OSError: AF_UNIX path too long #402
Description
Hi all,
I encountered this error:
[2024-07-28 08:43:11] INFO: CheckM v1.2.3
[2024-07-28 08:43:11] INFO: checkm lineage_wf -x fa reassembly_nus/reassembled_bins reassembly_nus/reassembled_bins.checkm -t 96 --tmpdir reassembly_nus/tmp --pplacer_threads 22
[2024-07-28 08:43:11] INFO: CheckM data: /mnt/cc061462-beb3-49ab-9318-5c7bf54d8588/database/checkm_database/checkm_data_2015_01_16
[2024-07-28 08:43:11] INFO: [CheckM - tree] Placing bins in reference genome tree.
[2024-07-28 08:43:21] INFO: Identifying marker genes in 609 bins with 96 threads:
Process SyncManager-1:
Traceback (most recent call last):
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/managers.py", line 591, in _run_server
server = cls._Server(registry, address, authkey, serializer)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/managers.py", line 156, in init
self.listener = Listener(address=address, backlog=128)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/connection.py", line 464, in init
self._listener = SocketListener(address, family, backlog)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/connection.py", line 608, in init
self._socket.bind(address)
OSError: AF_UNIX path too long
Unexpected error: <class 'EOFError'>
Traceback (most recent call last):
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/bin/checkm", line 856, in
checkmParser.parseOptions(args)
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/site-packages/checkm/main.py", line 979, in parseOptions
self.tree(options)
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/site-packages/checkm/main.py", line 157, in tree
binIdToModels = mgf.find(binFiles,
^^^^^^^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/site-packages/checkm/markerGeneFinder.py", line 68, in find
binIdToModels = mp.Manager().dict()
^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/context.py", line 57, in Manager
m.start()
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/managers.py", line 566, in start
self._address = reader.recv()
^^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/connection.py", line 250, in recv
buf = self._recv_bytes()
^^^^^^^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/connection.py", line 430, in _recv_bytes
buf = self._recv(4)
^^^^^^^^^^^^^
File "/home/e2s2/miniconda3/envs/metawrap_reassembly/lib/python3.12/multiprocessing/connection.py", line 399, in _recv
raise EOFError
EOFError
Any ideas on how to fix it? Many thanks!