Crash when attempting search

Issue #7 new
Anonymous created an issue

Hi,

I was intending to try out identipy but I just get this result:

PS C:\<...>\220618 - sample with iRT> identipy -cfg .\identipy.cfg .\QE20180621_003.mgf
INFO: [19:28:28] Reading defaults from c:\python27\lib\site-packages\identipy\default.cfg
INFO: [19:28:28] Reading config from .\identipy.cfg
INFO: [19:28:28] Setting legend: {'!': ('ox', 'M', ''), 'oxM': '!'}
INFO: [19:28:28] Writing .\QE20180621_003.pep.xml ...
INFO: [19:28:28] Reading spectra ...
INFO: [19:28:28] 169 spectra pass quality criteria.
INFO: [19:28:28] Running the search ...
Traceback (most recent call last):
  File "C:\Python27\Scripts\identipy-script.py", line 11, in <module>
    load_entry_point('identipy==0.2', 'console_scripts', 'identipy')()
  File "c:\python27\lib\site-packages\identipy\cli.py", line 209, in run
    utils.write_output(inputfile, settings, main.process_file(inputfile, settings))
  File "c:\python27\lib\site-packages\identipy\utils.py", line 1410, in write_output
    return writer(inputfile, settings, results)
  File "c:\python27\lib\site-packages\identipy\utils.py", line 1119, in write_pepxml
    results = [x for x in results if x['candidates'].size]
  File "c:\python27\lib\site-packages\identipy\peptide_centric.py", line 254, in process_peptides
    for y in utils.multimap(n, func, peps, **kwargs):
  File "c:\python27\lib\site-packages\identipy\utils.py", line 850, in multimap
    p.start()
  File "c:\python27\lib\multiprocessing\process.py", line 130, in start
    self._popen = Popen(self)
  File "c:\python27\lib\multiprocessing\forking.py", line 277, in __init__
    dump(process_obj, to_child, HIGHEST_PROTOCOL)
  File "c:\python27\lib\multiprocessing\forking.py", line 199, in dump
    ForkingPickler(file, protocol).dump(obj)
  File "c:\python27\lib\pickle.py", line 224, in dump
    self.save(obj)
  File "c:\python27\lib\pickle.py", line 331, in save
    self.save_reduce(obj=obj, *rv)
  File "c:\python27\lib\pickle.py", line 425, in save_reduce
    save(state)
  File "c:\python27\lib\pickle.py", line 286, in save
    f(self, obj) # Call unbound method with explicit self
  File "c:\python27\lib\pickle.py", line 655, in save_dict
    self._batch_setitems(obj.iteritems())
  File "c:\python27\lib\pickle.py", line 687, in _batch_setitems
    save(v)
  File "c:\python27\lib\pickle.py", line 286, in save
    f(self, obj) # Call unbound method with explicit self
  File "c:\python27\lib\pickle.py", line 754, in save_global
    (obj, module, name))
pickle.PicklingError: Can't pickle <function worker at 0x0000000002C04518>: it's not found as identipy.utils.worker
PS C:\<...>\220618 - sample with iRT> Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "c:\python27\lib\multiprocessing\forking.py", line 381, in main
    self = load(from_parent)
  File "c:\python27\lib\pickle.py", line 1384, in load
    return Unpickler(file).load()
  File "c:\python27\lib\pickle.py", line 864, in load
    dispatch[key](self)
  File "c:\python27\lib\pickle.py", line 886, in load_eof
    raise EOFError
EOFError

Can you help me out with that? It's a windows PC with latest identipy commit and python 2.7.

Best regards, Jonas

Comments (5)

  1. Lev Levitsky repo owner

    Hi, thank you for your interest in IdentiPy. Unfortunately, concurrent processing is not currently supported on Windows. To make it work, try adding the following in identipy.cfg:

    [performance]
    processes = 1
    

    I will add a platform check so that multiprocessing is disabled automatically on Windows until it is supported.

  2. jonasfoe

    Hey so now I get:

    PS C:\<...>\QE20180621_003.mzML
    INFO: [14:59:01] Reading defaults from c:\python27\lib\site-packages\identipy\default.cfg
    INFO: [14:59:01] Reading config from .\identipy.cfg
    INFO: [14:59:01] Setting legend: {'!': ('ox', 'M', ''), 'oxM': '!'}
    INFO: [14:59:01] Writing .\QE20180621_003.pep.xml ...
    INFO: [14:59:01] Reading spectra ...
    INFO: [14:59:41] 169 spectra pass quality criteria.
    INFO: [14:59:41] Running the search ...
    Traceback (most recent call last):
      File "C:\Python27\Scripts\identipy-script.py", line 11, in <module>
        load_entry_point('identipy==0.2', 'console_scripts', 'identipy')()
      File "c:\python27\lib\site-packages\identipy\cli.py", line 209, in run
        utils.write_output(inputfile, settings, main.process_file(inputfile, settings))
      File "c:\python27\lib\site-packages\identipy\utils.py", line 1410, in write_output
        return writer(inputfile, settings, results)
      File "c:\python27\lib\site-packages\identipy\utils.py", line 1119, in write_pepxml
        results = [x for x in results if x['candidates'].size]
      File "c:\python27\lib\site-packages\identipy\peptide_centric.py", line 255, in process_peptides
        for x in y:
    TypeError: 'NoneType' object is not iterable
    

    I was trying to just straight up find peptides by using a fasta file like this:

    > iRT 1 LGGNEQVTR
    LGGNEQVTR
    > iRT 2 GAGSSEPVTGLDAK
    GAGSSEPVTGLDAK
    > iRT 3 VEATFGVDESNAK
    VEATFGVDESNAK
    

    Not sure if that is valid but should probably not error out.

    Cheers

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