verylili
commented
1 year ago This error occurred on a server, not a personal computer. And I met the error when the number of genomes is large.
Open verylili opened 1 year ago
verylili
commented
1 year ago This error occurred on a server, not a personal computer. And I met the error when the number of genomes is large.
Hi, I was running PEPPAN on ~1700 E. coli genomes. I met an error as follows: Traceback (most recent call last): File "/home/LL/miniconda3/envs/PEPPAN/bin/PEPPAN", line 8, in
sys.exit(ortho())
^^^^^^^
File "/home/LL/miniconda3/envs/PEPPAN/lib/python3.11/site-packages/PEPPAN/PEPPAN.py", line 1916, in ortho
filt_genes(tab_conn, np.load(params['self_bsn'], allow_pickle=True), params['global'], params['map_bsn']+'.conflicts.npz', priorities, gene_scores, encodes)
File "/home/LL/miniconda3/envs/PEPPAN/lib/python3.11/site-packages/PEPPAN/PEPPAN.py", line 732, in filt_genes
mat_out.append([pangene_name, gene_name, min_rank, mat])
File "", line 2, in append
File "/home/LL/miniconda3/envs/PEPPAN/lib/python3.11/multiprocessing/managers.py", line 821, in _callmethod
conn.send((self._id, methodname, args, kwds))
File "/home/LL/miniconda3/envs/PEPPAN/lib/python3.11/multiprocessing/connection.py", line 205, in send
self._send_bytes(_ForkingPickler.dumps(obj))
File "/home/LL/miniconda3/envs/PEPPAN/lib/python3.11/multiprocessing/connection.py", line 410, in _send_bytes
self._send(header + buf)
File "/home/LL/miniconda3/envs/PEPPAN/lib/python3.11/multiprocessing/connection.py", line 367, in _send
n = write(self._handle, buf)
^^^^^^^^^^^^^^^^^^^^^^^^
BrokenPipeError: [Errno 32] Broken pipe