ValueError: cannot set a frame with no defined index and a scalar

[Hang0918]

Starting Apex for /hwfssz5/ST_CANCER/CGR/USER/zhengzetian/MS/PXD001170_result/txt_data/AML-272.txt ...
moff Input file: /hwfssz5/ST_CANCER/CGR/USER/zhengzetian/MS/PXD001170_result/txt_data/AML-272.txt  XIC_tol 10.0 XIC_win 4.0000 moff_rtWin_peak 0.3300
RAW file from folder :  /zfssz3/pub/database/ftp.pride.ebi.ac.uk/pride/data/archive/2017/02/PXD001170
Output file in :  /hwfssz5/ST_CANCER/CGR/USER/zhengzetian/MS/PXD001170_result/output
starting  peptide quantification (ms2 / matched ) ..
Traceback (most recent call last):
  File "/hwfssz5/ST_CANCER/CGR/USER/zhuyafeng/moFF/moFF/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/hwfssz1/ST_CANCER/POL/SHARE/tools/miniconda3/lib/python3.6/site-packages/pandas/core/indexing.py", line 189, in __setitem__
    self._setitem_with_indexer(indexer, value)
  File "/hwfssz1/ST_CANCER/POL/SHARE/tools/miniconda3/lib/python3.6/site-packages/pandas/core/indexing.py", line 356, in _setitem_with_indexer
    raise ValueError("cannot set a frame with no "
ValueError: cannot set a frame with no defined index and a scalar
end apex quantification (ms2 / matched ) peptides
computational time (sec):  1.9446
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/hwfssz1/ST_CANCER/POL/SHARE/tools/miniconda3/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/hwfssz5/ST_CANCER/CGR/USER/zhuyafeng/moFF/moFF/moff.py", line 888, in apex_multithr
    raise e
  File "/hwfssz5/ST_CANCER/CGR/USER/zhuyafeng/moFF/moFF/moff.py", line 870, in apex_multithr
    temp.ix[:, 'tol'] = int(tol)
  File "/hwfssz1/ST_CANCER/POL/SHARE/tools/miniconda3/lib/python3.6/site-packages/pandas/core/indexing.py", line 189, in __setitem__
    self._setitem_with_indexer(indexer, value)
  File "/hwfssz1/ST_CANCER/POL/SHARE/tools/miniconda3/lib/python3.6/site-packages/pandas/core/indexing.py", line 356, in _setitem_with_indexer
    raise ValueError("cannot set a frame with no "
ValueError: cannot set a frame with no defined index and a scalar
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/hwfssz5/ST_CANCER/CGR/USER/zhuyafeng/moFF/moFF/moff.py", line 133, in save_moff_apex_result
    if result[df_index].get()[1] == -1:
  File "/hwfssz1/ST_CANCER/POL/SHARE/tools/miniconda3/lib/python3.6/multiprocessing/pool.py", line 644, in get
    raise self._value
ValueError: cannot set a frame with no defined index and a scalar
multiprocessing.pool.RemoteTraceback:

[Hang0918]

AML272_2.txt config_AML.ini.txt Hi, there, could anyone help me solve this? I am running moff_all.py with the following command:

python moff_all.py --config_file config_AML.ini

Thank you Best

[Maux82]

Hi,

Can you write also the command that you use ?

[Maux82]

All your input list contains only few psms ? like this one

AML272_2.txt or this just a sample of your input ?

If you have just few psms, try to adjust the cpu parameter to 1 or 2. and let me know

[Hang0918]

All your input list contains only few psms ? like this one

AML272_2.txt or this just a sample of your input ?

If you have just few psms, try to adjust the cpu parameter to 1 or 2. and let me know

Hi, Maux, that's right my samples have just few psms. I set the cpu from 4 to 1 and it works, appreciate a lot for your kind help. By the way, would you mind give a hint that why this works? Thanks.

[Maux82]

Well, moFF splits the input data with respect to the number of cpu given in input or present in your machine. If the number of psm is small (6 psm / 4 cpu= 1.5 ) , some worker gets an empty dataframe and so moFF complains about it. I will try to fixit in one of the next release. However, six psm is quite small compared to "standard" shotgun experiments :)

[Hang0918]

Well, moFF splits the input data with respect to the number of cpu given in input or present in your machine. If the number of psm is small (6 psm / 4 cpu= 1.5 ) , some worker gets an empty dataframe and so moFF complains about it. I will try to fixit in one of the next release. However, six psm is quite small compared to "standard" shotgun experiments :)

Yeah, I will recheck my data then. Thanks very much for your answer, that really helps me a lot.