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TypeError: 'NoneType' object is not subscriptable #49

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jawad9-11 opened this issue Sep 11, 2024 · 1 comment
Open

TypeError: 'NoneType' object is not subscriptable #49

jawad9-11 opened this issue Sep 11, 2024 · 1 comment

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@jawad9-11
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Whenever i give command to straglr
"straglr.py HGDP00776.bam hg38.fa 776 --min_str_len 2 --max_str_len 100 --min_ins_size 100 --genotype_in_size --min_support 2 --max_num_clusters 2 --nprocs 32" as i dont want to specify any region and want to scan whole region. everytime it says:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/work/home/jawad/miniconda3/envs/straglr/lib/python3.12/site-packages/src/ins.py", line 93, in find_ins
batched_results = parallel_process(self.examine_regions, batches, self.nprocs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/work/home/jawad/miniconda3/envs/straglr/lib/python3.12/site-packages/src/utils.py", line 21, in parallel_process
results = p.map(func, args)
^^^^^^^^^^^^^^^^^
File "/work/home/jawad/miniconda3/envs/straglr/lib/python3.12/site-packages/pathos/multiprocessing.py", line 154, in map
return _pool.map(star(f), zip(*args), **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/work/home/jawad/miniconda3/envs/straglr/lib/python3.12/site-packages/multiprocess/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/work/home/jawad/miniconda3/envs/straglr/lib/python3.12/site-packages/multiprocess/pool.py", line 774, in get
raise self._value
TypeError: 'NoneType' object is not subscriptable

@readmanchiu
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Does your computer have enough (>=32) cores?
Can you run with --debug --tmpdir <custom_tmp_dir>, and zip up <custom_tmp_dir> for me to take a look?

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