error in breadth_and_depth_output function from metapop_filter.py

[beacamara]

Hi everyone,

I have run metapop y I obtained this error:

#######################################################
Getting breadth and depth of coverage for: TS_sept_cat.fa starting at: 01/06/2023 10:02:16
Filtering by genome for: TS_sept_cat.fa starting at: 01/06/2023 10:02:16
Completed preprocessing for: TS_sept_cat.fa at: 01/06/2023 10:02:16
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/emm4/anaconda3/envs/metapop/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/emm4/anaconda3/envs/metapop/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/emm4/anaconda3/envs/metapop/lib/python3.7/site-packages/metapop/metapop_filter.py", line 292, in parse_reads
breadth_and_depth_output(current_depths, contig_length_dict[contig], contig, truncation, breadth_and_depth_fh)
UnboundLocalError: local variable 'contig' referenced before assignment
"""

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

Traceback (most recent call last):
File "/home/emm4/anaconda3/envs/metapop/bin/metapop", line 8, in
sys.exit(main())
File "/home/emm4/anaconda3/envs/metapop/lib/python3.7/site-packages/metapop/metapop_main.py", line 297, in main
metapop.metapop_filter.filt(original_bams, filter_command_base, bdb, threads, mag_contig_dict, mag_length_dict, joined_fastas)
File "/home/emm4/anaconda3/envs/metapop/lib/python3.7/site-packages/metapop/metapop_filter.py", line 167, in filt
p.map(parse_reads, commands)
File "/home/emm4/anaconda3/envs/metapop/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/emm4/anaconda3/envs/metapop/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
UnboundLocalError: local variable 'contig' referenced before assignment

#############################################

I have realized that the function breadth_and_depth_output in metapop_filter.py script (line 292) is calling for the "contig" argument outside the for loop where this parameter is defined. Enclosed you will find a screenshot

Maybe removing line 292

[bayknight]

HI @beacamara , Im getting the same issue with the test data. Were you able to resolve this?