PhenoGenius issue

[lgmgeo]

PhenoGenius issue

[jammywwh]

Do you have git-lfs installed?

I installed it with conda and confirmed that git-lfs (3.5.1) was installed successfully.

Hi!

Not sure that git-lfs installed by conda makes it.

conda/conda-build#1462

Could you try to install it directly ?

Thanks, Kevin

According https://github.com/git-lfs/git-lfs/wiki/Installation described "On all operating systems, once git-lfs is downloaded, git lfs install must be run. ", I execute

git lfs install
git clone https://github.com/kyauy/PhenoGenius.git

It works!
Thank you.

[kyauy]

Hi @abrusell and @lgmgeo !

It seems that this file is corrupted in your clone repository ("data/resources/Homo_sapiens.gene_info.gz" -> gzip.BadGzipFile: Not a gzipped file (b've')).

Errors may have happen during the download, can you reinstall ? (https://github.com/kyauy/PhenoGenius.git) or replace the corresponding file (https://github.com/kyauy/PhenoGenius/blob/main/data/resources/Homo_sapiens.gene_info.gz) ?

[abrusell]

Finally got it working!
I had to manually re-download every file in PhenoGenius/data/resources

Thank you @kyauy and @lgmgeo !
Best

[jammywwh]

I'm sorry, I went ahead and tested it and it's working now. Thanks.
$ANNOTSV/bin/AnnotSV -SVinputFile ./input/PKD1.bed -outputFile "./output/PKD1.annotated.tsv" -svtbedcol 4 -genomeBuild GRCh38 -hpo "HP:0000107,HP:0000108,HP:0001407,HP:0005562"

Hi, @lgmgeo Thanks for your reply, I re-executed as you said, but this log file still shows the same message as before.

git clone https://github.com/lgmgeo/AnnotSV.git
cd ${ANNOTSV}
make PREFIX=. install
make PREFIX=. install-human-annotation
git lfs install
mkdir -p ${ANNOTSV}/share/python3/phenogenius ; cd ${ANNOTSV}/share/python3/phenogenius
${ANNOTSV}/share/bash/AnnotSV/checkPhenoGeniusInstall.sh

the ${ANNOTSV}/share/python3/phenogenius/PhenoGenius.install.log shows:

Cloning into 'PhenoGenius'...
Note: switching to 'fd7e63c7192c968a054cf0c0f0e7f6421326e7ce'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false

[lgmgeo]

1- Can you share your $ANNOTSV/share/python3/phenogenius/PhenoGenius.install.log file?

2- Can you share your $ANNOTSV/share/python3/phenogenius/poetry_install.log file?

3- Is this the same user installing and running AnnotSV?
If not, can you try changing the permissions in the PhenoGenius installation?
chmod -R 777 $ANNOTSV/share/python3/phenogenius/

4- Did you run AnnotSV from the same environment (python...) as that used during installation?

5- Another question, did you run AnnotSV with bioconda?
Same feelings regarding permissions in the "conda_env_share" you are using

[abrusell]

1- Even though phenogenius seems to have been installed whithout errors, I haven't got a PhenoGenius.install.log... I don't know why!
2- I have 2 poetry_install.log: one in the $ANNOTSV/share/python3/phenogenius/ directory :
Updating dependencies Resolving dependencies... Writing lock file No dependencies to install or update Installing the current project: PhenoGenius_app (0.1.0)

and one in $ANNOTSV/share/ directory:
Poetry could not find a pyproject.toml file in $ANNOTSV/share/python3 or its parents
This one seems to have encountered some problems...

3- YES
4- YES
5- NO, I've installed it from source

Thank you

[lgmgeo]

Can you run the following commands and show me each result:

bash
cd $ANNOTSV/share/python3/phenogenius/PhenoGenius
poetry --version 
python --version
python3 --version
poetry install
poetry run python3 phenogenius_cli.py --help
poetry run python3 phenogenius_cli.py --hpo_list HP:0000107,HP:0000108,HP:0001407,HP:0005562 --result_file PKD1.tsv

[abrusell]

$ cd $ANNOTSV/share/python3/phenogenius/PhenoGenius
$ poetry --version
Poetry (version 1.2.2)
$ python --version
Python 3.9.15
$ python3 --version
Python 3.9.15
$ poetry install

Installing dependencies from lock file

No dependencies to install or update

Installing the current project: PhenoGenius_app (0.1.0)

$ poetry run python3 phenogenius_cli.py --help

Usage: phenogenius_cli.py [OPTIONS]

Options:
  --version           Show the version and exit.
  --result_file TEXT  Output file name, default = match.tsv
  --hpo_list TEXT     (Mandatory) List of HPO terms to match, separated with
                      commas
  --gene_list TEXT    (Optional) List of genes in NCBI ID format to match,
                      separated with commas
  --help              Show this message and exit.

$ poetry run python3 phenogenius_cli.py --hpo_list HP:0000107,HP:0000108,HP:0001407,HP:0005562 --result_file PKD1.tsv

Traceback (most recent call last):
  File "phenogenius_cli.py", line 245, in <module>
    evaluate_matching()
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "phenogenius_cli.py", line 141, in evaluate_matching
    ncbi, symbol = symbol_to_id_to_dict()
  File "phenogenius_cli.py", line 38, in symbol_to_id_to_dict
    ncbi_df = pd.read_csv("data/resources/Homo_sapiens.gene_info.gz", sep="\t")
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1679, in _make_engine
    return mapping[engine](f, **self.options)
  File "/g100/home/userexternal/abrusell/.cache/pypoetry/virtualenvs/phenogenius-app-3ZtR_Fj0-py3.8/lib/python3.8/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas/_libs/parsers.pyx", line 550, in pandas._libs.parsers.TextReader.__cinit__
  File "pandas/_libs/parsers.pyx", line 639, in pandas._libs.parsers.TextReader._get_header
  File "pandas/_libs/parsers.pyx", line 850, in pandas._libs.parsers.TextReader._tokenize_rows
  File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._check_tokenize_status
  File "pandas/_libs/parsers.pyx", line 2021, in pandas._libs.parsers.raise_parser_error
  File "/g100_work/PROJECTS/spack/v0.17/prod/0.17.1/install/0.17/linux-centos8-cascadelake/intel-2021.4.0/python-3.8.12-tvg3jcaazvbwlpwrdeiyin4rjulbae26/lib/python3.8/_compression.py", line 68, in readinto
    data = self.read(len(byte_view))
  File "/g100_work/PROJECTS/spack/v0.17/prod/0.17.1/install/0.17/linux-centos8-cascadelake/intel-2021.4.0/python-3.8.12-tvg3jcaazvbwlpwrdeiyin4rjulbae26/lib/python3.8/gzip.py", line 479, in read
    if not self._read_gzip_header():
  File "/g100_work/PROJECTS/spack/v0.17/prod/0.17.1/install/0.17/linux-centos8-cascadelake/intel-2021.4.0/python-3.8.12-tvg3jcaazvbwlpwrdeiyin4rjulbae26/lib/python3.8/gzip.py", line 427, in _read_gzip_header
    raise BadGzipFile('Not a gzipped file (%r)' % magic)
gzip.BadGzipFile: Not a gzipped file (b've')

[lgmgeo]

Can you try the same command with python == 3.8?

Else, @kyauy, can you help us please?

[abrusell]

Same output with python-3.8.12

[lgmgeo]

Ok, waiting for help from the PhenoGenius developper (@kyauy)

[lgmgeo]

Do you have git-lfs installed?

which git-lfs

Because the resource files in the PhenoGenius GitHub are hosted via git-lfs

[abrusell]

No,
I didn't have it...

Thank you
Alessandro

[lgmgeo]

Thanks for the feed-back, I will update the README.

Have fun with PhenoGenius and AnnotSV!

[jammywwh]

Hi @abrusell and @lgmgeo !

It seems that this file is corrupted in your clone repository ("data/resources/Homo_sapiens.gene_info.gz" -> gzip.BadGzipFile: Not a gzipped file (b've')).

Errors may have happen during the download, can you reinstall ? (https://github.com/kyauy/PhenoGenius.git) or replace the corresponding file (https://github.com/kyauy/PhenoGenius/blob/main/data/resources/Homo_sapiens.gene_info.gz) ?

Hi @kyauy,
I got same issue. I use "git clone https://github.com/kyauy/PhenoGenius.git", but files are empty in data/ directory.
Only "wget https://github.com/kyauy/PhenoGenius/blob/main/data/resources/Homo_sapiens.gene_info.gz" is work.
How can i get all correct files once.
Thanks, looking forward to your reply!

[lgmgeo]

Do you have git-lfs installed?

[jammywwh]

Do you have git-lfs installed?

I installed it with conda and confirmed that git-lfs (3.5.1) was installed successfully.

I get the following message every time I run git clone https://github.com/kyauy/PhenoGenius.git.
Cloning into 'PhenoGenius'...
remote: Enumerating objects: 232, done.
remote: Counting objects: 100% (210/210), done.
remote: Compressing objects: 100% (128/128), done.
remote: Total 232 (delta 99), reused 183 (delta 77), pack-reused 22
Receiving objects: 100% (232/232), 84.46 KiB | 426.00 KiB/s, done.
Resolving deltas: 100% (115/115), done.

[kyauy]

Do you have git-lfs installed?

I installed it with conda and confirmed that git-lfs (3.5.1) was installed successfully.

Hi!

Not sure that git-lfs installed by conda makes it.

conda/conda-build#1462

Could you try to install it directly ?

Thanks,
Kevin

[jammywwh]

Hi, @kyauy @lgmgeo
I got a new issue, when I execute
$ANNOTSV/bin/AnnotSV -SVinputFile ./input/PKD1.bed -outputFile "./output/PKD1.annotated.tsv" -svtbedcol 4 -genomeBuild GRCh38 -hpo "HP:0000107,HP:0000108,HP:0001407,HP:0005562"
It will re-download PhenoGenius, PhenoGenius.install.log, and poetry_install.log under the current path, then output

WARNING: No PhenoGenius installation available for the phenotype-driven analysis.
cf $ANNOTSV/share/python3/phenogenius/*.log

PhenoGenius.install.log

Cloning into 'PhenoGenius'...
Note: switching to 'fd7e63c7192c968a054cf0c0f0e7f6421326e7ce'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

git switch -c

Or undo this operation with:

git switch -

Turn off this advice by setting config variable advice.detachedHead to false

Filtering content: 100% (22/22), 160.66 MiB | 2.96 MiB/s, done.

poetry_install.log

Updating dependencies
Resolving dependencies...

No dependencies to install or update

Writing lock file

Installing the current project: PhenoGenius_app (0.1.0)

What's this about, what am I doing wrong?
Thanks, looking forward to your reply!

[lgmgeo]

Hi,

When HPO terms are given as input, AnnotSV checks if the PhenoGenius installation is correct.
=> To do this, AnnotSV executes the file $ANNOTSV/share/bash/AnnotSV/checkPhenoGeniusInstall.sh
=> The results are in $ANNOTSV/share/python3/phenogenius/*.log

The result of git clone https://github.com/kyauy/PhenoGenius --branch v1.0.0 is strange:

=> The problem seems to be with your git clone command.

Ok, can you run the following commands:

echo $ANNOTSV
cd $ANNOTSV/share/python3/phenogenius
chmod -R 777 PhenoGenius* poetry_install.log
rm -r  PhenoGenius* poetry_install.log
$ANNOTSV/share/bash/AnnotSV/checkPhenoGeniusInstall.sh

[jammywwh]

Hi, @lgmgeo
Thanks for your reply, I re-executed as you said, but this log file still shows the same message as before.

git clone https://github.com/lgmgeo/AnnotSV.git
cd ${ANNOTSV}
make PREFIX=. install
make PREFIX=. install-human-annotation
git lfs install
mkdir -p ${ANNOTSV}/share/python3/phenogenius ; cd ${ANNOTSV}/share/python3/phenogenius
${ANNOTSV}/share/bash/AnnotSV/checkPhenoGeniusInstall.sh

the ${ANNOTSV}/share/python3/phenogenius/PhenoGenius.install.log shows:

Cloning into 'PhenoGenius'...
Note: switching to 'fd7e63c7192c968a054cf0c0f0e7f6421326e7ce'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

git switch -c

Or undo this operation with:

git switch -

Turn off this advice by setting config variable advice.detachedHead to false

[lgmgeo]

Great!