Problems using pheval

[seoanezonjic]

Hi Pheval authors Recently I've seen your paper in Researchgate and I'm very interested so I gave a try. Following the instructions here https://monarch-initiative.github.io/pheval/exomiser_pipeline (I use a previous exomiser version installed in my cluster) I've have the following problems:

• Tutorial saids in "5. Set PhEval Config YAML File" that exomiser directory program key is "exomiser" but it must be "exomiser-USED VERSION". If not set, it breaks with a dict key error.
• The dependency to j2cli to make j2 command works is not defined in poetry files so I have a j2 command not installed error. Maybe the snap version that you use contains jinja2 and j2 cli but I suggest to add "j2cli" to your depencies so all it's handled by python dependency manager
• pheval-utils create-spiked-vcfs gives the following error: "Error: No such option: --template-vcf-path (Possible options: --hg19-template-vcf, --hg38-template-vcf)". Downgrading pheval to 0.3.1 fix this error
• When I execute "make pheval run" the directory configurations/exomiser-13.1.0-default is created but later breaks because the file configurations/exomiser-13.1.0-default/config.yaml not exists. I think that this is counterintuitive, if the folder is created by pheval, I cannot create the config file in a folder that not exists. The same occurs for the preset-exome-analysis.yml file
• The pheval system make symlinks to exomiser configuration files but there is a stage that the file "application.properties" is accessed in write mode. As I work in a cluster and it's no sense install exomiser twice, I referenced the cluster installation that it's write protected so I have a Permission Error. If you simlink this file to write in it (that is not a good practice as the program is also used in other contexts), why not copy it? If you execute exomiser from configurations directory, it will access the copied file instead the original one, so the symlink is not necessary. In fact, I fixed this problem removing the symlink and copying the original "application.properties" file to the exomiser folder within configurations directory.
• Exomiser gives me file errors when with configurations/exomiser-13.1.0-default/2302_hg19/2302_hg19_transcripts_ensembl.ser and configurations/exomiser-13.1.0-default/2302_hg38/2302_hg38_transcripts_ensembl.ser. Pheval do NOT simlink these files or give any error about not finding them when simlinking. Simlink manually 2302_hg19 and 2302_hg38 folders from original exomiser installation fixed the problem.
• File errors with phenotype files. Pheval simlinks each file of phenotype folder instead simlink the folder. Simlink manually the phenotype folder within exomiser folder in configuration directory fixed the problem.
• Due to previous errors I've had several results folders with corrupted exomiser executions. If I execute "make pheval run", make execute and exits from pheval folder instead of resume exomiser execution. To do so, I have to remove manually the results folder. I think that the corresponding rule has to check if exomiser has generated the results files and if not, launch exomiser.

Once I've succesfully executed the pipeline, what is the next step to obtain the performance figures shown in the paper? Thank you very much in advance Pedro Seoane

[matentzn]

@seoanezonjic Thank you for your message, the whole team is OOO at the moment, but someone will come back to you when they are back!

[seoanezonjic]

Thank you @matentzn and @yaseminbridges , I''ll wait to the team and in the meantime I'm playing with the platform. In fact, another problem that I faced is that I'm executing in my university cluster but the computing nodes has not access to internet and the script create_noisy_phenopackets.py fails in the following line: resource = OntologyResource(slug="hp.obo", local=False) I think that the script should have an option to set "local" attribute to True and used a cached version of the ontology files in this computing environments (and I think that it will speeds up the execution avoiding repeated queries to servers) Thank you in advance Pedro Seoane

[yaseminbridges]

Hi, @seoanezonjic!

Thank you for documenting these problems in detail!

I think a lot of these issues may be due to the MakeFile pipeline needing to be updated to what we use in the paper. @souzadevinicius can you confirm?

[souzadevinicius]

Hello, @seoanezonjic,

Thank you for your message. I acknowledge that the PhEval pipeline documentation is outdated. I am currently working on updating it.

In the meantime, you can utilize a pipeline described in this repository: https://github.com/monarch-initiative/monarch_pheval. The repository contains different types of experiments, which can be edited by modifying the PhEval Config YAML File.

To execute all experiments outlined in the config file, please follow two steps provided in the pipeline documentation:

1. Run bash ./resources/generatemakefile.sh
2. Execute make pheval

I apologize for any inconvenience caused by the outdated documentation. If you happen to have any other issues, please feel free to reach out to me.

Thank you.

[julesjacobsen]

@souzadevinicius is the pheval Makefile needed any more if the monarch-pheval repo exists?

[souzadevinicius]

@souzadevinicius is the pheval Makefile needed any more if the monarch-pheval repo exists?

No, it's not, @julesjacobsen. I'm updating the PhEval pipeline documentation and removing these unnecessary files.

[yaseminbridges]

Hi, @seoanezonjic! Just a brief update:

• I have implemented an option to specify a local cached ontology file to the scramble-phenopackets command, allowing you to run in the computing environment you are using.
• There is now a docs page on how to execute a benchmark, this is a guide for how to produce performance figures shown in the paper.

These changes are implemented in v0.4.0

[seoanezonjic]

Hi @souzadevinicius and @yaseminbridges Thank you by your suggestions and code changes. First, I was toying with https://github.com/monarch-initiative/monarch_pheval but then Yasemin came around with her message and then I followed the tutorial that she point to me. So, using this tutorial I have the following problems:

• Again jinja2 problems: ./resources/generatemakefile.sh: línea 37: j2: command not found. I solved this with pip install j2cli whithin the poetry environment but again I strongly suggest to add this dependency to the project.
• Another error related with the yaml listed in the tutorial:

  
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval_monarch/pheval/resources/Makefile.j2", line 72, in top-level template code  configurations/{{ config.id }}/config.yaml:
         jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'id'

The line that makes reference: `Makefile.j2", line 72 -> configurations/{{ config.id }}/config.yaml:` . And config.id was not defined in yaml. I set it to `id: exomiser-13.2.0`

- Finally, the makefile has some problem because this error: `Makefile:149  *** target pattern contains no '%'. Stop.`. The mentioned makefile line contains:

prepare-corpora: corpora/small_test/scrambled-0.5/corpus.ymlcorpora/small_test/scrambled-0.7/corpus.yml: corpora/small_test/default/corpus.yml $(ROOT_DIR)/testdata/template_vcf/template_exome_hg19.vcf.gz test -d $(ROOT_DIR)/corpora/small_test/scrambled-0.7/ || mkdir -p $(ROOT_DIR)/corpora/small_test/scrambled-0.7/ test -L $(ROOT_DIR)/corpora/small_test/scrambled-0.7/template_exome_hg19.vcf.gz || ln -s $(ROOT_DIR)/testdata/template_vcf/template_exome_hg19.vcf.gz $(ROOT_DIR)/corpora/small_test/scrambled-0.7/template_exome_hg19.vcf.gz

If you could give some clue to fix this error I would thank you a lot.
Pedro Seoane

[yaseminbridges]

Hi @seoanezonjic

Apologies, just to clarify, did you face these errors when executing the pipeline here: https://github.com/monarch-initiative/monarch_pheval?

For the time being, you should use the instructions outlined in that repo and tailor it to the experiments that you want to run and ignore the docs regarding the MakeFile pipeline in this repo.

@souzadevinicius is OOO but he will be able to advise you further on your issues with the MakeFile once he returns

[seoanezonjic]

Hi @yaseminbridges I started in that repo BUT when you answered me with your message about pheval 0.4.0 and the new features I removed all files. From zero, I followed the instructions in https://monarch-initiative.github.io/pheval/executing_a_benchmark/ and I ended with the errors enumerated in my previous post and I expected a successful run. I do NOT mixed instructions or files from both repos. Thank you in advance Pedro Seoane

[yaseminbridges]

Hi @seoanezonjic Thank you for your patience on this and apologies for the misunderstanding. The instructions here: https://monarch-initiative.github.io/pheval/executing_a_benchmark/ are separate to the PhEval MakeFile pipeline. In order to execute a benchmark you must already have successfully run and have a directory or several directories of PhEval standardised TSV results. For example, after a single executed pheval run the output directory may look like so:

.
├── pheval_disease_results
│   ├── patient_1-pheval_disease_result.tsv
├── pheval_gene_results
│   ├── patient_1-pheval_gene_result.tsv
├── pheval_variant_results
│   ├── patient_1-pheval_variant_result.tsv
├── raw_results
│   ├── patient_1.json
├── results.yml
└── tool_input_commands
    └── tool_input_commands.txt

The MakeFile pipeline will automatically implement this command in its pipeline so you do not need to do so manually if you are planning to run the MakeFile.

[seoanezonjic]

Hi @yaseminbridges Now I'm understand and I apologize for my misunderstanding, I've a lot in my head the last weeks. I'll explain my steps with the aim of get a operational pheval in my cluster to benchmark my prioritizer. First, I need to get a working example with exomiser al least. My steps were:

• As you tell me that the pheval v0.4.0 has the option to use a local cached ontology file, I'm started from zero. I deleted all my work with https://github.com/monarch-initiative/monarch_pheval and I followed this guide: https://monarch-initiative.github.io/pheval/exomiser_pipeline/
• The errors listed in https://github.com/monarch-initiative/pheval/issues/347#issuecomment-2399813523 are from this fresh install and execution.
• I can't execute the instructions on https://monarch-initiative.github.io/pheval/executing_a_benchmark/ guide because the problems I've got with the Makefile

I hope that now it's clear my problem and I'm very sorry for the confusion Thank you in advance Pedro Seoane

[souzadevinicius]

Hi, @seoanezonjic.

I hope you have successfully run the PhEval pipeline. In any case, the https://monarch-initiative.github.io/pheval/executing_a_benchmark/ has been updated.

If you want to explore the pipeline process further, we have a dedicated repository available at https://github.com/monarch-initiative/monarch_pheval. This pipeline includes ready-to-use "recipes" structured with Makefile and YAML configuration files, designed to simplify each step. There is a branch specifically for PhEval paper experiments (the pheval-paper branch). We are actively updating the documentation to enhance usability, and your feedback is essential to this process.

Thank you!

[seoanezonjic]

Hi @souzadevinicius Thank you for the update but I've waiting a recommendation or fix for my problems listed in https://github.com/monarch-initiative/pheval/issues/347#issuecomment-2399813523 when I followed this guide: https://monarch-initiative.github.io/pheval/exomiser_pipeline. I'm stuck with this and I can't continue to the benchmark. If you want, you can point me to a guide for a Exomiser execution with pheval and another to make the benchmark to start from zero again. In this way, we all stay in the same page an we could debug together the bug origin. Thank you in advance Pedro Seoane

[souzadevinicius]

Hi @souzadevinicius Thank you for the update but I've waiting a recommendation or fix for my problems listed in #347 (comment) when I followed this guide: https://monarch-initiative.github.io/pheval/exomiser_pipeline. I'm stuck with this and I can't continue to the benchmark. If you want, you can point me to a guide for a Exomiser execution with pheval and another to make the benchmark to start from zero again. In this way, we all stay in the same page an we could debug together the bug origin. Thank you in advance Pedro Seoane

Hello, Pedro.

You're completely right about your suggestion of adding j2cli as a dependency and we did it. However, as I mentioned, we moved all pipeline code to a new repository to decouple this core PhEval repository from the pipeline code.

Additionally, in the updated documentation we don't mention j2 anymore because everything is encapsulated in Monarch PhEval repository. The Makefile generation is also fixed. If you have any other questions or issues, let us know.

[seoanezonjic]

Hi @souzadevinicius I've solved the j2cli and the yaml errors but the following it's blocking me (I write the text from the previous message):

• Finally, the makefile has some problem because this error: Makefile:149 *** target pattern contains no '%'. Stop.. The mentioned makefile line contains:

  
  prepare-corpora: corpora/small_test/scrambled-0.5/corpus.ymlcorpora/small_test/scrambled-0.7/corpus.yml: corpora/small_test/default/corpus.yml $(ROOT_DIR)/testdata/template_vcf/template_exome_hg19.vcf.gz
      test -d $(ROOT_DIR)/corpora/small_test/scrambled-0.7/ || mkdir -p $(ROOT_DIR)/corpora/small_test/scrambled-0.7/
      test -L $(ROOT_DIR)/corpora/small_test/scrambled-0.7/template_exome_hg19.vcf.gz || ln -s $(ROOT_DIR)/testdata/template_vcf/template_exome_hg19.vcf.gz $(ROOT_DIR)/corpora/small_test/scrambled-0.7/template_exome_hg19.vcf.gz

This error I'm unable to resolve it. Any suggestion?
Thank you in advance
Pedro Seoane

[souzadevinicius]

Hi @souzadevinicius I've solved the j2cli and the yaml errors but the following it's blocking me (I write the text from the previous message):

• Finally, the makefile has some problem because this error: Makefile:149 *** target pattern contains no '%'. Stop.. The mentioned makefile line contains:

prepare-corpora: corpora/small_test/scrambled-0.5/corpus.ymlcorpora/small_test/scrambled-0.7/corpus.yml: corpora/small_test/default/corpus.yml $(ROOT_DIR)/testdata/template_vcf/template_exome_hg19.vcf.gz
        test -d $(ROOT_DIR)/corpora/small_test/scrambled-0.7/ || mkdir -p $(ROOT_DIR)/corpora/small_test/scrambled-0.7/
        test -L $(ROOT_DIR)/corpora/small_test/scrambled-0.7/template_exome_hg19.vcf.gz || ln -s $(ROOT_DIR)/testdata/template_vcf/template_exome_hg19.vcf.gz $(ROOT_DIR)/corpora/small_test/scrambled-0.7/template_exome_hg19.vcf.gz

This error I'm unable to resolve it. Any suggestion? Thank you in advance Pedro Seoane

Hello, @seoanezonjic.

I recommend generating a new Makefile.

You can do this by cloning the monarch_pheval repository and regenerating the Makefile. Here are the steps to follow:

1. Run the command: git clone -b new-paper-2025 https://github.com/monarch-initiative/monarch_pheval.git
2. Access the created directory: cd monarch_pheval
3. Fill in the ./resources/pheval-config.yaml file with your experiment descriptions.
4. Execute the script by running: ./resources/generatemakefile.sh
5. Finally, type make pheval to compile.

Let me know if you have any questions!

[seoanezonjic]

Hi @souzadevinicius My problem is with the step 3, I have not clear documentation so to execute a exomiser run I've modified ./resources/pheval-config.yaml to:

directories:
  data: data
  tmp: data/tmp

corpora:
  - id: lirical
    custom_variants:
      - id: no_phenotype

configs:
  - tool: exomiser
    id: exomiser-14.0.0-2402_phenotype
    version: 14.0.0

runs:
  - tool: exomiser
    corpus: lirical
    corpusvariant: default
    version: 14.0.0
    phenotype: 2402
    configuration: exomiser-14.0.0-2402_phenotype

I've got this error:

mkdir -p /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype
pheval run \
 --input-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/configurations/exomiser-14.0.0-2402_phenotype \
 --testdata-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/corpora/lirical/default \
 --runner exomiserphevalrunner \
 --tmp-dir data/tmp/ \
 --version 14.0.0 \
 --output-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype
Traceback (most recent call last):
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/bin/pheval", line 8, in <module>
    sys.exit(pheval())
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/pheval/cli_pheval.py", line 87, in run
    runner_class = get_implementation_resolver().lookup(runner)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/class_resolver/api.py", line 182, in lookup
    return get_cls(
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/class_resolver/api.py", line 424, in get_cls
    raise KeyError(
KeyError: "Invalid PhEvalRunner name: exomiserphevalrunner (normalized to: exomiserphevalrunner). Valid choices are: ['defaultphevalrunner', 'templatephevalrunner']"
make[1]: *** [Makefile:69: /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype/results.yml] Error 1
make[1]: Leaving directory '/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval'
make: *** [Makefile:140: pheval] Error 2

A documentation explaining how works the file ./resources/pheval-config.yaml and how must be used would be very appreciated (not only examples but each section and attribute described to launch exomiser, lirical, gado and phen2gene programs I think that each one needs specific configuration). Thank you in advance Pedro Seoane

[souzadevinicius]

Hi @souzadevinicius My problem is with the step 3, I have not clear documentation so to execute a exomiser run I've modified ./resources/pheval-config.yaml to:

directories:
  data: data
  tmp: data/tmp

corpora:
  - id: lirical
    custom_variants:
      - id: no_phenotype

configs:
  - tool: exomiser
    id: exomiser-14.0.0-2402_phenotype
    version: 14.0.0

runs:
  - tool: exomiser
    corpus: lirical
    corpusvariant: default
    version: 14.0.0
    phenotype: 2402
    configuration: exomiser-14.0.0-2402_phenotype

I've got this error:

mkdir -p /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype
pheval run \
 --input-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/configurations/exomiser-14.0.0-2402_phenotype \
 --testdata-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/corpora/lirical/default \
 --runner exomiserphevalrunner \
 --tmp-dir data/tmp/ \
 --version 14.0.0 \
 --output-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype
Traceback (most recent call last):
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/bin/pheval", line 8, in <module>
    sys.exit(pheval())
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/pheval/cli_pheval.py", line 87, in run
    runner_class = get_implementation_resolver().lookup(runner)
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/class_resolver/api.py", line 182, in lookup
    return get_cls(
  File "/localscratch/users/pedro/pypoetry/virtualenvs/monarch-pheval-3lvLeukC-py3.10/lib/python3.10/site-packages/class_resolver/api.py", line 424, in get_cls
    raise KeyError(
KeyError: "Invalid PhEvalRunner name: exomiserphevalrunner (normalized to: exomiserphevalrunner). Valid choices are: ['defaultphevalrunner', 'templatephevalrunner']"
make[1]: *** [Makefile:69: /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype/results.yml] Error 1
make[1]: Leaving directory '/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval'
make: *** [Makefile:140: pheval] Error 2

A documentation explaining how works the file ./resources/pheval-config.yaml and how must be used would be very appreciated (not only examples but each section and attribute described to launch exomiser, lirical, gado and phen2gene programs I think that each one needs specific configuration). Thank you in advance Pedro Seoane

Hello, @seoanezonjic.

We are almost there. Your Makefile is correct. Now, you need the pheval.exomiser plugin, just installing it using poetry:

poetry add pheval.exomiser or pip: pip install pheval.exomiser

I'm adding to the documentation to make it clearer

[seoanezonjic]

Hi @souzadevinicius I've installed pheval.exomiser and then I've obtained the following errors:

    pheval run \
 --input-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/configurations/exomiser-14.0.0-2402_phenotype \
 --testdata-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/corpora/lirical/default \
 --runner exomiserphevalrunner \
 --tmp-dir data/tmp/ \
 --version 14.0.0 \
 --output-dir /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype
preparing
Traceback (most recent call last):
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/bin/pheval", line 8, in <module>
    sys.exit(pheval())
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pheval/cli_pheval.py", line 90, in run
    runner_instance.prepare()
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pheval_exomiser/runner.py", line 30, in prepare
    configurations=ExomiserConfigurations.parse_obj(
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pydantic/main.py", line 1162, in parse_obj
    return cls.model_validate(obj)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pydantic/main.py", line 596, in model_validate
    return cls.__pydantic_validator__.validate_python(
pydantic_core._pydantic_core.ValidationError: 3 validation errors for ExomiserConfigurations
application_properties.hg19_data_version
  Input should be a valid string [type=string_type, input_value=2402, input_type=int]
    For further information visit https://errors.pydantic.dev/2.9/v/string_type
application_properties.hg38_data_version
  Input should be a valid string [type=string_type, input_value=2402, input_type=int]
    For further information visit https://errors.pydantic.dev/2.9/v/string_type
application_properties.phenotype_data_version
  Input should be a valid string [type=string_type, input_value=2402, input_type=int]
    For further information visit https://errors.pydantic.dev/2.9/v/string_type
make: *** [Makefile:69: /mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/results/exomiser-14.0.0-2402_phenotype/results.yml] Error 1

This I 've fixed editing runners/configurations/exomiser-14.0.0-2402_phenotype.config.yaml and change 2402 to "2402" but then the following error arises:

Traceback (most recent call last):
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/bin/pheval", line 8, in <module>
    sys.exit(pheval())
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pheval/cli_pheval.py", line 91, in run
    runner_instance.run()
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pheval_exomiser/runner.py", line 49, in run
    run_exomiser(
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pheval_exomiser/run/run.py", line 208, in run_exomiser
    run_exomiser_local(
  File "/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/.venv/lib/python3.10/site-packages/pheval_exomiser/run/run.py", line 120, in run_exomiser_local
    exomiser_jar_file = [
IndexError: list index out of range

I've debugged line 117 from pheval_exomiser/run/run.py and a simple print as following:

    print(f"_{config.exomiser_software_directory}_", file=sys.stderr)
    print(f"_{input_dir.joinpath(config.exomiser_software_directory)}_", file=sys.stderr)

Shows this:

_._
_/mnt/home/users/pab_001_uma/pedro/proyectos/pheval/PIPELINE/monarch_pheval/configurations/exomiser-14.0.0-2402_phenotype_

This is a path error because exomiser is installed in the runners folder as I can see in my local installation of the monarch-pheval. Maybe is a misconfiguration in my yaml file? Thank you in advance Pedro Seoane

[souzadevinicius]

Yes maybe it is, please share your config.yaml file.

[seoanezonjic]

Hi @souzadevinicius Here it is:

directories:
  data: data
  tmp: data/tmp

corpora:
  - id: lirical
    custom_variants:
      - id: no_phenotype

configs:
  - tool: exomiser
    id: exomiser-14.0.0-2402_phenotype
    version: 14.0.0

runs:
  - tool: exomiser
    corpus: lirical
    corpusvariant: default
    version: 14.0.0
    phenotype: "2402"
    configuration: exomiser-14.0.0-2402_phenotype