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rderelle / Broccoli

orthology assignment using phylogenetic and network analyses

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Error

fmarletaz opened this issue · comments

commented

Hi,
Broccoli crashed at tep2 with the following error. I don't get what the problem could be. Thanks!

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/flash/RokhsarU/ferdi/miniconda3/envs/py37/lib/python3.7/multiprocessing/pool.py", line 121, in worker
    result = (True, func(*args, **kwds))
  File "/flash/RokhsarU/ferdi/miniconda3/envs/py37/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
    return list(map(*args))
  File "/flash/RokhsarU/ferdi/Genomes/Urchins/broccoli/Broccoli-1.2/scripts/broccoli_step2.py", line 402, in process_file
    prot = all_ref_prot[c]
IndexError: list index out of range
"""

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

Traceback (most recent call last):
  File "./Broccoli-1.2/broccoli.py", line 148, in <module>
    broccoli_step2.step2_phylomes(evalue, max_per_species, path_diamond, path_fasttree, trim_thres, phylo_method, nb_threads)
  File "/flash/RokhsarU/ferdi/Genomes/Urchins/broccoli/Broccoli-1.2/scripts/broccoli_step2.py", line 78, in step2_phylomes
    multithread_process_file(list_files, nb_threads)
  File "/flash/RokhsarU/ferdi/Genomes/Urchins/broccoli/Broccoli-1.2/scripts/broccoli_step2.py", line 151, in multithread_process_file
    results_2 = tmp_res.get()
  File "/flash/RokhsarU/ferdi/miniconda3/envs/py37/lib/python3.7/multiprocessing/pool.py", line 657, in get
    raise self._value
IndexError: list index out of range
commented

Hi,

my guess is that FastTree has generated some error messages that I'm not aware of, leading Broccoli to overestimate the number of phylogenetic trees.
I would need to run the FastTree analyses myself and have a look at the output. Would you have a way to share with me the alignment file ? It's probably the last that has been generated. For instance if index '8': the file 'step2/8/alis_8.phy'.

Romain

commented

if not possible, please try with FastTree 2.1.10. It should work fine.

I just saw that some warning messages have been added to the last version of FastTree (2.1.11). These could be the source of this issue if you have used that version.

commented

Thanks a lot Romain for your prompt reply. I don't mind at all sharing the alignment: https://www.dropbox.com/s/lu40m1i291k1ilq/alis_15.phy.gz?dl=0
I am retrying with FastTree 2.1.10, I will let you know!

Ferdi

commented

I just tried with FastTree 2.1.10 and reached the same error.

commented

I found the problem: one of your alignments generates the warning "WARNING! 100.0% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A PROTEIN ALIGNMENT?"

I have modified the script of step2 to ignore this warning message (tiny modification at line 384).
Unfortunately I would need the full dataset to test it. Could you please give it a try with the new file scripts/broccoli_step2.py and let me know ?

thanks
Romain

commented

Hello! I tried and it worked, thanks for the fix!