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Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi

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Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi


using a flag containing options "-dunbrack_prob_buried_semi 0.8" and "-dunbrack_prob_nonburied_semi 0.8", errors appear like:
File: /home/shanghai/RationalDesign/Rosetta3.9/rosetta_src_2018.09.60072_bundle/main/source/src/utility/options/
Option matching -dunbrack_prob_buried_semi not found in command line top-level context



the flags and log file were attached.

Please help, thanks




predictor_flags.txt325 bytes
log_semi.log1.22 KB
Post Situation: 
Fri, 2023-01-27 06:20

Looks like you're using Rosetta 3.9 (released late 2018) . It looks like the command line flags to control those options were't introduced until late 2019. It should be in weeklies after 2019.47 and numbered releases after 3.12

That said, prior to the addition of the semi flags, the values for the non-semi versions were used. Since you're setting them both the same, you probably can just omit the flags if you still want to use 3.9

Fri, 2023-01-27 07:58

Thanks very much, rmoretti !

You are absolutedly correct that I am using 3.9. After use of a newer version of rosetta_scripts (2022.41), previous errors disappeared !

However, new errors appeared as:


ERROR: -run:preserve_header is required for using "Tomponents". To avoid this message, include "-run:preserve_header true" in your flags.


After addition of "-run:preserve_header true" into predictor.flags, this error still appeared.

New predictor.flags and the crash file is attached

Again, please help, thanks !

Fri, 2023-01-27 19:02

Rosetta appends crashes to the ROSETTA_CRASH.log file, it doesn't overwrite them. So your most recent error is at the end of the file.

[FILE]: src/core/io/external/
[LINE]: 341
[ ERROR ] UtilityExitException
ERROR: Failed to run the psipred command, which was "/home/shanghai/RationalDesign/Rosetta3.9/psipred/runpsipred_single SEDETIKKLV_RCR6QVHC.fasta > /dev/null". Something went wrong. Make sure you specified the full path to the psipred command in your XML file. Return code=256


My guess is that the path to your psipred command is incorrect. (If not, try running the command specified directly, without the `< /dev/null` bit. Take a look for any warnings or errors which may have occured.

Mon, 2023-01-30 08:04