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View Code? Open in Web Editor NEWzol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
License: BSD 3-Clause "New" or "Revised" License
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
License: BSD 3-Clause "New" or "Revised" License
This issue/ticket is to track ideas for downstream improvement of the suite:
Please feel free to add suggestions or make pull requests if you want to implement them yourselves!
I have been trying to run Zol through the prepTG/fai/zol pipeline, but I am always facing the same issue after Step 4 (Identifying homologous gene-cluster segments) starts. The run always generates the error below (independently if I am trying to use any of the 3 input types):
โ fai -pq cluster_ptn.faa -tg prepTG_DB -o fai_Results/ -c 3 -gp
Output directory exists. Overwriting in 5 seconds ...
Running fai version '1.02'
Beginning fai searches using protein queries FASTA file at: cluster_ptn.faa
--------------------
Step 1
--------------------
Getting protein sequences of known gene-cluster instance(s).
--------------------
Step 2
--------------------
Running DIAMOND BLASTp and Processing Results.
--------------------
Step 3
--------------------
Loading target genomes database prepared by prepTG.
--------------------
Step 4
--------------------
Identifying homologous gene-cluster segments.
Issues with managing running of HMM to find gene-cluster homolog segments.
'NoneType' object is not subscriptable
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/Volumes/Expansion/fai/zol/zol/fai.py", line 649, in identify_gc_instances
for scaffold in hgs_ordered_dict[sample]:
TypeError: 'NoneType' object is not subscriptable
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Volumes/Expansion/fai/zol/zol/fai.py", line 631, in identifyGCInstances
p.map(identify_gc_instances, identify_gc_segments_input)
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
TypeError: 'NoneType' object is not subscriptable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Volumes/Expansion/fai/zol/zol_conda_env/bin/fai", line 7, in <module>
exec(compile(f.read(), __file__, 'exec'))
File "/Volumes/Expansion/fai/zol/bin/fai", line 527, in <module>
faiMain()
File "/Volumes/Expansion/fai/zol/bin/fai", line 494, in faiMain
fai.identifyGCInstances(query_information, target_information, diamond_results, hmm_work_dir, logObject,
File "/Volumes/Expansion/fai/zol/zol/fai.py", line 641, in identifyGCInstances
raise RuntimeError(traceback.format_exc())
RuntimeError: multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/Volumes/Expansion/fai/zol/zol/fai.py", line 649, in identify_gc_instances
for scaffold in hgs_ordered_dict[sample]:
TypeError: 'NoneType' object is not subscriptable
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Volumes/Expansion/fai/zol/zol/fai.py", line 631, in identifyGCInstances
p.map(identify_gc_instances, identify_gc_segments_input)
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Volumes/Expansion/fai/zol/zol_conda_env/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
TypeError: 'NoneType' object is not subscriptable
Any ideas of what might be happening?
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