PanicException: called Result::unwrap() on an Err value: ParseIntError { kind: InvalidDigit } #221
Description
Hello
I run the folowing code and found this error:
Could you let me know how can I solve it?
Thanks
from pycisTopic.pseudobulk_peak_calling import export_pseudobulk
os.makedirs(os.path.join(out_dir, "consensus_peak_calling"), exist_ok = True)
os.makedirs(os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bed_files"), exist_ok = True)
os.makedirs(os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bw_files"), exist_ok = True)
bw_paths, bed_paths = export_pseudobulk(
input_data = cell_data,
variable = "Clusters2",
sample_id_col = "Sample2",
chromsizes = chromsizes,
bed_path = os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bed_files"),
bigwig_path = os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bw_files"),
path_to_fragments = fragments_dict,
n_cpu = 10,
normalize_bigwig = True,
#temp_dir = "/tmp",
#split_pattern = "-"
)
2025-12-23 11:16:19,058 cisTopic INFO Splitting fragments by cell type.
thread '<unnamed>' panicked at src/aggregate_fragments.rs:78:56:
called `Result::unwrap()` on an `Err` value: ParseIntError { kind: InvalidDigit }
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
---------------------------------------------------------------------------
_RemoteTraceback Traceback (most recent call last)
_RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/dan/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 463, in _process_worker
r = call_item()
^^^^^^^^^^^
File "/home/dan/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 291, in __call__
return self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dan/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in __call__
return [func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^
File "/home/dan/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py", line 589, in <listcomp>
return [func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
pyo3_runtime.PanicException: called `Result::unwrap()` on an `Err` value: ParseIntError { kind: InvalidDigit }
"""
The above exception was the direct cause of the following exception:
PanicException Traceback (most recent call last)
Cell In[62], line 7
3 os.makedirs(os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bed_files"), exist_ok = True)
4 os.makedirs(os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bw_files"), exist_ok = True)
----> 7 bw_paths, bed_paths = export_pseudobulk(
8 input_data = cell_data,
9 variable = "Clusters2",
10 sample_id_col = "Sample2",
11 chromsizes = chromsizes,
12 bed_path = os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bed_files"),
13 bigwig_path = os.path.join(out_dir, "consensus_peak_calling/pseudobulk_bw_files"),
14 path_to_fragments = fragments_dict,
15 n_cpu = 10,
16 normalize_bigwig = True,
17 #temp_dir = "/tmp",
18 #split_pattern = "-"
19 )
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/pseudobulk_peak_calling.py:162](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/pycisTopic/pseudobulk_peak_calling.py#line=161), in export_pseudobulk(input_data, variable, chromsizes, bed_path, bigwig_path, path_to_fragments, sample_id_col, n_cpu, normalize_bigwig, split_pattern, temp_dir)
159 # For each sample, get fragments for each cell type
161 log.info("Splitting fragments by cell type.")
--> 162 split_fragment_files_by_cell_type(
163 sample_to_fragment_file = path_to_fragments,
164 path_to_temp_folder = temp_dir,
165 path_to_output_folder = bed_path,
166 sample_to_cell_type_to_cell_barcodes = sample_to_cell_type_to_barcodes,
167 chromsizes = chromsizes_dict,
168 n_cpu = n_cpu,
169 verbose = False,
170 clear_temp_folder = True
171 )
173 bed_paths = {}
174 for cell_type in cell_data[variable].unique():
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scatac_fragment_tools/library/split/split_fragments_by_cell_type.py:100](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/scatac_fragment_tools/library/split/split_fragments_by_cell_type.py#line=99), in split_fragment_files_by_cell_type(sample_to_fragment_file, path_to_temp_folder, path_to_output_folder, sample_to_cell_type_to_cell_barcodes, chromsizes, n_cpu, verbose, clear_temp_folder)
98 if verbose:
99 print("Merging fragments ...")
--> 100 joblib.Parallel(n_jobs=n_cpu)(
101 joblib.delayed(_rust_scatac_fragment_tools.merge_fragment_files)
102 (
103 path_to_fragment_files = cell_type_to_fragment_files[cell_type],
104 path_to_output_file = os.path.join(path_to_output_folder, f"{cell_type}.fragments.tsv.gz"),
105 number_of_threads = NUMBER_OF_WRITER_THREADS,
106 verbose = verbose
107 )
108 for cell_type in cell_type_to_fragment_files
109 )
111 # Check wether all files were create successfully
112 for cell_type in cell_type_to_fragment_files:
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py:1952](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py#line=1951), in Parallel.__call__(self, iterable)
1946 # The first item from the output is blank, but it makes the interpreter
1947 # progress until it enters the Try/Except block of the generator and
1948 # reach the first `yield` statement. This starts the aynchronous
1949 # dispatch of the tasks to the workers.
1950 next(output)
-> 1952 return output if self.return_generator else list(output)
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py:1595](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py#line=1594), in Parallel._get_outputs(self, iterator, pre_dispatch)
1592 yield
1594 with self._backend.retrieval_context():
-> 1595 yield from self._retrieve()
1597 except GeneratorExit:
1598 # The generator has been garbage collected before being fully
1599 # consumed. This aborts the remaining tasks if possible and warn
1600 # the user if necessary.
1601 self._exception = True
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py:1699](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py#line=1698), in Parallel._retrieve(self)
1692 while self._wait_retrieval():
1693
1694 # If the callback thread of a worker has signaled that its task
1695 # triggered an exception, or if the retrieval loop has raised an
1696 # exception (e.g. `GeneratorExit`), exit the loop and surface the
1697 # worker traceback.
1698 if self._aborting:
-> 1699 self._raise_error_fast()
1700 break
1702 # If the next job is not ready for retrieval yet, we just wait for
1703 # async callbacks to progress.
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py:1734](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py#line=1733), in Parallel._raise_error_fast(self)
1730 # If this error job exists, immediatly raise the error by
1731 # calling get_result. This job might not exists if abort has been
1732 # called directly or if the generator is gc'ed.
1733 if error_job is not None:
-> 1734 error_job.get_result(self.timeout)
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py:736](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py#line=735), in BatchCompletionCallBack.get_result(self, timeout)
730 backend = self.parallel._backend
732 if backend.supports_retrieve_callback:
733 # We assume that the result has already been retrieved by the
734 # callback thread, and is stored internally. It's just waiting to
735 # be returned.
--> 736 return self._return_or_raise()
738 # For other backends, the main thread needs to run the retrieval step.
739 try:
File [~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py:754](http://localhost:8888/lab/tree/~/miniconda3/envs/scenicplus/lib/python3.11/site-packages/joblib/parallel.py#line=753), in BatchCompletionCallBack._return_or_raise(self)
752 try:
753 if self.status == TASK_ERROR:
--> 754 raise self._result
755 return self._result
756 finally:
PanicException: called `Result::unwrap()` on an `Err` value: ParseIntError { kind: InvalidDigit }