local variable 'xic_data' referenced before assignment

[Cheng111]

Hi, when I try to run the moff on Ubuntu, there is a error report "local variable 'xic_data' referenced before assignment". It looks like that something wrong with the get_xic_data function. Is there anything I didn't wrong. Thank you so much.

The command I used is "python3 ./moff_all.py --mbr off --tsv_list moff_input.tsv --raw_list *.mzML --rt_peak_win 0.75 --tol 10 --loc_out ./moff/ --xic_length 3"

I attached part of the error report here. It's same error appear several times. Traceback (most recent call last): File "/usr/lib/python3.5/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/home/cades/tools/moFF/moff.py", line 838, in apex_multithr raise e File "/home/cades/tools/moFF/moff.py", line 829, in apex_multithr flag_mzml, flag_windows, temp, loc_output, name_file, txic_path, loc, 0) File "/home/cades/tools/moFF/moff.py", line 1005, in get_xic_data return xic_data UnboundLocalError: local variable 'xic_data' referenced before assignment """

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

Traceback (most recent call last): File "./moff_all.py", line 416, in result = moff.save_moff_apex_result(result) File "/home/cades/tools/moFF/moff.py", line 144, in save_moff_apex_result raise e File "/home/cades/tools/moFF/moff.py", line 133, in save_moff_apex_result if result[df_index].get()[1] == -1: File "/usr/lib/python3.5/multiprocessing/pool.py", line 608, in get raise self._value UnboundLocalError: local variable 'xic_data' referenced before assignment

[Maux82]

Hi ,

Thanks for reporting this. I am aware of this bug. Actually , I am still fixing the access to the mzML file in this new version. I hope to solve this for the end of the next week. In the meantine you can use moFFwith Thermo raw file.

[subinamehta]

Hi , I am also finding this issue using moFF...could you please let me know when this is fixed!! Thanks, Subina

[Maux82]

Hi @subinamehta ,

The last version in the master branch should work with mzML. Let me know if you if you get the same error .

[Maux82]

Hi, @Cheng111
now moFF should work with mzML , let me know if you find other issue with mzML.

[subinamehta]

I still get the same error..so I did conda update moff and then ran this "python moff_all.py --mbr off --tsv_list jrudney_chenx096_20141205_14469_737NS_08_23.tabular --raw_list jrudney_chenx096_20141205_14469_737NS_08_23.mzml --tol 10 --loc_out output_moFF1" and it gives me the error "UnboundLocalError: local variable 'xic_data' referenced before assignment"

[Maux82]

@subinamehta ARe you sure that you are using the last version from the master branch ? you can try to pull it down again? I tried your command and for me it work.

[subinamehta]

Let me give it a try once more

On Mon, Oct 15, 2018, 3:43 PM Maux82 notifications@github.com wrote:

@subinamehta https://github.com/subinamehta ARe you sure that you are using the last version from the master branch ? you can try to pull it down again? I tried your command and for me it work.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/compomics/moFF/issues/39#issuecomment-429987323, or mute the thread https://github.com/notifications/unsubscribe-auth/AZ-wfYaM2jUy4yLN4_xza-Sg_yzvq6Vvks5ulOVQgaJpZM4XK-QI .

[Maux82]

@subinamehta here is my last commit (in moff.py )where I fixed the mzml part https://github.com/compomics/moFF/commit/3e9b9b22a4f79052c5c284a6da9fbda9fd597674.

[subinamehta]

@Maux82 so I have sent u few files regarding the error I have been getting!

[subinamehta]

Could you check the bioconda version of moFF???