Rosetta 4.20

Message boards : RALPH@home bug list : Rosetta 4.20

To post messages, you must log in.

AuthorMessage
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6835 - Posted: 20 Jun 2020, 12:48:12 UTC

Today a lot of "validation error"
5163767
5163769
etc

<stderr_txt>
command: projects/ralph.bakerlab.org/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol lance_hbnet_boinc_v1.xml @flags_hb_100 -in:file:silent hbnet_surface_design_100_SAVE_ALL_OUT_IGNORE_THE_REST_1hr5gj0m.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip hbnet_surface_design_100_SAVE_ALL_OUT_IGNORE_THE_REST_1hr5gj0m.zip @hbnet_surface_design_100_SAVE_ALL_OUT_IGNORE_THE_REST_1hr5gj0m.flags -nstruct 10000 -cpu_run_time 3600 -boinc:max_nstruct 5000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3959001
Using database: database_357d5d93529_n_methylminirosetta_database
======================================================
DONE :: 22 starting structures 14123.8 cpu seconds
This process generated 22 decoys from 22 attempts
======================================================
BOINC :: WS_max 5.92327e+08
10:38:20 (10652): called boinc_finish(0)

</stderr_txt>
ID: 6835 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6839 - Posted: 2 Jul 2020, 18:45:38 UTC
Last modified: 2 Jul 2020, 18:45:58 UTC

All "CJG0001_SAVE_ALL_OUT" errors after few seconds

<stderr_txt>
command: projects/ralph.bakerlab.org/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol jhr_boinc_v5.xml @flags -in:file:silent CJG0001_SAVE_ALL_OUT_IGNORE_THE_REST_8dc9jy8d.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip CJG0001_SAVE_ALL_OUT_IGNORE_THE_REST_8dc9jy8d.zip @CJG0001_SAVE_ALL_OUT_IGNORE_THE_REST_8dc9jy8d.flags -nstruct 10000 -cpu_run_time 3600 -boinc:max_nstruct 5000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3949529
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: no such file /home/cjg263/de_novo_dna/results/struct_profile_constraints/200628/1BLO_C/run_1/1BLO_C_design_start_0120_0001.profile
ERROR:: Exit from: ......srccorescoringconstraintsSequenceProfileConstraint.cc line: 175
BOINC:: Error reading and gzipping output datafile: default.out
20:27:25 (6768): called boinc_finish(1)

</stderr_txt>
ID: 6839 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6862 - Posted: 21 Aug 2020, 7:10:31 UTC

These wus are validated (so it helps), but in the log there is this error:

[ ERROR ]: Caught exception:


File: ......srcprotocolsmotif_graftingmoversMotifGraftMover.cc:537
For this scaffold there are not suitable scaffold grafts within your constrains
------------------------ Begin developer's backtrace -------------------------
BACKTRACE:
------------------------- End developer's backtrace --------------------------


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

ID: 6862 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6864 - Posted: 21 Aug 2020, 19:26:26 UTC

All "docktst_" errors after few seconds.


command: projects/ralph.bakerlab.org/rosetta_4.20_windows_x86_64.exe @docktst_2008899_0000_global_dock_flags -in:file:boinc_wu_zip asym_dock_docktst_2008899_0000_data.zip -patchdock docktst_2008899_0000_patchdock.patchdock -patchdock_random_entry 1 4026 -in:file:s docktst_2008899_0000_patchdock.pdb -nstruct 10000 -cpu_run_time 3600 -boinc:max_nstruct 5000 -checkpoint_interval 120 -mute all -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3939048
Using database: database_357d5d93529_n_methylminirosetta_database

[ ERROR ]: Caught exception:


File: ......srcprotocolsrosetta_scriptsRosettaScriptsParser.cc:1313
Input rosetta scripts XML file "asym_dock_global.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema <output filename> to output the schema to a file to see all valid options.
Your XML has failed validation. The error message below will tell you where in your XML file the error occurred. Here's how to fix it:

1) If the validation fails on something obvious, like an illegal attribute due to a spelling error (perhaps you used scorefnction instead of scorefunction), then you need to fix your XML file.
2) If you haven&#226;&#128;&#153;t run the XML rewriter script and this might be pre-2017 Rosetta XML, run the rewriter script (tools/xsd_xrw/rewrite_rosetta_script.py) on your input XML first. The attribute values not being in quotes (scorefunction=talaris2014 instead of scorefunction="talaris2014") is a good indicator that this is your problem.
3) If you are a developer and neither 1 nor 2 worked - email the developer&#226;&#128;&#153;s mailing list or try Slack.
4) If you are an academic or commercial user - try the Rosetta Forums https://www.rosettacommons.org/forum


Error messages were:
Error: AttValue: " or ' expected

1: <ROSETTASCRIPTS>
2: <SCOREFXNS>
3: <fullatom weights=talaris2013 symmetric=0>
4: </fullatom>
5: </SCOREFXNS>
6:
7: <FILTERS>
8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/>
Error: attributes construct error

1: <ROSETTASCRIPTS>
2: <SCOREFXNS>
3: <fullatom weights=talaris2013 symmetric=0>
4: </fullatom>
5: </SCOREFXNS>
6:
7: <FILTERS>
8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/>
Error: Couldn't find end of Start Tag fullatom line 3

1: <ROSETTASCRIPTS>
2: <SCOREFXNS>
3: <fullatom weights=talaris2013 symmetric=0>
4: </fullatom>
5: </SCOREFXNS>
6:
7: <FILTERS>
8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/>
Error: Opening and ending tag mismatch: SCOREFXNS line 2 and fullatom

1: <ROSETTASCRIPTS>
2: <SCOREFXNS>
3: <fullatom weights=talaris2013 symmetric=0>
4: </fullatom>
5: </SCOREFXNS>
6:
7: <FILTERS>
8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/>
9: <Sasa name=sasa confidence=0/>
Error: Opening and ending tag mismatch: ROSETTASCRIPTS line 1 and SCOREFXNS

1: <ROSETTASCRIPTS>
2: <SCOREFXNS>
3: <fullatom weights=talaris2013 symmetric=0>
4: </fullatom>
5: </SCOREFXNS>
6:
7: <FILTERS>
8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/>
9: <Sasa name=sasa confidence=0/>
10: <ShapeComplementarity name=shape verbose=1 confidence=0 jump=1/>
Error: Extra content at the end of the document

2: <SCOREFXNS>
3: <fullatom weights=talaris2013 symmetric=0>
4: </fullatom>
5: </SCOREFXNS>
6:
7: <FILTERS>
8: <Ddg name=Isc scorefxn=fullatom threshold=0 jump=1 repeats=1 repack=0 confidence=1/>
9: <Sasa name=sasa confidence=0/>
10: <ShapeComplementarity name=shape verbose=1 confidence=0 jump=1/>
11: </FILTERS>
12:
------------------------------------------------------------
Warning messages were:
------------------------------------------------------------

------------------------ Begin developer's backtrace -------------------------
BACKTRACE:
------------------------- End developer's backtrace --------------------------


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.


DummyMover::apply() should never have been called! (JobDistributor/Parser should have replaced DummyMover.)

ERROR: Function not implemented.
ERROR:: Exit from: ......srcappspublicboincminirosetta.cc line: 101
21:23:06 (15472): called boinc_finish(0)

</stderr_txt>
ID: 6864 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6906 - Posted: 10 Nov 2020, 19:11:51 UTC

A lot of errors, after 2/3 minutes:
5199235
5199144
5198711

<stderr_txt>
ERROR: Bad equation in CalculatorFilter: - 1 / ( 1 + EXP( -( contact_molecular_surface - 400.67596 ) input 0.01416 ) ) input 1 / ( 1 + EXP( -( contact_patch - 248.35528 ) input 0.04437 ) ) input 1 / ( 1 + EXP( -( contact_patch - 248.35528 ) input 0.04437 ) ) input 1 / ( 1 + EXP( -( score_per_res - -2.38225 ) input -7.98873 ) ) input 1 / ( 1 + EXP( -( ddg_norepack - -41.20216 ) input -0.06781 ) )
ERROR:: Exit from: ......srcprotocolsfiltersCalculatorFilter.cc line: 178
BOINC:: Error reading and gzipping output datafile: default.out
20:02:35 (3636): called boinc_finish(1)
</stderr_txt>


ERROR: Bad equation in CalculatorFilter: - 1 / ( 1 + EXP( -( ddg_norepack - -35.92195 ) input -0.15280 ) ) input 1 / ( 1 + EXP( -( contact_molecular_surface - 372.57248 ) input 0.02193 ) ) input 1 / ( 1 + EXP( -( score_per_res - -2.40579 ) input -6.50904 ) ) input 1 / ( 1 + EXP( -( contact_patch - 215.72044 ) input 0.05354 ) ) input 1 / ( 1 + EXP( -( contact_patch - 215.72044 ) input 0.05354 ) )
ERROR:: Exit from: ......srcprotocolsfiltersCalculatorFilter.cc line: 178
BOINC:: Error reading and gzipping output datafile: default.out
19:59:53 (10160): called boinc_finish(1)


ERROR: Bad equation in CalculatorFilter: - 1 / ( 1 + EXP( -( score_per_res - -2.43173 ) input -6.40169 ) ) input 1 / ( 1 + EXP( -( ddg_norepack - -39.61585 ) input -0.12913 ) ) input 1 / ( 1 + EXP( -( contact_molecular_surface - 370.39337 ) input 0.01232 ) ) input 1 / ( 1 + EXP( -( contact_patch - 252.95528 ) input 0.02638 ) ) input 1 / ( 1 + EXP( -( contact_patch - 252.95528 ) input 0.02638 ) )
ERROR:: Exit from: ......srcprotocolsfiltersCalculatorFilter.cc line: 178
BOINC:: Error reading and gzipping output datafile: default.out
20:03:00 (17628): called boinc_finish(1)
ID: 6906 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6907 - Posted: 10 Nov 2020, 19:16:25 UTC

Also a LOT of validation error:
5199240
5199030
5199226

[ ERROR ]: Caught exception:


File: ......srcprotocolsmotif_graftingmoversMotifGraftMover.cc:537
For this scaffold there are not suitable scaffold grafts within your constrains
------------------------ Begin developer's backtrace -------------------------
BACKTRACE:
------------------------- End developer's backtrace --------------------------


AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
ID: 6907 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6916 - Posted: 15 Dec 2020, 11:37:07 UTC
Last modified: 15 Dec 2020, 11:37:24 UTC

Screensaver crashes on all wus
ID: 6916 · Report as offensive    Reply Quote
Profile Maurice Goulois

Send message
Joined: 23 May 15
Posts: 3
Credit: 84,619
RAC: 2,279
Message 6919 - Posted: 15 Dec 2020, 15:23:40 UTC

Hello, all wus seem to error :(

<core_client_version>7.16.6</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)</message>
<stderr_txt>
command: ../../projects/ralph.bakerlab.org/rosetta_4.20_x86_64-pc-linux-gnu -run:protocol jd2_scripting -parser:protocol design.xml @flags_norn_sIaaUAESrJPM -in:file:silent 165_0_0.45_1_6_7404_0_0.35_1_W17_Y33_Q117d1ohpa__clean_0001_N22.rd1.silent_norn_sIaaUAESrJPM_SAVE_ALL_OUT_IGNORE_THE_REST_5ik1xb8p.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 165_0_0.45_1_6_7404_0_0.35_1_W17_Y33_Q117d1ohpa__clean_0001_N22.rd1.silent_norn_sIaaUAESrJPM_SAVE_ALL_OUT_IGNORE_THE_REST_5ik1xb8p.zip -nstruct 10000 -cpu_run_time 3600 -boinc:max_nstruct 5000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3896392
Using database: database_357d5d93529_n_methyl/minirosetta_database

ERROR: Cannot find file '-extra_res_fa or minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types/-extra_res_fa'
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 144
BOINC:: Error reading and gzipping output datafile: default.out
16:06:20 (762737): called boinc_finish(1)

</stderr_txt>
]]>

ID: 6919 · Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 9 Apr 08
Posts: 700
Credit: 1,370,153
RAC: 3,827
Message 6920 - Posted: 15 Dec 2020, 20:20:02 UTC - in response to Message 6919.  
Last modified: 15 Dec 2020, 20:20:49 UTC

<stderr_txt>
command: ../../projects/ralph.bakerlab.org/rosetta_4.20_x86_64-pc-linux-gnu -run:protocol jd2_scripting -parser:protocol design.xml @flags_norn_sIaaUAESrJPM -in:file:silent 165_0_0.45_1_6_7404_0_0.35_1_W17_Y33_Q117d1ohpa__clean_0001_N22.rd1.silent_norn_sIaaUAESrJPM_SAVE_ALL_OUT_IGNORE_THE_REST_5ik1xb8p.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 165_0_0.45_1_6_7404_0_0.35_1_W17_Y33_Q117d1ohpa__clean_0001_N22.rd1.silent_norn_sIaaUAESrJPM_SAVE_ALL_OUT_IGNORE_THE_REST_5ik1xb8p.zip -nstruct 10000 -cpu_run_time 3600 -boinc:max_nstruct 5000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3896392
Using database: database_357d5d93529_n_methyl/minirosetta_database

ERROR: Cannot find file '-extra_res_fa or minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types/-extra_res_fa'
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 144
BOINC:: Error reading and gzipping output datafile: default.out
16:06:20 (762737): called boinc_finish(1)

</stderr_txt>


Same here, some errors after few seconds, but in Windows

(0x1) - exit code 1 (0x1)</message>
<stderr_txt>
command: projects/ralph.bakerlab.org/rosetta_4.20_windows_x86_64.exe -run:protocol jd2_scripting -parser:protocol design.xml @flags_norn_xvodZzWrzbOk -in:file:silent 1725_0_0.35_2_668_0_0.05_2_Y17_H101_W103d1gy7a__clean_0001_D21_H66.rd1.silent_norn_xvodZzWrzbOk_SAVE_ALL_OUT_IGNORE_THE_REST_9ay3mf1k.silent -in:file:silent_struct_type binary -silent_gz -mute all -silent_read_through_errors true -out:file:silent_struct_type binary -out:file:silent default.out -in:file:boinc_wu_zip 1725_0_0.35_2_668_0_0.05_2_Y17_H101_W103d1gy7a__clean_0001_D21_H66.rd1.silent_norn_xvodZzWrzbOk_SAVE_ALL_OUT_IGNORE_THE_REST_9ay3mf1k.zip -nstruct 10000 -cpu_run_time 3600 -boinc:max_nstruct 5000 -checkpoint_interval 120 -database minirosetta_database -in::file::zip minirosetta_database.zip -boinc::watchdog -boinc::cpu_run_timeout 36000 -run::rng mt19937 -constant_seed -jran 3916109
Using database: database_357d5d93529_n_methylminirosetta_database

ERROR: Cannot find file '-extra_res_fa or minirosetta_databasechemical/residue_type_sets/fa_standard/residue_types/-extra_res_fa'
ERROR:: Exit from: ......srccorechemicalresidue_io.cc line: 144
BOINC:: Error reading and gzipping output datafile: default.out
21:04:48 (6092): called boinc_finish(1)
ID: 6920 · Report as offensive    Reply Quote
Profile Maurice Goulois

Send message
Joined: 23 May 15
Posts: 3
Credit: 84,619
RAC: 2,279
Message 6921 - Posted: 16 Dec 2020, 9:54:54 UTC

Hello :) problem seems to be solved :) no errors on last batch of 4.20.
ID: 6921 · Report as offensive    Reply Quote

Message boards : RALPH@home bug list : Rosetta 4.20



©2021 University of Washington
http://www.bakerlab.org