kalan-lab / zol Goto Github PK

→ 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