N E X T F L O W ~ version 24.04.4
Launching /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/meta/mock.nf [prickly_leavitt] DSL2 - revision: 6a2b47e621
Creating env using conda: conda-forge::decoupler-py=1.6.0 [cache /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/conda/env-e8572468eaade6843c07829a0101aaf2]
[63/ce7666] Submitted process > DECOUPLER (test)
ERROR ~ Error executing process > 'DECOUPLER (test)'
Caused by:
Process DECOUPLER (test) terminated with an error exit status (1)
mat = pd.read_csv("expression.tsv", sep=" ", index_col=0)
net = pd.read_csv("network.tsv", sep=" ", index_col=0)
Parsing arguments
args = {'min_n': 1}
parsedargs = {'args': {}}
for k, v in args.items():
Specific method argument
if k.split('_')[0] in methods:
meth = k.split('_')[0]
arg = '_'.join(k.split('_')[1:])
if meth not in args['args'].keys():
parsedargs['args'][meth] = {arg: v}
else:
parsedargs['args'][meth].update({arg: v})
# Generic argument
else:
parsedargs[k] = v
results = dc.decouple(
mat=mat,
net=net,
Of which 2 did not match due to:
Overload in function 'np_arange': File: numba/np/arrayobj.py: Line 4760.
With argument(s): '(start=int64, stop=int64, step=int64, dtype=class(float32))':
Rejected as the implementation raised a specific error:
TypingError: got some positional-only arguments passed as keyword arguments: 'start'
raised from /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/conda/env-e8572468eaade6843c07829a0101aaf2/lib/python3.12/site-packages/numba/core/typing/templates.py:783
During: resolving callee type: Function()
During: typing of call at /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/conda/env-e8572468eaade6843c07829a0101aaf2/lib/python3.12/site-packages/decoupler/method_gsva.py (86)
File "../../conda/env-e8572468eaade6843c07829a0101aaf2/lib/python3.12/site-packages/decoupler/method_gsva.py", line 86:
def nb_get_D_I(mat):
n = mat.shape[1]
rev_idx = np.abs(np.arange(start=n, stop=0, step=-1, dtype=nb.f4) - n / 2)
^
Work dir:
/home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/63/ce7666b5e282eae692d5bdab4f1143
Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
-- Check '/home/ubuntu/tests/949573c551759dbba21b380d94c814b5/meta/nextflow.log' file for details
WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
Assertion failed:
edmundmiller
commented
3 days ago
Have you checked the docs?
Description of the bug
Test [949573c5] 'decoupler_test'
assert process.success | | | false DECOUPLER
Command used and terminal output
No response
Relevant files
No response
System information
No response