error in detect_leaf_markers

[xyang2uchicago]

Hi,
My code running the Jupyter Notebook is:

st.detect_leaf_markers(adata,marker_list=adata.uns['var_genes'],cutoff_zscore=1.0,cutoff_pvalue=0.01,
... percentile_expr=90, min_num_cells=25,
... root='S0',n_jobs=1)

The error outputs are:

Scanning the specified marker list ...
Filtering out markers that are expressed in less than 25 cells ...
1 cpus are being used ...
Traceback (most recent call last):
File "", line 3, in
File "/project/xyang2/software-packages/env/stream/lib/python3.7/site-packages/stream/core.py", line 3807, in detect_leaf_markers
results = pool.map(scale_marker_expr,params)
File "/project/xyang2/software-packages/env/stream/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/project/xyang2/software-packages/env/stream/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
File "/project/xyang2/software-packages/env/stream/lib/python3.7/multiprocessing/pool.py", line 431, in _handle_tasks
put(task)
File "/project/xyang2/software-packages/env/stream/lib/python3.7/multiprocessing/connection.py", line 206, in send
self._send_bytes(_ForkingPickler.dumps(obj))
File "/project/xyang2/software-packages/env/stream/lib/python3.7/multiprocessing/connection.py", line 393, in _send_bytes
header = struct.pack("!i", n)
struct.error: 'i' format requires -2147483648 <= number <= 2147483647

Anyone can help?

[braaist]

Hello!
I have the same problem. It looks like an issue with pool multiprocessing which was fixed in py3.8. However, STREAM 1.1 only supports py3.7. As a temporary fix, I reduced the number of genes (marker_list parameter).