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HyPhy: Hypothesis testing using Phylogenies
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Error when using RELAX #1698

Closed Oswaldz closed 1 month ago

Oswaldz commented 4 months ago

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 commented 4 months ago

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 commented 4 months ago

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).

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

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

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:

spond@temple.edu spond@temple.edu

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

spond commented 4 months ago

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 commented 3 months ago

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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