Open RalfG opened 1 year ago
Hi @JB91451,
Thanks for testing and reporting back! The generated new fontManager
message could indicate an issue with matplotlib. Is the Windows server a headless environment with only the CLI active and now graphical environment?
Could you provide a list of all package versions used in the environment (e.g. with pip freeze
or conda list
? A full log might also help me in figuring out the source of the issue.
Thanks! Ralf
Hi Ralf,
No, the Windows server has a gui and I connect via the remote-desktop tool.
The output from pip freeze is as follows:
E:\JB>E:\JB\ms2pip\venv\Scripts\activate.bat
Parameterformat falsch - 437. # this is an error message related to the usage of _venv_ in German Windows versions but should not cause any issues according to https://bugs.python.org/issue35148
(venv) E:\JB>pip freeze
absl-py==1.4.0
astunparse==1.6.3
biopython==1.81
cachetools==5.3.0
certifi==2022.12.7
charset-normalizer==3.1.0
click==8.1.3
colorama==0.4.6
cycler==0.11.0
deeplc==1.2.1
deeplcretrainer==0.1.13
flatbuffers==23.3.3
fonttools==4.38.0
future==0.18.3
gast==0.4.0
google-auth==2.16.2
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
greenlet==2.0.2
grpcio==1.51.3
h5py==3.8.0
idna==3.4
importlib-metadata==6.0.0
joblib==1.2.0
keras==2.11.0
kiwisolver==1.4.4
libclang==15.0.6.1
llvmlite==0.39.1
lxml==4.9.2
Markdown==3.4.1
markdown-it-py==2.2.0
MarkupSafe==2.1.2
matplotlib==3.5.3
mdurl==0.1.2
ms2pip==3.11.0
numba==0.56.4
numexpr==2.8.4
numpy==1.21.6
oauthlib==3.2.2
opt-einsum==3.3.0
packaging==23.0
pandas==1.3.5
Pillow==9.4.0
progressbar2==4.2.0
protobuf==3.19.6
pyasn1==0.4.8
pyasn1-modules==0.2.8
pydantic==1.10.6
pygam==0.8.0
Pygments==2.14.0
pyparsing==3.0.9
pyteomics==4.5.6
python-dateutil==2.8.2
python-utils==3.5.2
pytz==2022.7.1
requests==2.28.2
requests-oauthlib==1.3.1
rich==13.3.2
rsa==4.9
scikit-learn==1.0.2
scipy==1.7.3
six==1.16.0
spectrum-utils==0.3.5
SQLAlchemy==1.4.46
tables==3.7.0
tensorboard==2.11.2
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorflow==2.11.0
tensorflow-estimator==2.11.0
tensorflow-intel==2.11.0
tensorflow-io-gcs-filesystem==0.31.0
termcolor==2.2.0
threadpoolctl==3.1.0
tomlkit==0.11.6
tqdm==4.65.0
typing_extensions==4.5.0
urllib3==1.26.14
Werkzeug==2.2.3
wrapt==1.15.0
xgboost==1.6.2
zipp==3.15.0
(venv) E:\JB>python -v
import _frozen_importlib # frozen
import _imp # builtin
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import '_warnings' # <class '_frozen_importlib.BuiltinImporter'>
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
# installing zipimport hook
import 'zipimport' # <class '_frozen_importlib.BuiltinImporter'>
# installed zipimport hook
import '_frozen_importlib_external' # <class '_frozen_importlib.FrozenImporter'>
import '_io' # <class '_frozen_importlib.BuiltinImporter'>
import 'marshal' # <class '_frozen_importlib.BuiltinImporter'>
import 'nt' # <class '_frozen_importlib.BuiltinImporter'>
import _thread # previously loaded ('_thread')
import '_thread' # <class '_frozen_importlib.BuiltinImporter'>
import _weakref # previously loaded ('_weakref')
import '_weakref' # <class '_frozen_importlib.BuiltinImporter'>
import 'winreg' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program Files\Python3\lib\encodings\__pycache__\__init__.cpython-37.pyc matches C:\Program Files\Python3\lib\encodings\__init__.py
# code object from 'C:\\Program Files\\Python3\\lib\\encodings\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program Files\Python3\lib\__pycache__\codecs.cpython-37.pyc matches C:\Program Files\Python3\lib\codecs.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\codecs.cpython-37.pyc'
import '_codecs' # <class '_frozen_importlib.BuiltinImporter'>
import 'codecs' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1B52E8>
# C:\Program Files\Python3\lib\encodings\__pycache__\aliases.cpython-37.pyc matches C:\Program Files\Python3\lib\encodings\aliases.py
# code object from 'C:\\Program Files\\Python3\\lib\\encodings\\__pycache__\\aliases.cpython-37.pyc'
import 'encodings.aliases' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1CAE10>
import 'encodings' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1986A0>
# C:\Program Files\Python3\lib\encodings\__pycache__\utf_8.cpython-37.pyc matches C:\Program Files\Python3\lib\encodings\utf_8.py
# code object from 'C:\\Program Files\\Python3\\lib\\encodings\\__pycache__\\utf_8.cpython-37.pyc'
import 'encodings.utf_8' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1DAEB8>
import '_signal' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program Files\Python3\lib\encodings\__pycache__\latin_1.cpython-37.pyc matches C:\Program Files\Python3\lib\encodings\latin_1.py
# code object from 'C:\\Program Files\\Python3\\lib\\encodings\\__pycache__\\latin_1.cpython-37.pyc'
import 'encodings.latin_1' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1DE320>
# C:\Program Files\Python3\lib\__pycache__\io.cpython-37.pyc matches C:\Program Files\Python3\lib\io.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\io.cpython-37.pyc'
# C:\Program Files\Python3\lib\__pycache__\abc.cpython-37.pyc matches C:\Program Files\Python3\lib\abc.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\abc.cpython-37.pyc'
import '_abc' # <class '_frozen_importlib.BuiltinImporter'>
import 'abc' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1DE8D0>
import 'io' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1DE518>
# C:\Program Files\Python3\lib\__pycache__\site.cpython-37.pyc matches C:\Program Files\Python3\lib\site.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\site.cpython-37.pyc'
# C:\Program Files\Python3\lib\__pycache__\os.cpython-37.pyc matches C:\Program Files\Python3\lib\os.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\os.cpython-37.pyc'
# C:\Program Files\Python3\lib\__pycache__\stat.cpython-37.pyc matches C:\Program Files\Python3\lib\stat.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\stat.cpython-37.pyc'
import '_stat' # <class '_frozen_importlib.BuiltinImporter'>
import 'stat' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B597B38>
# C:\Program Files\Python3\lib\__pycache__\ntpath.cpython-37.pyc matches C:\Program Files\Python3\lib\ntpath.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\ntpath.cpython-37.pyc'
# C:\Program Files\Python3\lib\__pycache__\genericpath.cpython-37.pyc matches C:\Program Files\Python3\lib\genericpath.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\genericpath.cpython-37.pyc'
import 'genericpath' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B5A59E8>
import 'ntpath' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B5A1208>
# C:\Program Files\Python3\lib\__pycache__\_collections_abc.cpython-37.pyc matches C:\Program Files\Python3\lib\_collections_abc.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\_collections_abc.cpython-37.pyc'
import '_collections_abc' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B5A5FD0>
import 'os' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1EE748>
# C:\Program Files\Python3\lib\__pycache__\_sitebuiltins.cpython-37.pyc matches C:\Program Files\Python3\lib\_sitebuiltins.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\_sitebuiltins.cpython-37.pyc'
import '_sitebuiltins' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1EEB38>
# C:\Program Files\Python3\lib\__pycache__\_bootlocale.cpython-37.pyc matches C:\Program Files\Python3\lib\_bootlocale.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\_bootlocale.cpython-37.pyc'
import '_locale' # <class '_frozen_importlib.BuiltinImporter'>
import '_bootlocale' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B592E80>
# C:\Program Files\Python3\lib\encodings\__pycache__\cp1252.cpython-37.pyc matches C:\Program Files\Python3\lib\encodings\cp1252.py
# code object from 'C:\\Program Files\\Python3\\lib\\encodings\\__pycache__\\cp1252.cpython-37.pyc'
import 'encodings.cp1252' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B6EE160>
# E:\JB\ms2pip\venv\lib\site-packages\_distutils_hack\__pycache__\__init__.cpython-37.pyc matches E:\JB\ms2pip\venv\lib\site-packages\_distutils_hack\__init__.py
# code object from 'E:\\JB\\ms2pip\\venv\\lib\\site-packages\\_distutils_hack\\__pycache__\\__init__.cpython-37.pyc'
import '_distutils_hack' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B6F5358>
# C:\Program Files\Python3\lib\__pycache__\types.cpython-37.pyc matches C:\Program Files\Python3\lib\types.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\types.cpython-37.pyc'
import 'types' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B6FCBE0>
# C:\Program Files\Python3\lib\importlib\__pycache__\__init__.cpython-37.pyc matches C:\Program Files\Python3\lib\importlib\__init__.py
# code object from 'C:\\Program Files\\Python3\\lib\\importlib\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program Files\Python3\lib\__pycache__\warnings.cpython-37.pyc matches C:\Program Files\Python3\lib\warnings.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\warnings.cpython-37.pyc'
import 'warnings' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B701C50>
import 'importlib' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B701860>
# C:\Program Files\Python3\lib\importlib\__pycache__\util.cpython-37.pyc matches C:\Program Files\Python3\lib\importlib\util.py
# code object from 'C:\\Program Files\\Python3\\lib\\importlib\\__pycache__\\util.cpython-37.pyc'
# C:\Program Files\Python3\lib\importlib\__pycache__\abc.cpython-37.pyc matches C:\Program Files\Python3\lib\importlib\abc.py
# code object from 'C:\\Program Files\\Python3\\lib\\importlib\\__pycache__\\abc.cpython-37.pyc'
# C:\Program Files\Python3\lib\importlib\__pycache__\machinery.cpython-37.pyc matches C:\Program Files\Python3\lib\importlib\machinery.py
# code object from 'C:\\Program Files\\Python3\\lib\\importlib\\__pycache__\\machinery.cpython-37.pyc'
import 'importlib.machinery' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B715828>
import 'importlib.abc' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B70BF98>
# C:\Program Files\Python3\lib\__pycache__\contextlib.cpython-37.pyc matches C:\Program Files\Python3\lib\contextlib.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\contextlib.cpython-37.pyc'
# C:\Program Files\Python3\lib\collections\__pycache__\__init__.cpython-37.pyc matches C:\Program Files\Python3\lib\collections\__init__.py
# code object from 'C:\\Program Files\\Python3\\lib\\collections\\__pycache__\\__init__.cpython-37.pyc'
# C:\Program Files\Python3\lib\__pycache__\operator.cpython-37.pyc matches C:\Program Files\Python3\lib\operator.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\operator.cpython-37.pyc'
import '_operator' # <class '_frozen_importlib.BuiltinImporter'>
import 'operator' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B747DA0>
# C:\Program Files\Python3\lib\__pycache__\keyword.cpython-37.pyc matches C:\Program Files\Python3\lib\keyword.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\keyword.cpython-37.pyc'
import 'keyword' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B751F60>
# C:\Program Files\Python3\lib\__pycache__\heapq.cpython-37.pyc matches C:\Program Files\Python3\lib\heapq.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\heapq.cpython-37.pyc'
import '_heapq' # <class '_frozen_importlib.BuiltinImporter'>
import 'heapq' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B758978>
import 'itertools' # <class '_frozen_importlib.BuiltinImporter'>
# C:\Program Files\Python3\lib\__pycache__\reprlib.cpython-37.pyc matches C:\Program Files\Python3\lib\reprlib.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\reprlib.cpython-37.pyc'
import 'reprlib' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B758F60>
import '_collections' # <class '_frozen_importlib.BuiltinImporter'>
import 'collections' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B72AFD0>
# C:\Program Files\Python3\lib\__pycache__\functools.cpython-37.pyc matches C:\Program Files\Python3\lib\functools.py
# code object from 'C:\\Program Files\\Python3\\lib\\__pycache__\\functools.cpython-37.pyc'
import '_functools' # <class '_frozen_importlib.BuiltinImporter'>
import 'functools' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B72E400>
import 'contextlib' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B715400>
import 'importlib.util' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B70B080>
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\google
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\mpl_toolkits
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\google
# destroy google
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\pyteomics
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\google
# destroy google
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\mpl_toolkits
# destroy mpl_toolkits
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\google
# destroy google
# possible namespace for E:\JB\ms2pip\venv\lib\site-packages\pyteomics
# destroy pyteomics
import 'site' # <_frozen_importlib_external.SourceFileLoader object at 0x000002016B1E43C8>
Python 3.7.2 (tags/v3.7.2:9a3ffc0492, Dec 23 2018, 23:09:28) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
import 'atexit' # <class '_frozen_importlib.BuiltinImporter'>
exit()
...
(venv) E:\JB>systeminfo
Hostname: REMOVED
Betriebssystemname: Microsoft Windows 10 Enterprise N 2016 LTSB
Betriebssystemversion: 10.0.14393 Nicht zutreffend Build 14393
Betriebssystemhersteller: Microsoft Corporation
Betriebssystemkonfiguration: Eigenständige Arbeitsstation
Betriebssystem-Buildtyp: Multiprocessor Free
Registrierter Benutzer: Windows-Benutzer
Registrierte Organisation:
Produkt-ID: REMOVED
Ursprüngliches Installationsdatum: 3/7/2019, 11:16:02 AM
Systemstartzeit: 3/21/2023, 12:44:36 PM
Systemhersteller: QEMU
Systemmodell: Standard PC (Q35 + ICH9, 2009)
Systemtyp: x64-based PC
Prozessor(en): 1 Prozessor(en) installiert.
[01]: Intel64 Family 15 Model 6 Stepping 1 GenuineIntel ~2000 MHz
BIOS-Version: REMOVED
Windows-Verzeichnis: C:\Windows
System-Verzeichnis: C:\Windows\system32
Startgerät: \Device\HarddiskVolume2
Systemgebietsschema: en-us;Englisch (Vereinigte Staaten)
Eingabegebietsschema: en-us;Englisch (Vereinigte Staaten)
Zeitzone: (UTC+01:00) Belgrad, Bratislava (Pressburg), Budapest, Ljubljana, Prag
Gesamter physischer Speicher: 127,994 MB
Verfügbarer physischer Speicher: 123,445 MB
Virtueller Arbeitsspeicher: Maximale Größe: 146,426 MB
Virtueller Arbeitsspeicher: Verfügbar: 141,934 MB
Virtueller Arbeitsspeicher: Zurzeit verwendet: 4,492 MB
Auslagerungsdateipfad(e): E:\pagefile.sys
Domäne: REMOVED
Anmeldeserver: REMOVED
Hotfix(es): 29 Hotfix(e) installiert.
[01]: KB4033631
[02]: KB4054590
[03]: KB4485447
[04]: KB4498947
[05]: KB4503537
[06]: KB4509091
[07]: KB4512574
[08]: KB4520724
[09]: KB4521858
[10]: KB4524244
[11]: KB4535680
[12]: KB4540723
[13]: KB4550994
[14]: KB4562561
[15]: KB4565912
[16]: KB4576750
[17]: KB4589210
[18]: KB4601392
[19]: KB5001078
[20]: KB5001402
[21]: KB5005698
[22]: KB5011570
[23]: KB5012170
[24]: KB5014026
[25]: KB5016058
[26]: KB5017095
[27]: KB5017396
[28]: KB5023788
[29]: KB5023697
Netzwerkkarte(n): 1 Netzwerkadapter installiert.
[01]: Intel(R) PRO/1000 MT Network Connection
Verbindungsname: Ethernet
DHCP aktiviert: Ja
DHCP-Server: REMOVED
IP-Adresse(n)
[01]: REMOVED
Anforderungen für Hyper-V: Es wurde ein Hypervisor erkannt. Features, die für Hyper-V erforderlich sind, werden nicht angezeigt.
(venv) E:\JB>cd E:\JB\ms2pip\semiTry
(venv) E:\JB\ms2pip\semiTry>E:\JB\ms2pip\venv\Scripts\fasta2speclib.exe -o E:\JB\ms2pip\semiTry\ms2pipTest -c E:\JB\ms2pip\semiTry\MS2PIP_Test_cpuCount10.json E:\JB\ms2pip\semiTry\Test.fasta
2023-03-21 13:21:25 INFO Starting library generation pipeline...
INFO Preparing search space...
Digesting proteins... ---------------------------------------- 0% -:--:--
At this step the prediction stops without any notice. However, I waited several hours and the computer seems to be idle during the complete time as there is no cpu, I/O or RAM activity from any of the python processes that were started. When I repeat the process with with an altered config file with only one cpu, the digestion and modification assignment works, but ms2pip does not proceed after retention time prediction (or spectrum prediction if DeepLC is disabled):
(venv) E:\JB\ms2pip\semiTry>E:\JB\ms2pip\venv\Scripts\fasta2speclib.exe -o E:\JB\ms2pip\semiTry\ms2pipTest -c E:\JB\ms2pip\semiTry\MS2PIP_Test_cpuCount10.json E:\JB\ms2pip\semiTry\Test.fasta
2023-03-21 15:04:09 INFO Starting library generation pipeline...
INFO Preparing search space...
2023-03-21 15:09:38 INFO Search space contains 2722016 peptides.
2023-03-21 15:09:39 INFO Processing batch 1/273...
INFO Generating MS²PIP input...
2023-03-21 15:09:45 INFO Chunk contains 128924 peptidoforms.
2023-03-21 15:09:49 INFO Filtered batch on precursor m/z: 128924 -> 128340
INFO Predicting retention times with DeepLC...
Please note that the prediction for this first chunk seems to work as the counter that displays ETA, etc. runs down and disapears before the computer turns idle.
Best, Juergen