SpecLib Problem w/ FP24

[jjGG]

- Upload your log file

FP24_specLibError_log_p36602.txt

I still do have issues with the spectrum library generation:

this issue relates to -> #2076 (comment)
(I cannot reopen it)

Hello @guoci,

Unfortunately I still get an error that I cannot troubleshoot..

'E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\python.exe' -I 'E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Scripts\fragpipe-speclib.exe' library --psmtsv 'E:\projects\p36602\FragPipe\jaruschkaTestRun_FP24\psm.tsv' --peptidetsv 'E:\projects\p36602\FragPipe\jaruschkaTestRun_FP24\peptide.tsv' --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.01 'E:\projects\p36602\FragPipe\jaruschkaTestRun_FP24\filelist_easypqp_library.txt'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Scripts\fragpipe-speclib.exe\__main__.py", line 4, in <module>
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Lib\site-packages\easypqp\main.py", line 9, in <module>
    from .convert import conversion, basename_spectralfile, conversion_psm, drop_psm_columns
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Lib\site-packages\easypqp\convert.py", line 18, in <module>
    import pyopenms as po
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Lib\site-packages\pyopenms\__init__.py", line 109, in <module>
    raise e
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Lib\site-packages\pyopenms\__init__.py", line 67, in <module>
    from ._all_modules import *  # pylint: disable=wildcard-import; lgtm(py/polluting-import)
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Lib\site-packages\pyopenms\_all_modules.py", line 1, in <module>
    from ._pyopenms_1 import *  # pylint: disable=wildcard-import; lgtm(py/polluting-import)
    ^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: DLL load failed while importing _pyopenms_1: The specified procedure could not be found.
Traceback (most recent call last):
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\tools\speclib\gen_con_spec_lib.py", line 604, in <module>
    main()
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\tools\speclib\gen_con_spec_lib.py", line 576, in main
    main_easypqp(params, irt_df, allcmds, easypqp_convert_cmds)
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\tools\speclib\gen_con_spec_lib.py", line 323, in main_easypqp
    subprocess.run([sys.executable, *(["-I"] if sys.platform == 'win32' else []), os.fspath(params.easypqp), '--version'], check=True)
  File "E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Lib\subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['E:\\software\\FragPipe_versions\\FP24\\cleanFragPipe-24.0\\python\\python.exe', '-I', 'E:\\software\\FragPipe_versions\\FP24\\cleanFragPipe-24.0\\python\\Scripts\\fragpipe-speclib.exe', '--version']' returned non-zero exit status 1.

======================================================================
Error when loading pyOpenMS libraries!
Libraries could not be found / could not be loaded.

To debug this error, please run ldd (on linux), otool -L (on macOS) or dependency walker (on windows) on 

E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python\Lib\site-packages\pyopenms\pyopenms*.so

======================================================================
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 7 remaining tasks

here the output of the command above:

E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0>cd pytho

E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python>p
show --files fragpipe-speclib
Name: fragpipe-speclib
Version: 0.1.58
Summary: FragPipe-SpecLib: Simple library generation for FragP
Home-page: https://github.com/Nesvilab/FragPipe-SpecLib
Author:
Author-email:
License:
Location: E:\software\FragPipe_versions\FP24\cleanFragPipe-24.
packages
Requires: biopython, Click, matplotlib, numba, numpy, pandas,
earn, scipy, seaborn, statsmodels, tqdm
Required-by:
Files:
  ..\..\Scripts\fragpipe-speclib.exe
  easypqp\__init__.py
  easypqp\convert.py
  easypqp\data\unimod.xml
  easypqp\library.py
  easypqp\main.py
  easypqp\openswathassaygenerator.py
  easypqp\openswathdecoygenerator.py
  easypqp\targetedfileconverter.py
  easypqp\unimoddb.py
  easypqp\util.py
  fragpipe_speclib-0.1.58.dist-info\INSTALLER
  fragpipe_speclib-0.1.58.dist-info\METADATA
  fragpipe_speclib-0.1.58.dist-info\RECORD
  fragpipe_speclib-0.1.58.dist-info\REQUESTED
  fragpipe_speclib-0.1.58.dist-info\WHEEL
  fragpipe_speclib-0.1.58.dist-info\entry_points.txt
  fragpipe_speclib-0.1.58.dist-info\licenses\LICENSE
  fragpipe_speclib-0.1.58.dist-info\top_level.txt
  fragpipe_speclib-0.1.58.dist-info\uv_build.json
  fragpipe_speclib-0.1.58.dist-info\uv_cache.json

E:\software\FragPipe_versions\FP24\cleanFragPipe-24.0\python>

Complete Log-file is also attached.

best regards

jonas

[guoci]

@jjGG The error originates from OpenMS, please post an issue at https://github.com/OpenMS/OpenMS/issues.

[guoci]

@jjGG While we wait for the OpenMS developers to fix that issue. I would suggest you try our fix. We reverted PyOpenMS to an older version (3.4.0 to 3.3.0).
Please use the following link to get it: https://drive.google.com/drive/folders/1yLxJmXjN8tHpOos_eFRRfz4WjlMoAtV7?usp=sharing

[jjGG]

Hello @guoci,

We did install and test the 24.1 build 6 version.

Unfortunately I still get some errors also here: Any idea what I could test/try?

ImportError: DLL load failed while importing lib: The specified procedure could not be found.
Traceback (most recent call last):
  File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\tools\speclib\gen_con_spec_lib.py", line 633, in <module>
    main()
  File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\tools\speclib\gen_con_spec_lib.py", line 605, in main
    main_easypqp(params, irt_df, allcmds, easypqp_convert_cmds)
  File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\tools\speclib\gen_con_spec_lib.py", line 337, in main_easypqp
    subprocess.run([sys.executable, *(["-I"] if sys.platform == 'win32' else []), os.fspath(params.easypqp), '--version'], check=True)
  File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\subprocess.py", line 571, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['E:\\software\\FragPipe_versions\\FP24\\FragPipe-24.1-build6\\python\\python.exe', '-I', 'E:\\software\\FragPipe_versions\\FP24\\FragPipe-24.1-build6\\python\\Scripts\\fragpipe-speclib.exe', '--version']' returned non-zero exit status 1.
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

~~~~~~~~~~~~~~~~~~~~
Cancelling 9 remaining tasks

[guoci]

@jjGG Can you give me the lines starting from Traceback (most recent call last):?

[jjGG]

Hello @guoci

find here the part from the log:

`Traceback (most recent call last):
File "", line 198, in run_module_as_main
File "", line 88, in run_code
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Scripts\fragpipe-speclib.exe_main.py", line 4, in
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\easypqp\main.py", line 10, in
from .library import generate
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\easypqp\library.py", line 19, in
from sklearn import preprocessing
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn_init.py", line 73, in
from .base import clone # noqa: E402
^^^^^^^^^^^^^^^^^^^^^^^
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn\base.py", line 19, in
from .utils._metadata_requests import _MetadataRequester, routing_enabled
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn\utils_init.py", line 9, in
from ._chunking import gen_batches, gen_even_slices
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn\utils_chunking.py", line 11, in
from ._param_validation import Interval, validate_params
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn\utils_param_validation.py", line 17, in
from .validation import _is_arraylike_not_scalar
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn\utils\validation.py", line 21, in
from ..utils._array_api import _asarray_with_order, is_numpy_namespace, get_namespace
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn\utils_array_api.py", line 20, in
from .fixes import parse_version
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\sklearn\utils\fixes.py", line 421, in
import pyarrow
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-packages\pyarrow_init.py", line 73, in
import pyarrow.lib as _lib
ImportError: DLL load failed while importing lib: The specified procedure could not be found.
Traceback (most recent call last):
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\tools\speclib\gen_con_spec_lib.py", line 633, in
main()
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\tools\speclib\gen_con_spec_lib.py", line 605, in main
main_easypqp(params, irt_df, allcmds, easypqp_convert_cmds)
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\tools\speclib\gen_con_spec_lib.py", line 337, in main_easypqp
subprocess.run([sys.executable, *(["-I"] if sys.platform == 'win32' else []), os.fspath(params.easypqp), '--version'], check=True)
File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\python.exe', '-I', 'E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Scripts\fragpipe-speclib.exe', '--version']' returned non-zero exit status 1.
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

Cancelling 9 remaining tasks

`
Plus the complete log-file here: 

[log_2026-02-03_15-45.txt](https://github.com/user-attachments/files/25214158/log_2026-02-03_15-45.txt)

thanks for looking into it.
jonas

[guoci]

@jjGG Can you start the Python interpreter E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\python.exe
then enter this code below?
import pyarrow

[jjGG]

Hello @guoci,

This is what I get:

C:\Users\fragpipe_user>
C:\Users\fragpipe_user>E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\p
ython\python.exe
Python 3.11.11 (main, Dec  6 2024, 18:05:41) [MSC v.1942 64 bit (AMD64)] on win3
2
Type "help", "copyright", "credits" or "license" for more information.
>>> a = 3
>>> print(a)
>>>
>>> import pyarrow
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "E:\software\FragPipe_versions\FP24\FragPipe-24.1-build6\python\Lib\site-
packages\pyarrow\__init__.py", line 73, in <module>
    import pyarrow.lib as _lib
ImportError: DLL load failed while importing lib: The specified procedure could
not be found.
>>>

[fcyu]

Hi @jjGG ,

Guo Ci downgraded pyarrow. Hopefully it will resolve the issue. Here is the link to download the pre-released version.

https://www.dropbox.com/scl/fi/96hdjyhpkdilos09sa02r/FragPipe-24.1-build8-installer.exe?rlkey=tspzgkng3s6lnz1hx8km1ukp3&st=mhz01nt1&dl=1

Thanks,

Fengchao

[jjGG]

Hello @guoci,

Thanks for the comment, for downgrading pyarrow and for another installer of FragPipe.

Unfortunately I cannot send the mail for the license agreement... it refuses to send the request with a Connetion time out.
The computer is connected to the internet. I do not see if this now on our hardware side (I dont think so, on your side or inside this FragPipe version.. )
-> any idea what else I could try & test?

Best regards
jonas

[fcyu]

any idea what else I could try & test?

You could just copy the MSFragger folder, IonQuant jar file, and diaTracer jar file from the old version of FragPipe's tool folder to this version's.

And restart FragPipe.

Best,

Fengchao

[marilyvm]

Dear developers,
I'm writing to this loop as the problem that we face in my team is also relatable to SpecLib generation.

Specifically, for 3 days now in almost any analysis that we launch, we face the following error:

"File list provided
Traceback (most recent call last):
File "C:\FragPipe\FragPipe-24.0\tools\speclib\gen_con_spec_lib.py", line 604, in
main()
File "C:\FragPipe\FragPipe-24.0\tools\speclib\gen_con_spec_lib.py", line 528, in main
assert len(iproph_pep_xmls) > 0, params.iproph_RT_aligned
^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: C:\DATA_TRANSFER\NKUABiology\ZoidakisMakis\0-Fragpipe_Saliva_manyprojects\output"

Here you may find also the error log:
Error_log_2026-02-18_12-04-44.txt

Thank you a lot in advance for your help!