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pinellolab / dictys

Context specific and dynamic gene regulatory network reconstruction and analysis
GNU Affero General Public License v3.0
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Creating .h5 output file #49

Closed e-arslan closed 6 months ago

e-arslan commented 6 months ago

Hi thanks for the method.

I'm having an issue while running Aggregating network part

make -f makefiles/static.mk combine

mkdir -p output/ OPENBLAS_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1 MKL_NUM_THREADS=1 OPENBLAS_MAX_THREADS=1 NUMEXPR_MAX_THREADS=1 MKL_MAX_THREADS=1 python3 -m dictys network tofile data tmp_static data/subsets.txt output/static.h5 WARNING:27658:2024-01-07 18:59:19,742:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c1d1 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:27658:2024-01-07 18:59:19,743:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c1d1 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:27658:2024-01-07 18:59:19,743:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c1d3 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:27658:2024-01-07 18:59:19,744:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c1d3 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:27658:2024-01-07 18:59:19,744:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c1d8 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:27658:2024-01-07 18:59:19,744:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c1d8 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:27658:2024-01-07 18:59:19,745:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c2d1 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:27658:2024-01-07 18:59:19,745:/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset pt_28_c2d1 due to error: FileNotFoundError(2, 'No such file or directory') Traceback (most recent call last): File "/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/main.py", line 13, in docstringrunner(package) File "/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 340, in docstringrunner run_args(pkgname,funcs,args) File "/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 330, in run_args return func(a,ka) File "/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/network.py", line 1074, in tofile n=network.from_folders(diri_data,diri_work,fi_subsets,dynamic=dynamic,nettype=nettype,optional=optional,fi_c=fi_c) File "/Users/earslan/opt/anaconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py", line 407, in from_folders raise RuntimeError('No network found.') RuntimeError: No network found. make: [makefiles/common.mk:178: output/static.h5] Error 1

lingfeiwang commented 6 months ago

Hi, thanks for the interest. Did you run the tutorial successfully?