run error #109
Description
Dear Prof. @spond,
Please see below:
hivtrace -i TEST.FASTA -a resolve -r HXB2_prrt -t .015 -m 500 -g .05 -c
Traceback (most recent call last):
File "/Users/liam/opt/miniconda3/bin/bealign", line 16, in <module>
from BioExt.scorematrices import (
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/BioExt/scorematrices/__init__.py", line 4, in <module>
from BioExt.scorematrices._scorematrix import *
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/BioExt/scorematrices/_scorematrix.py", line 12, in <module>
from BioExt.optimize import minimize_bfgs
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/BioExt/optimize/__init__.py", line 193, in <module>
tol=1e-5, norm=numpy.Inf, eps=_epsilon, maxiter=None,
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/numpy/__init__.py", line 397, in __getattr__
raise AttributeError(
AttributeError: `np.Inf` was removed in the NumPy 2.0 release. Use `np.inf` instead.
Traceback (most recent call last):
File "/Users/liam/opt/miniconda3/bin/hivtrace", line 8, in <module>
sys.exit(main())
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 793, in main
results = hivtrace(
File "/Users/liam/opt/miniconda3/lib/python3.9/site-packages/hivtrace/hivtrace.py", line 438, in hivtrace
subprocess.check_call(bealign_process, stdout=DEVNULL)
File "/Users/liam/opt/miniconda3/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/Users/liam/opt/miniconda3/bin/bealign', '-q', '-r', 'HXB2_prrt', '-m', 'HIV_BETWEEN_F', '-R', 'TEST.FASTA', '/var/folders/q4/gvrdsnj94vl527nfhj25rxh40000gn/T/hivtrace-pa1fw79s/TEST.FASTA_output.bam']' returned non-zero exit status 1.