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Error when using RELAX #1698

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Oswaldz opened this issue Mar 7, 2024 · 4 comments
Open

Error when using RELAX #1698

Oswaldz opened this issue Mar 7, 2024 · 4 comments

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@Oswaldz
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Oswaldz commented Mar 7, 2024

Hi,

I'm using RELAX to analyse over 500 genes of 11 insect species, but have some problems. Apologize that I have no bioinformatics background, but I cannot find what caused the problem.

Thank you very much.

Following is what's in my error.log.
Error:'RPN:"mUyYPLdU.tree_id_0"|"hanni"|{
"empirical":9,
"global":{
"Mixture auxiliary weight for category 1":"relax.ge.bsrel_mixture_aux_0",
"Mixture auxiliary weight for category 2":"relax.ge.bsrel_mixture_aux_1",
"Substitution rate from nucleotide A to nucleotide C":"relax.ge.theta_AC",
"Substitution rate from nucleotide A to nucleotide G":"relax.ge.theta_AG",
"Substitution rate from nucleotide A to nucleotide T":"relax.ge.theta_AT",
"Substitution rate from nucleotide C to nucleotide G":"relax.ge.theta_CG",
"Substitution rate from nucleotide C to nucleotide T":"relax.ge.theta_CT",
"Substitution rate from nucleotide G to nucleotide T":"relax.ge.theta_GT",
"non-synonymous/synonymous rate ratio for category 1":"relax.ge.omega1",
"non-synonymous/synonymous rate ratio for category 2":"relax.ge.omega2",
"non-synonymous/synonymous rate ratio for category 3":"relax.ge.omega3"
},
"local":{
"relaxation or intensification parameter":"k",
"synonymous rate":"t"
}
}|0|relax.set.k' evaluated with errors Unconsumed values on the stack
[2]------------------
hanni.{
"empirical":9,
"global":{
"Mixture auxiliary weight for category 1":"relax.ge.bsrel_mixture_aux_0",
"Mixture auxiliary weight for category 2":"relax.ge.bsrel_mixture_aux_1",
"Substitution rate from nucleotide A to nucleotide C":"relax.ge.theta_AC",
"Substitution rate from nucleotide A to nucleotide G":"relax.ge.theta_AG",
"Substitution rate from nucleotide A to nucleotide T":"relax.ge.theta_AT",
"Substitution rate from nucleotide C to nucleotide G":"relax.ge.theta_CG",
"Substitution rate from nucleotide C to nucleotide T":"relax.ge.theta_CT",
"Substitution rate from nucleotide G to nucleotide T":"relax.ge.theta_GT",
"non-synonymous/synonymous rate ratio for category 1":"relax.ge.omega1",
"non-synonymous/synonymous rate ratio for category 2":"relax.ge.omega2",
"non-synonymous/synonymous rate ratio for category 3":"relax.ge.omega3"
},
"local":{
"relaxation or intensification parameter":"k",
"synonymous rate":"t"
}
}.0
[1]------------------
hanni.{
"empirical":9,
"global":{
"Mixture auxiliary weight for category 1":"relax.ge.bsrel_mixture_aux_0",
"Mixture auxiliary weight for category 2":"relax.ge.bsrel_mixture_aux_1",
"Substitution rate from nucleotide A to nucleotide C":"relax.ge.theta_AC",
"Substitution rate from nucleotide A to nucleotide G":"relax.ge.theta_AG",
"Substitution rate from nucleotide A to nucleotide T":"relax.ge.theta_AT",
"Substitution rate from nucleotide C to nucleotide G":"relax.ge.theta_CG",
"Substitution rate from nucleotide C to nucleotide T":"relax.ge.theta_CT",
"Substitution rate from nucleotide G to nucleotide T":"relax.ge.theta_GT",
"non-synonymous/synonymous rate ratio for category 1":"relax.ge.omega1",
"non-synonymous/synonymous rate ratio for category 2":"relax.ge.omega2",
"non-synonymous/synonymous rate ratio for category 3":"relax.ge.omega3"
},
"local":{
"relaxation or intensification parameter":"k",
"synonymous rate":"t"
}
}.0
'RPN:"mUyYPLdU.tree_id_0"|"hanni"|{
"empirical":9,
"global":{
"Mixture auxiliary weight for category 1":"relax.ge.bsrel_mixture_aux_0",
"Mixture auxiliary weight for category 2":"relax.ge.bsrel_mixture_aux_1",
"Substitution rate from nucleotide A to nucleotide C":"relax.ge.theta_AC",
"Substitution rate from nucleotide A to nucleotide G":"relax.ge.theta_AG",
"Substitution rate from nucleotide A to nucleotide T":"relax.ge.theta_AT",
"Substitution rate from nucleotide C to nucleotide G":"relax.ge.theta_CG",
"Substitution rate from nucleotide C to nucleotide T":"relax.ge.theta_CT",
"Substitution rate from nucleotide G to nucleotide T":"relax.ge.theta_GT",
"non-synonymous/synonymous rate ratio for category 1":"relax.ge.omega1",
"non-synonymous/synonymous rate ratio for category 2":"relax.ge.omega2",
"non-synonymous/synonymous rate ratio for category 3":"relax.ge.omega3"
},
"local":{
"relaxation or intensification parameter":"k",
"synonymous rate":"t"
}
}|0|relax.set.k' evaluated with errors Unconsumed values on the stack
[2]------------------
hanni.{
"empirical":9,
"global":{
"Mixture auxiliary weight for category 1":"relax.ge.bsrel_mixture_aux_0",
"Mixture auxiliary weight for category 2":"relax.ge.bsrel_mixture_aux_1",
"Substitution rate from nucleotide A to nucleotide C":"relax.ge.theta_AC",
"Substitution rate from nucleotide A to nucleotide G":"relax.ge.theta_AG",
"Substitution rate from nucleotide A to nucleotide T":"relax.ge.theta_AT",
"Substitution rate from nucleotide C to nucleotide G":"relax.ge.theta_CG",
"Substitution rate from nucleotide C to nucleotide T":"relax.ge.theta_CT",
"Substitution rate from nucleotide G to nucleotide T":"relax.ge.theta_GT",
"non-synonymous/synonymous rate ratio for category 1":"relax.ge.omega1",
"non-synonymous/synonymous rate ratio for category 2":"relax.ge.omega2",
"non-synonymous/synonymous rate ratio for category 3":"relax.ge.omega3"
},
"local":{
"relaxation or intensification parameter":"k",
"synonymous rate":"t"
}
}.0
[1]------------------
hanni.{
"empirical":9,
"global":{
"Mixture auxiliary weight for category 1":"relax.ge.bsrel_mixture_aux_0",
"Mixture auxiliary weight for category 2":"relax.ge.bsrel_mixture_aux_1",
"Substitution rate from nucleotide A to nucleotide C":"relax.ge.theta_AC",
"Substitution rate from nucleotide A to nucleotide G":"relax.ge.theta_AG",
"Substitution rate from nucleotide A to nucleotide T":"relax.ge.theta_AT",
"Substitution rate from nucleotide C to nucleotide G":"relax.ge.theta_CG",
"Substitution rate from nucleotide C to nucleotide T":"relax.ge.theta_CT",
"Substitution rate from nucleotide G to nucleotide T":"relax.ge.theta_GT",
"non-synonymous/synonymous rate ratio for category 1":"relax.ge.omega1",
"non-synonymous/synonymous rate ratio for category 2":"relax.ge.omega2",
"non-synonymous/synonymous rate ratio for category 3":"relax.ge.omega3"
},
"local":{
"relaxation or intensification parameter":"k",
"synonymous rate":"t"
}
}.0
@spond
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spond commented Mar 7, 2024

Dear @Oswaldz,

This is an odd-looking error, I am not sure what caused it. Could you include

  1. The version of HyPhy you are using (hyphy --version)
  2. The command you are using to run RELAX
  3. The output you see printed to the console (screen), not the errors.log file?

Best,
Sergei

@Oswaldz
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Author

Oswaldz commented Mar 8, 2024

Hi Sergei,

I'm using HYPHY 2.5.59(MP) for Darwin on arm64 ARM Neon SIMD zlib (v1.2.12).

And command is:
hyphy Direction/to/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.fasta --tree foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log

Following is the print on the console:
Analysis DescriptionAnalysis Description

Analysis Description

Analysis Description

RELAX (a random effects test of selection relaxation) uses a random
effects branch-site model framework to test whether a set of 'Test'
branches evolves under relaxed selection relative to a set of
'Reference' branches (R), as measured by the relaxation parameter (K).
RELAX (a random effects test of selection relaxation) uses a random
Version 2.1 adds a check for stability in K estimates to try to mitigate
effects branch-site model framework to test whether a set of 'Test'
RELAX (a random effects test of selection relaxation) uses a random
convergence problems. Version 3 provides support for >2 branch sets.
branches evolves under relaxed selection relative to a set of
effects branch-site model framework to test whether a set of 'Test'
Version 3.1 adds LHC + Nedler-Mead initial fit phase and keyword support'Reference' branches (R), as measured by the relaxation parameter (K).
branches evolves under relaxed selection relative to a set of
Version 2.1 adds a check for stability in K estimates to try to mitigate

RELAX (a random effects test of selection relaxation) uses a random
'Reference' branches (R), as measured by the relaxation parameter (K).
convergence problems. Version 3 provides support for >2 branch sets.
Version 2.1 adds a check for stability in K estimates to try to mitigate
effects branch-site model framework to test whether a set of 'Test'
Version 3.1 adds LHC + Nedler-Mead initial fit phase and keyword supportconvergence problems. Version 3 provides support for >2 branch sets.
branches evolves under relaxed selection relative to a set of

Version 3.1 adds LHC + Nedler-Mead initial fit phase and keyword support'Reference' branches (R), as measured by the relaxation parameter (K).

  • Requirements: Version 2.1 adds a check for stability in K estimates to try to mitigate

convergence problems. Version 3 provides support for >2 branch sets.
Version 3.1 adds LHC + Nedler-Mead initial fit phase and keyword support

  • Requirements: - Requirements:

  • Requirements: in-frame codon alignment and a phylogenetic tree, with at least two
    groups of branches defined using the {} notation (one group can be
    defined as all unlabeled branches)
    in-frame codon alignment and a phylogenetic tree, with at least two
    in-frame codon alignment and a phylogenetic tree, with at least two
    groups of branches defined using the {} notation (one group can be
    groups of branches defined using the {} notation (one group can be
    defined as all unlabeled branches)defined as all unlabeled branches)

  • Citation: - Citation: - Citation: in-frame codon alignment and a phylogenetic tree, with at least two
    RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015).
    RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015).
    groups of branches defined using the {} notation (one group can be
    Mol Biol Evol 32 (3): 820-832Mol Biol Evol 32 (3): 820-832defined as all unlabeled branches)

  • Written by: - Written by:

  • Citation: RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015).
    Mol Biol Evol 32 (3): 820-832

Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM /

  • Written by: UCSD viral evolution group
    RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015).
    Mol Biol Evol 32 (3): 820-832

  • Contact Information:

  • Written by: spond@temple.edu
    Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM /
    UCSD viral evolution group

  • Analysis Version:

  • Contact Information: 3.1

spond@temple.eduSergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM /

UCSD viral evolution groupSergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM /

UCSD viral evolution group- Analysis Version:

  • Contact Information:
    3.1- Contact Information:

spond@temple.edu
spond@temple.edu

  • Analysis Version:
  • Analysis Version: 3.13.1

codecodecodecode => => => => UniversalUniversalUniversal

Universal

Error:
Could not find source dataset file "PROMPT_FOR_FILE" (resolved to '/Users/zzha8134/Desktop/Genome/Zhuzhi_single-copy-BUSCOs/shared/alignment/3')
Error:
Error:
Path stack:
Could not find source dataset file "PROMPT_FOR_FILE" (resolved to '/Users/zzha8134/Desktop/Genome/Zhuzhi_single-copy-BUSCOs/shared/alignment/3')
Could not find source dataset file "PROMPT_FOR_FILE" (resolved to '/Users/zzha8134/Desktop/Genome/Zhuzhi_single-copy-BUSCOs/shared/alignment/3')
/Users/zzha8134/Desktop/Tech/hyphy-master/installation/share/hyphy/
Error:
Path stack:
Path stack:
/Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/
Could not find source dataset file "PROMPT_FOR_FILE" (resolved to '/Users/zzha8134/Desktop/Genome/Zhuzhi_single-copy-BUSCOs/shared/alignment/3')
/Users/zzha8134/Desktop/Tech/hyphy-master/installation/share/hyphy/
/Users/zzha8134/Desktop/Tech/hyphy-master/installation/share/hyphy/

Path stack:
/Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/
/Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/
Function call stack
/Users/zzha8134/Desktop/Tech/hyphy-master/installation/share/hyphy/

1 : [namespace = PMtSzZTO] DataSet ^dataset_name = ReadDataFile(PROMPT_FOR_FILE);
/Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/
Function call stack
Function call stack

1 : [namespace = huDGPZAh] DataSet ^dataset_name = ReadDataFile(PROMPT_FOR_FILE);
1 : [namespace = xisvZUbY] DataSet ^dataset_name = ReadDataFile(PROMPT_FOR_FILE);

Keyword arguments:

Keyword arguments:
	{
Keyword arguments:
	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

Function call stack
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
}
{
}

	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

	}

2 : [namespace = EHXHsOTS] code_info=alignments.LoadGeneticCode(None);
1 : [namespace = IhwcjYkQ] DataSet ^dataset_name = ReadDataFile(PROMPT_FOR_FILE);
2 : [namespace = kshSkrkP] code_info=alignments.LoadGeneticCode(None);

2 : [namespace = avLvqFqI] code_info=alignments.LoadGeneticCode(None);
Keyword arguments:

	{
Keyword arguments:
Keyword arguments:
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
	}
Keyword arguments:
	{

	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

3 : [namespace = QDjnhiws] return alignments.ReadCodonDataSetFromPath(dataset_name,None);
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
}

	}

Keyword arguments:

3 : [namespace = zNnJeTlt] return alignments.ReadCodonDataSetFromPath(dataset_name,None);
{
3 : [namespace = XgNpaQaz] return alignments.ReadCodonDataSetFromPath(dataset_name,None);

	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

Keyword arguments:
	}
Keyword arguments:
	{

	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

4 : r "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
}
{
eturn alignments.LoadCodonDataFile(dataset_name,datafilter_name,alignments.ReadCodonDataSet(dataset_name));
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
}

	}

4 : return alignments.LoadCodonDataFile(dataset_name,datafilter_name,alignments.ReadCodonDataSet(dataset_name));
Keyword arguments:

4 : return alignments.LoadCodonDataFile(dataset_name,datafilter_name,alignments.ReadCodonDataSet(dataset_name));

	{

2 : [namespace = PxhFWIGD] code_info=alignments.LoadGeneticCode(None);

Keyword arguments:
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

Keyword arguments:
	{
	}
	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
Keyword arguments:

	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
	}
	{

5 : [namespace = relax] codon_data_info=alignments.PromptForGeneticCodeAndAlignment(prefix+".codon_data",prefix+".codon_filter");
}

	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

5 : [namespace = relax] codon_data_info=alignments.PromptForGeneticCodeAndAlignment(prefix+".codon_data",prefix+".codon_filter");
}
Keyword arguments:
5 : [namespace = relax] codon_data_info=alignments.PromptForGeneticCodeAndAlignment(prefix+".codon_data",prefix+".codon_filter");

	{

3 : [namespace = iywFKazF] return alignments.ReadCodonDataSetFromPath(dataset_name,None);
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

Keyword arguments:

	}
Keyword arguments:
	{
Keyword arguments:

	{
	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

6 : [namespace = relax] load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
}

	}
	}

Keyword arguments:

6 : [namespace = relax] load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});
{
6 : [namespace = relax] load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});

	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

4 : return alignments.LoadCodonDataFile(dataset_name,datafilter_name,alignments.ReadCodonDataSet(dataset_name));

Keyword arguments:
	}

Keyword arguments:
	{

Keyword arguments:
	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

7 : namespace
{
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

	}
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
	}

Step 0.LoadFunctionLibrary("SelectionAnalyses/modules/shared-load-file.bf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);

	}

7 : namespace
7 : namespace
5 : [namespace = relax] codon_data_info=alignments.PromptForGeneticCodeAndAlignment(prefix+".codon_data",prefix+".codon_filter");

Step 1.load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});

Step 0.LoadFunctionLibrary("SelectionAnalyses/modules/shared-load-file.bf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);
Step 0.LoadFunctionLibrary("SelectionAnalyses/modules/shared-load-file.bf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);

Keyword arguments:

	{

Step 2.LoadFunctionLibrary("SelectionAnalyses/modules/grid_compute.ibf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);;
Step 1.load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
Step 1.load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});

	}
Keyword arguments:

Step 2.LoadFunctionLibrary("SelectionAnalyses/modules/grid_compute.ibf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);;

	{

Step 2.LoadFunctionLibrary("SelectionAnalyses/modules/grid_compute.ibf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);;

6 : [namespace = relax] load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});
"tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

Keyword arguments:

	}
Keyword arguments:
	{
Keyword arguments:

	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
	}
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"

	}
	}

7 : namespace

Step 0.LoadFunctionLibrary("SelectionAnalyses/modules/shared-load-file.bf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);

Step 1.load_file({utility.getGlobalValue("terms.prefix"):"relax",utility.getGlobalValue("terms.settings"):{utility.getGlobalValue("terms.settings.branch_selector"):"relax.select_branches"}});

Step 2.LoadFunctionLibrary("SelectionAnalyses/modules/grid_compute.ibf", /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/);;

Keyword arguments:
	{
	 "tree":"/Users/zzha8134/Desktop/Genome/BUSCO analysis/topology"
	}

Check errors.log for execution error details.

Check errors.log for execution error details.

Check errors.log for execution error details.

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.msa --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/topology_coakroach_Z.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log"

dquote>
dquote>
dquote> y
dquote>
dquote>
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.msa --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/topology_coakroach_Z.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.msa --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log

^C
Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.msa --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
^C
Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.msa --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
2

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.msa --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
2

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.fasta --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
2

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.fasta --tree /Users/zzha8134/Desktop/Genome/BUSCO\ analysis/foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
2

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888_10.fasta --tree foreground_10.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
2

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888_9.fasta --tree foreground_9.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
2

Check errors.log for execution error details.
zzha8134@AC07HL1KJQ6P0 alignment % /Users/zzha8134/Desktop/Tech/hyphy-master/hyphy /Users/zzha8134/Desktop/Tech/hyphy/RELAX-mod/RELAX.bf --alignment 888aligned-cds.fasta --tree foreground.nwk --code Universal --branches Foreground --multiple-hits None --kill-zero-lengths No > 888_HyPhy-output.log
2

Check errors.log for execution error details.

Thanks for your reply,

Best wishes,
Zhuzhi

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spond commented Mar 8, 2024

Dear @Oswaldz,

The error indicates that HyPhy is unable to find the alignment file. But it's looking for it in an odd place

Could not find source dataset file "PROMPT_FOR_FILE" (resolved to '/Users/zzha8134/Desktop/Genome/Zhuzhi_single-copy-BUSCOs/shared/alignment/3')

My suspicion is that something in the RELAX-mod/RELAX.bf may be a bit off (since this is not a standard library analysis). Unfortunately, without looking at RELAX-mod/RELAX.bf, I don't think I can be of much further help. Could you share it as a .txt attachment here?

Best,
Sergei

@Oswaldz
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Oswaldz commented Mar 10, 2024

Hi Sergei,

Thanks. I downloaded the file from the code here, It's in the attachment.
RELAX.txt

Best wishes,
Zhuzhi

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