RELAX Error: Matrix/List LHS expected but not supplied

[lrschaff]

Hello hyphy team,

I am attempting to run RELAX on HPC and looks like RELAX is almost done running but then I am getting the error:

Error:
Matrix/List LHS expected but not supplied.

Function call stack
1 :  ((json[terms.json.analysis])[terms.settings])[key]=value;

	Keyword arguments:
		{
		 "keepident":"true",
		 "multiple-hit":"Double+Triple"
		}
-------
2 :  selection.io.json_store_setting(relax.json,"convergence-flat-surface",relax.best_samples[1]-relax.best_samples[0]);

	Keyword arguments:
		{
		 "keepident":"true",
		 "multiple-hit":"Double+Triple"
		}
-------
3 :  relax.FitMainTestPair(relax.loop_passes==1);

	Keyword arguments:
		{
		 "keepident":"true",
		 "multiple-hit":"Double+Triple"
		}
-------

This is the input as well:
hyphy RELAX --alignment ./gene_167.fa --tree ./536mammals_ML_tree.nwk --test ProgHigh --models All --srv Branch-site --multiple-hit "Double+Triple" --keepident true

I am also using the 2.5.64 version of hyphy.

Do you have any insight on how to fix this error?

Thank you,
Lillie

[spond]

Dear @lrschaff,

This specific error is because the Settings field in the result dictionary isn't initialized properly before the RELAX analysis tries to write to it. I also see that this happens because your specific srv setting triggers a branch in the analysis that creates this situation. I should also note that --srv Branch-site is an "experimental" option which I have not extensively tested. Please report other issues if you find them.

I am going to release 2.5.65 tonight or tomorrow (with some other code changes) that fixes this issue.
You can also drop the attached file (after decompressing it) into res/TemplateBatchFiles/SelectionAnalyses (and rerun make install) if you want to try it out sooner.

Best,
Sergei

RELAX.bf.zip

P.S. keepident is not a supported keyword (unless you modified the analyses). I don't think it will do anything.

[lrschaff]

Thank you for the quick response Sergei! I will try this new version out.

I appreciate the help,

Lillie

[lrschaff]

Hi Sergei,

When building 2.5.65, the version identifies as 2.5.64 and fails as before:

$ hyphy RELAX --alignment ./gene_167.fa --tree ./536mammals_ML_tree_BG.nwk --test ProgHigh --models All --srv Branch-site --multiple-hit "Double+Triple" --keepident true

Function call stack
1 : ((json[terms.json.analysis])[terms.settings])[key]=value;

Keyword arguments:
    {
     "keepident":"true",
     "multiple-hit":"Double+Triple"
    }

---

2 : selection.io.json_store_setting(relax.json,"convergence-flat-surface",relax.best_samples[1]-relax.best_samples[0]);

Keyword arguments:
    {
     "keepident":"true",
     "multiple-hit":"Double+Triple"
    }

---

3 : relax.FitMainTestPair(relax.loop_passes==1);

Keyword arguments:
    {
     "keepident":"true",
     "multiple-hit":"Double+Triple"
    }

---

Is it possible that the update hasn't fully propagated yet or might I be missing a step to ensure the right version is installed?

Thanks,

Lillie

[spond]

Dear @lrschaff,

Ooops! My mistake (messed up code merges). I re-released 2.5.65, please try again.

Best,
Sergei