New install, will not run

[hwa2Hu]

Hi Arun,
I go it to run with your help last time by bypass samtools. I try to update cutadapt to use it globally and it will not run anymore.

Please help. Thanks a lot.

Gui

---

owner@P700:~/miRge3$ pyenv versions
system
2.7.15

• 3.8.0 (set by /home/owner/miRge3/.python-version)
  3.12.8
  3.13.1

owner@P700:~/miRge3$ which cutadapt
/usr/bin/cutadapt

owner@P700:~/miRge3$ cutadapt --version
4.9

owner@P700:~/miRge3$ which python
/home/owner/.pyenv/shims/python

owner@P700:~/miRge3$ python -V
Python 3.8.0

---

owner@P700:~/miRge3$ miRge3.0 -s SRR772403.fastq.gz, -lib miRge3_Lib -on human -db mirbase -o output_dir -gff -nmir -trf -ai -cpu 16 -a illumina

/home/owner/.local/lib/python3.8/site-packages/pandas/_testing.py:24: FutureWarning: In the future np.bool will be defined as the corresponding NumPy scalar.
import pandas._libs.testing as _testing
Traceback (most recent call last):
File "/home/owner/.local/bin/miRge3.0", line 5, in
from mirge.main import main
File "/home/owner/.local/lib/python3.8/site-packages/mirge/main.py", line 12, in
import pandas as pd
File "/home/owner/.local/lib/python3.8/site-packages/pandas/init.py", line 180, in
import pandas.testing
File "/home/owner/.local/lib/python3.8/site-packages/pandas/testing.py", line 5, in
from pandas._testing import (
File "/home/owner/.local/lib/python3.8/site-packages/pandas/_testing.py", line 24, in
import pandas._libs.testing as _testing
File "pandas/_libs/testing.pyx", line 10, in init pandas._libs.testing
File "/home/owner/.local/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'bool'.
np.bool was a deprecated alias for the builtin bool. To avoid this error in existing code, use bool by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.bool_ here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

[arunhpatil]

Hi Guihua,

This error is due to Numpy version, can you downgrade the currently installed Numpy?

python3.8 -m pip install numpy==1.19

Thank you,
Arun.

[hwa2Hu]

Hi Arun,
Solved. Thanks!

Guihua

[arunhpatil]

Hi Guihua,

Great. Glad it worked.

Thank you,
Arun.