concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/process.py", line 254, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/process.py", line 203, in _process_chunk
return [fn(*args) for args in chunk]
~~^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/parallel_workers.py", line 326, in construct_models_in_parallel
model_reads_printer.add_read_info(ma)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/assignment/assignment_io.py", line 430, in add_read_info
self._write_unmatched(read_assignment)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/assignment/assignment_io.py", line 404, in _write_unmatched
self._get_canonical(read_introns, read_assignment, strand), # canonical
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/assignment/assignment_io.py", line 361, in _get_canonical
if not self.params.check_canonical or not read_assignment.gene_info or not read_assignment.gene_info.reference_region:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'GeneInfo' object has no attribute 'reference_region'. Did you mean: 'get_gene_region'?
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant.py", line 1433, in main_entry
main(sys.argv[1:])
~~~~^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant.py", line 1427, in main
run_pipeline(args)
~~~~~~~~~~~~^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant.py", line 1340, in run_pipeline
dataset_processor.process_all_samples(args.input_data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/dataset_processor.py", line 136, in process_all_samples
self.process_sample(sample)
~~~~~~~~~~~~~~~~~~~^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/dataset_processor.py", line 236, in process_sample
self.process_assigned_reads(sample, saves_file)
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/dataset_processor.py", line 474, in process_assigned_reads
for read_stat_counter, tsc in results:
^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/process.py", line 617, in _chain_from_iterable_of_lists
for element in iterable:
^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 619, in result_iterator
yield _result_or_cancel(fs.pop())
~~~~~~~~~~~~~~~~~^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 317, in _result_or_cancel
return fut.result(timeout)
~~~~~~~~~~^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
~~~~~~~~~~~~~~~~~^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
AttributeError: 'GeneInfo' object has no attribute 'reference_region'
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/process.py", line 254, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/process.py", line 203, in _process_chunk
return [fn(*args) for args in chunk]
~~^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/parallel_workers.py", line 326, in construct_models_in_parallel
model_reads_printer.add_read_info(ma)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/assignment/assignment_io.py", line 430, in add_read_info
self._write_unmatched(read_assignment)
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/assignment/assignment_io.py", line 404, in _write_unmatched
self._get_canonical(read_introns, read_assignment, strand), # canonical
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/assignment/assignment_io.py", line 361, in _get_canonical
if not self.params.check_canonical or not read_assignment.gene_info or not read_assignment.gene_info.reference_region:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'GeneInfo' object has no attribute 'reference_region'. Did you mean: 'get_gene_region'?
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant.py", line 1433, in main_entry
main(sys.argv[1:])
~~~~^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant.py", line 1427, in main
run_pipeline(args)
~~~~~~~~~~~~^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant.py", line 1340, in run_pipeline
dataset_processor.process_all_samples(args.input_data)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/dataset_processor.py", line 136, in process_all_samples
self.process_sample(sample)
~~~~~~~~~~~~~~~~~~~^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/dataset_processor.py", line 236, in process_sample
self.process_assigned_reads(sample, saves_file)
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/site-packages/isoquant_lib/dataset_processor.py", line 474, in process_assigned_reads
for read_stat_counter, tsc in results:
^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/process.py", line 617, in _chain_from_iterable_of_lists
for element in iterable:
^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 619, in result_iterator
yield _result_or_cancel(fs.pop())
~~~~~~~~~~~~~~~~~^^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 317, in _result_or_cancel
return fut.result(timeout)
~~~~~~~~~~^^^^^^^^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
~~~~~~~~~~~~~~~~~^^
File "/mnt/dfc_data1/home/zhoujj/anaconda2/envs/rnaseq-long/lib/python3.13/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
AttributeError: 'GeneInfo' object has no attribute 'reference_region'