Comments (22)
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.
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.
from annotsv.
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) ?
from annotsv.
Finally got it working!
I had to manually re-download every file in PhenoGenius/data/resources
Thank you @kyauy and @lgmgeo !
Best
from annotsv.
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
from annotsv.
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
from annotsv.
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
from annotsv.
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
from annotsv.
$ 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')
from annotsv.
Can you try the same command with python == 3.8?
Else, @kyauy, can you help us please?
from annotsv.
Same output with python-3.8.12
from annotsv.
Ok, waiting for help from the PhenoGenius developper (@kyauy)
from annotsv.
Do you have git-lfs installed?
which git-lfs
Because the resource files in the PhenoGenius GitHub are hosted via git-lfs
from annotsv.
No,
I didn't have it...
Thank you
Alessandro
from annotsv.
Thanks for the feed-back, I will update the README.
Have fun with PhenoGenius and AnnotSV!
from annotsv.
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!
from annotsv.
Do you have git-lfs installed?
from annotsv.
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.
from annotsv.
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.
Could you try to install it directly ?
Thanks,
Kevin
from annotsv.
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!
from annotsv.
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
from annotsv.
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
from annotsv.
Great!
from annotsv.
Related Issues (20)
- Unusual large memory needed for very large sized coupled BNDs HOT 4
- Why is there never a class 2 in ACMG_class? HOT 1
- CytoBand appear... HOT 3
- MAF in gnomAD HOT 1
- Is there a way to include ensembl_ids and/or hgnc_ids along with gene_name? HOT 3
- New long-read population reference HOT 1
- Question about reverse strand genes HOT 7
- Rogue double quote in PRDM10 HOT 6
- custom bed annotation. overlap within n bases HOT 2
- Multiple column and tab errors with CNVkit vcf output HOT 4
- left gene HOT 15
- Mapping of structural variant to intron or coding regions HOT 2
- exomiser error: connect failed connection refused HOT 2
- vcf errors HOT 1
- AnnotSV passing wrong arguments to variant convert HOT 5
- Keep AnnotSV_ID consistent with SV_chrom HOT 10
- frameshift between full and split mode HOT 5
- UCSC link failed to open the correct position HOT 5
- AnnotSV" line 283 HOT 3
- VCF for false positive deletion and for compund etherozygosity
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from annotsv.