kalan-lab / zol Goto Github PK
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
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?
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!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.