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two runs for the same hyphy relax command, but the results are different #62

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aaannaw opened this issue Nov 26, 2024 · 0 comments
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@aaannaw
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aaannaw commented Nov 26, 2024

Dear author,
For some genes, when I first run the hyphy relax command:
/data/01/p1/user157/software/hyphy/bin/hyphy relax --alignment /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/07.deletestopcodon/evm.model.ptg000026l.297.fa --tree /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/00.mark.tree/evm.model.ptg000026l.297.fa.treefile.mark --test FG1 --reference FG2 --output /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.socialtest.relax.out/evm.model.ptg000026l.297.json > /data/01/p1/user157/Bathyergidae-sociaty/2024812.newcactus/03.proteincoding-selected-analysis/01.getgene/13.hyphy/02.relax/01.socialtest.relax.out/evm.model.ptg000026l.297.log 2>&1

The error occurs in the log file:

Error:
Internal error 
Constrained optimization failed, since a starting point within the domain specified for the variables couldn't be found.
Set it by hand, or check your constraints for compatibility.
Failed constraint: relax.ge.omega2:=1/0.3652980831447958 must be in [0,10000]. Current value = 1.

Then I rerun the the same command, the error disappears and the dN/dS distribution for models is shown in the log file:

### Fitting the alternative model to test K != 1
* Log(L) =  -941.31, AIC-c =  1969.90 (42 estimated parameters)
* Relaxation/intensification parameter (K) =     0.01
* The following rate distribution was inferred for **test** branches

|          Selection mode           |     dN/dS     |Proportion, %|               Notes               |
|-----------------------------------|---------------|-------------|-----------------------------------|
|        Negative selection         |     0.976     |   39.361    |                                   |
|        Negative selection         |     0.976     |   37.942    |       Collapsed rate class        |
|         Neutral evolution         |     1.000     |   22.697    |       Collapsed rate class        |

* The following rate distribution was inferred for **reference** branches

|          Selection mode           |     dN/dS     |Proportion, %|               Notes               |
|-----------------------------------|---------------|-------------|-----------------------------------|
|        Negative selection         |     0.045     |   39.361    |                                   |
|        Negative selection         |     0.088     |   37.942    |                                   |
|         Neutral evolution         |     1.000     |   22.697    |                                   |

The difference for two runs is obvious and which result could I trust?

The input files are attached.

Could you give me any suggestions?
Looking forward with your reply.

Best wishes,
Na Wan
evm.model.ptg000026l.297.json
evm.model.ptg000026l.297.log
evm.model.ptg000026l.297.fa.treefile.mark.txt
evm.model.ptg000026l.297.fa.txt

@aaannaw aaannaw changed the title two runs for the same hyphy relax command, and the results are different two runs for the same hyphy relax command, but the results are different Nov 26, 2024
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