicker: 54% done at 1zud
protocols.frag_picker.FragmentPicker: 55% done at 2a5y
protocols.frag_picker.FragmentPicker: 56% done at 2aja
protocols.frag_picker.FragmentPicker: 57% done at 2aze
protocols.frag_picker.FragmentPicker: 58% done at 2bay
protocols.frag_picker.FragmentPicker: 59% done at 2bmb
protocols.frag_picker.FragmentPicker: 60% done at 2c1x
protocols.frag_picker.FragmentPicker: 61% done at 2cgh
protocols.frag_picker.FragmentPicker: 62% done at 2cx1
protocols.frag_picker.FragmentPicker: 63% done at 2dbb
protocols.frag_picker.FragmentPicker: 64% done at 2dqw
protocols.frag_picker.FragmentPicker: 65% done at 2e4u
protocols.frag_picker.FragmentPicker: 66% done at 2et1
protocols.frag_picker.FragmentPicker: 67% done at 2f6h
protocols.frag_picker.FragmentPicker: 68% done at 2fh5
protocols.frag_picker.FragmentPicker: 69% done at 2fsu
protocols.frag_picker.FragmentPicker: 70% done at 2g5g
protocols.frag_picker.FragmentPicker: 71% done at 2gia
protocols.frag_picker.FragmentPicker: 72% done at 2gtr
protocols.frag_picker.FragmentPicker: 73% done at 2h5e
protocols.frag_picker.FragmentPicker: 74% done at 2hev
protocols.frag_picker.FragmentPicker: 75% done at 2hqt
protocols.frag_picker.FragmentPicker: 76% done at 2i3t
protocols.frag_picker.FragmentPicker: 77% done at 2ics
protocols.frag_picker.FragmentPicker: 78% done at 2inp
protocols.frag_picker.FragmentPicker: 79% done at 2j01
protocols.frag_picker.FragmentPicker: 80% done at 2jae
protocols.frag_picker.FragmentPicker: 81% done at 2nnr
protocols.frag_picker.FragmentPicker: 82% done at 2nwh
protocols.frag_picker.FragmentPicker: 83% done at 2o3i
protocols.frag_picker.FragmentPicker: 84% done at 2obw
protocols.frag_picker.FragmentPicker: 85% done at 2ols
protocols.frag_picker.FragmentPicker: 86% done at 2oyc
protocols.frag_picker.FragmentPicker: 87% done at 2p6r
protocols.frag_picker.FragmentPicker: 88% done at 2ph3
protocols.frag_picker.FragmentPicker: 89% done at 2pu9
protocols.frag_picker.FragmentPicker: 90% done at 2q4e
protocols.frag_picker.FragmentPicker: 91% done at 2qg7
protocols.frag_picker.FragmentPicker: 92% done at 2qqh
protocols.frag_picker.FragmentPicker: 93% done at 2qzb
protocols.frag_picker.FragmentPicker: 94% done at 2rio
protocols.frag_picker.FragmentPicker: 95% done at 2v1x
protocols.frag_picker.FragmentPicker: 96% done at 2yxb
protocols.frag_picker.FragmentPicker: 97% done at 3b57
protocols.frag_picker.FragmentPicker: 98% done at 3bja
protocols.frag_picker.FragmentPicker: 99% done at 5nul
protocols.frag_picker.FragmentPicker: ... done. Processed 13717 chunks. Time elapsed: 2659 seconds.
protocols.frag_picker.FragmentPicker: Saving Fragments...
Segmentation fault (core dumped)

Issue History
Date Modified	Username	Field	Change
2013-09-06 09:42	kimdn	New Issue
2013-09-06 09:42	kimdn	File Added: crmsd_has_1_wt_and_1_max_seg_fault.zip
2013-09-06 09:45	kimdn	Steps to Reproduce Updated	View Revisions

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