I'm running the dev branch of mhcquant under the test profile on my local server:
git clone --branch dev --single-branch git@github.com:nf-core/mhcquant.git mhcquant
nextflow run ./main.nf -profile test,docker --outdir test
And keep running into the same error:
Apr-25 13:01:55.598 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE (HepG2_1)'
Caused by:
Process `NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE (HepG2_1)` terminated with an error exit status (1)
Command executed:
ms2rescore_cli.py \
--psm_file HepG2_1.idXML \
--spectrum_path . \
--output_path HepG2_1_ms2rescore.idXML \
--processes 2 \
--ms2_tolerance 0.02 --ms2pip_model Immuno-HCD --rescoring_engine percolator --feature_generators deeplc,ms2pip
cat <<-END_VERSIONS > versions.yml
"NFCORE_MHCQUANT:MHCQUANT:MS2RESCORE":
MS²Rescore: $(echo $(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \(v\K[^\)]+' ))
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
File "/usr/local/lib/python3.10/socket.py", line 824, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
File "/usr/local/lib/python3.10/socket.py", line 955, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno -3] Temporary failure in name resolution
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data2023/suna/proj/mhcquant/bin/ms2rescore_cli.py", line 175, in <module>
sys.exit(main())
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/data2023/suna/proj/mhcquant/bin/ms2rescore_cli.py", line 171, in main
rescore_idxml(kwargs["psm_file"], kwargs["output_path"], config)
File "/data2023/suna/proj/mhcquant/bin/ms2rescore_cli.py", line 81, in rescore_idxml
rescore(config, psm_list)
File "/usr/local/lib/python3.10/site-packages/ms2rescore/core.py", line 80, in rescore
fgen.add_features(psm_list)
File "/usr/local/lib/python3.10/site-packages/ms2rescore/feature_generators/ms2pip.py", line 190, in add_features
ms2pip_results = correlate(
File "/usr/local/lib/python3.10/site-packages/ms2pip/core.py", line 178, in correlate
ms2pip_parallelized = _Parallelized(
File "/usr/local/lib/python3.10/site-packages/ms2pip/core.py", line 383, in __init__
validate_requested_xgb_model(
File "/usr/local/lib/python3.10/site-packages/ms2pip/_utils/xgb_models.py", line 21, in validate_requested_xgb_model
_download_model(model_file, xgboost_model_hashes[model_file], model_dir)
File "/usr/local/lib/python3.10/site-packages/ms2pip/_utils/xgb_models.py", line 98, in _download_model
urllib.request.urlretrieve(
File "/usr/local/lib/python3.10/urllib/request.py", line 241, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
File "/usr/local/lib/python3.10/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
File "/usr/local/lib/python3.10/urllib/request.py", line 519, in open
response = self._open(req, data)
File "/usr/local/lib/python3.10/urllib/request.py", line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/usr/local/lib/python3.10/urllib/request.py", line 496, in _call_chain
result = func(*args)
File "/usr/local/lib/python3.10/urllib/request.py", line 1377, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/usr/local/lib/python3.10/urllib/request.py", line 1351, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -3] Temporary failure in name resolution>
In my case, when pipeline module calls ms2rescore_cli.py script, the ms2rescore.rescore is trying to download a xgboost file (in this case its size is 300MB) into the docker container, which cause error when the network condition is not that good.
My request is can we have an option for ms2rescore to use a preparable cache?
Kinda like what nfcore/mag do to BUSCO lineage dataset. When params.busco_db is set to a local path, the process will try to read the local dir or tar.gz archive and if success, skip downloading. Otherwise if params.busco_db is a url, the process will try to download BUSCO reference from there.
I'm not familiar with python, but this approach is possible as far as I know.
I think add the model_dir argument in here in ms2rescore/core.py is a must-done. Update nextflow.config accordingly on our side is easy, but can we ask the manager of compomics/ms2rescore accept this request?
Description of feature
I'm running the
devbranch ofmhcquantunder the test profile on my local server:And keep running into the same error:
In my case, when pipeline module calls
ms2rescore_cli.pyscript, thems2rescore.rescoreis trying to download a xgboost file (in this case its size is 300MB) into the docker container, which cause error when the network condition is not that good.ms2rescoreis hereMy request is can we have an option for
ms2rescoreto use a preparable cache?nfcore/magdo to BUSCO lineage dataset. Whenparams.busco_dbis set to a local path, the process will try to read the local dir or tar.gz archive and if success, skip downloading. Otherwise ifparams.busco_dbis a url, the process will try to download BUSCO reference from there.model_dirargument in here in ms2rescore/core.py is a must-done. Update nextflow.config accordingly on our side is easy, but can we ask the manager of compomics/ms2rescore accept this request?