enasearch
enasearch copied to clipboard
Published
20 hours ago •
bebatut
bebatut
requests.exceptions.HTTPError: 500 Server Error
>>> enasearch.retrieve_run_report(accession="ERR1558694", fields="run_accession,instrument_platform,library_strategy,read_count,fastq_ftp")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/ebio/abt3_projects/software/dev/miniconda3_dev/envs/database/lib/python2.7/site-packages/enasearch/__init__.py", line 737, in retrieve_run_report
file=file)
File "/ebio/abt3_projects/software/dev/miniconda3_dev/envs/database/lib/python2.7/site-packages/enasearch/__init__.py", line 721, in retrieve_filereport
return request_url(url, "text", file)
File "/ebio/abt3_projects/software/dev/miniconda3_dev/envs/database/lib/python2.7/site-packages/enasearch/__init__.py", line 375, in request_url
r.raise_for_status()
File "/ebio/abt3_projects/software/dev/miniconda3_dev/envs/database/lib/python2.7/site-packages/requests/models.py", line 943, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: https://www.ebi.ac.uk/ena/portal/api/filereport
conda env
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
backports 1.0 py27_1 conda-forge
biopython 1.76 py27h516909a_0 conda-forge
blas 1.0 mkl
brotlipy 0.7.0 py27h516909a_1000 conda-forge
ca-certificates 2021.7.5 h06a4308_1
certifi 2020.6.20 pyhd3eb1b0_3
cffi 1.14.0 py27he30daa8_1
chardet 3.0.4 py27h8c360ce_1006 conda-forge
click 8.0.0 pyhd3eb1b0_0
configparser 4.0.2 py27_0
contextlib2 0.6.0.post1 py_0 conda-forge
cryptography 2.8 py27h2c19f6a_2 conda-forge
dicttoxml 1.7.4 py27_0 conda-forge
enasearch 0.2.2 py27_1 bioconda
enum34 1.1.10 py27h8c360ce_1 conda-forge
flake8 3.8.3 pyh9f0ad1d_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
importlib-metadata 1.5.0 py27h8c360ce_1 conda-forge
intel-openmp 2021.3.0 h06a4308_3350
ipaddress 1.0.23 py_0 conda-forge
libffi 3.3 h58526e2_2 conda-forge
libgcc-ng 11.1.0 hc902ee8_8 conda-forge
libgfortran-ng 7.5.0 h14aa051_19 conda-forge
libgfortran4 7.5.0 h14aa051_19 conda-forge
libgomp 11.1.0 hc902ee8_8 conda-forge
libstdcxx-ng 11.1.0 h56837e0_8 conda-forge
mccabe 0.6.1 py27_0 conda-forge
mkl 2020.2 256
mkl-service 2.3.0 py27he904b0f_0
mkl_fft 1.0.15 py27ha843d7b_0
mkl_random 1.1.0 py27hd6b4f25_0
more-itertools 5.0.0 py_0 conda-forge
ncurses 6.2 h58526e2_4 conda-forge
numpy 1.16.6 py27hbc911f0_0
numpy-base 1.16.6 py27hde5b4d6_0
openssl 1.1.1k h7f98852_1 conda-forge
pathlib2 2.3.5 py27h8c360ce_1 conda-forge
pip 20.1.1 pyh9f0ad1d_0 conda-forge
pycodestyle 2.6.0 pyh9f0ad1d_0 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pyflakes 2.2.0 pyh9f0ad1d_0 conda-forge
pyopenssl 20.0.1 pyhd3eb1b0_1
pysocks 1.7.1 py27h8c360ce_1 conda-forge
python 2.7.18 ha1903f6_2
python_abi 2.7 1_cp27mu conda-forge
readline 8.1 h46c0cb4_0 conda-forge
requests 2.25.1 pyhd3deb0d_0 conda-forge
scandir 1.10.0 py27hdf8410d_1 conda-forge
setuptools 44.0.0 py27_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.36.0 h9cd32fc_0 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
urllib3 1.26.6 pyhd8ed1ab_0 conda-forge
wheel 0.37.0 pyhd8ed1ab_1 conda-forge
xmltodict 0.12.0 py_0 conda-forge
zipp 1.0.0 py_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
Also, curl "https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=ERR1558694&result=read_run&fields=run_accession,instrument_platform,library_strategy,read_count,fastq_ftp" (as written in the docs) returns nothing, instead of:
ERR1558694 ILLUMINA WGS 1259641 ftp.sra.ebi.ac.uk/vol1/fastq/ERR155/004/ERR1558694/ERR1558694_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR155/004/ERR1558694/ERR1558694_2.fastq.gz
Changing line 706 in __init__.py to url = baseUrl + "portal/api/filereport?" fixes the issue. enasearch has the old url hardcoded