Hello!
Can we please get full log (of why the script crashed) of our submission?
Thank you!
Created by gmurtaza Thank you for your prompt response!
Hi @gmurtaza,
The following errors were received for subID 9761293:
```
WARNING: adata.X seems to be already log-transformed.
Warning: StackingClassifier not available. Relying on dummy class.
--- Starting Prediction (Strategy 1 Model) ---
Target Class: Non-neuronal and Non-neural
Found model files.
Step 1: Loading test data from /input/data.h5ad...
Step 2: Processing test data for 'Non-neuronal and Non-neural'...
Normalizing and log1p...
Running pseudobulk aggregation...
Starting pseudobulk aggregation on 'log1p_norm'...
Grouping by: ['Class', 'library_prep']
/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/backend/utils.py:63: UserWarning: Failed to kill subprocesses on this platform. Please installpsutil: https://github.com/giampaolo/psutil
Details:
Traceback (most recent call last):
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/backend/utils.py", line 60, in _kill_process_tree_without_psutil
_posix_recursive_kill(process.pid)
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/backend/utils.py", line 111, in _posix_recursive_kill
children_pids = subprocess.check_output(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/subprocess.py", line 466, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/subprocess.py", line 548, in run
with Popen(*popenargs, **kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/local/lib/python3.11/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'pgrep'
warnings.warn(
Exception in thread ExecutorManagerThread:
Traceback (most recent call last):
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/backend/utils.py", line 60, in _kill_process_tree_without_psutil
_posix_recursive_kill(process.pid)
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/backend/utils.py", line 111, in _posix_recursive_kill
children_pids = subprocess.check_output(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/subprocess.py", line 466, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/subprocess.py", line 548, in run
with Popen(*popenargs, **kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/subprocess.py", line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/local/lib/python3.11/subprocess.py", line 1955, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'pgrep'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.11/threading.py", line 1045, in _bootstrap_inner
self.run()
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 635, in run
self.flag_executor_shutting_down()
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 856, in flag_executor_shutting_down
self.kill_workers(reason="executor shutting down")
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/process_executor.py", line 866, in kill_workers
kill_process_tree(p)
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/backend/utils.py", line 21, in kill_process_tree
_kill_process_tree_without_psutil(process)
File "/home/user/.local/lib/python3.11/site-packages/joblib/externals/loky/backend/utils.py", line 73, in _kill_process_tree_without_psutil
process.kill()
File "/usr/local/lib/python3.11/multiprocessing/process.py", line 140, in kill
self._popen.kill()
^^^^^^^^^^^^^^^^
AttributeError: 'Popen' object has no attribute 'kill'
ERROR: Pseudobulk aggregation failed. Could not pickle the task to send it to the workers.
FATAL ERROR: Pseudobulk aggregation failed on test data.
```