Hi, apparently I have a multiprocess error when running adVNTR ; the command :
advntr genotype --alignment_file $bam --working_directory $advntrDir/$bam_name --vntr_id 25561 --pacbio --frameshift -m ../hg19_selected_VNTRs_Pacbio.db -t $Ncpu
the error :
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 14991 reads
Process Process-1009:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 749, in _callmethod
conn = self._tls.connection
AttributeError: 'ForkAwareLocal' object has no attribute 'connection'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 264, in check_if_pacbio_read_spans_vntr
self.check_if_flanking_regions_align_to_str(str(read.seq).upper(), length_distribution, spanning_reads)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 260, in check_if_flanking_regions_align_to_str
spanning_reads.append(read_str[left_align[3]:right_align[3]+flanking_region_size])
File "", line 2, in append
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 753, in _callmethod
self._connect()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 740, in _connect
conn = self._Client(self._token.address, authkey=self._authkey)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 487, in Client
c = SocketClient(address)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 614, in SocketClient
s.connect(address)
FileNotFoundError: [Errno 2] No such file or directory
Process Process-1017:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 749, in _callmethod
conn = self._tls.connection
AttributeError: 'ForkAwareLocal' object has no attribute 'connection'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 264, in check_if_pacbio_read_spans_vntr
self.check_if_flanking_regions_align_to_str(str(read.seq).upper(), length_distribution, spanning_reads)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 260, in check_if_flanking_regions_align_to_str
spanning_reads.append(read_str[left_align[3]:right_align[3]+flanking_region_size])
File "", line 2, in append
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 753, in _callmethod
self._connect()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 740, in _connect
conn = self._Client(self._token.address, authkey=self._authkey)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 487, in Client
c = SocketClient(address)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 614, in SocketClient
s.connect(address)
FileNotFoundError: [Errno 2] No such file or directory
Process Process-1010:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 749, in _callmethod
conn = self._tls.connection
AttributeError: 'ForkAwareLocal' object has no attribute 'connection'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 264, in check_if_pacbio_read_spans_vntr
self.check_if_flanking_regions_align_to_str(str(read.seq).upper(), length_distribution, spanning_reads)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 260, in check_if_flanking_regions_align_to_str
spanning_reads.append(read_str[left_align[3]:right_align[3]+flanking_region_size])
File "", line 2, in append
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 753, in _callmethod
self._connect()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 740, in _connect
conn = self._Client(self._token.address, authkey=self._authkey)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 487, in Client
c = SocketClient(address)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 614, in SocketClient
s.connect(address)
FileNotFoundError: [Errno 2] No such file or directory
Process Process-994:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 749, in _callmethod
conn = self._tls.connection
AttributeError: 'ForkAwareLocal' object has no attribute 'connection'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 264, in check_if_pacbio_read_spans_vntr
self.check_if_flanking_regions_align_to_str(str(read.seq).upper(), length_distribution, spanning_reads)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 260, in check_if_flanking_regions_align_to_str
spanning_reads.append(read_str[left_align[3]:right_align[3]+flanking_region_size])
File "", line 2, in append
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 753, in _callmethod
self._connect()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 740, in _connect
conn = self._Client(self._token.address, authkey=self._authkey)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 487, in Client
c = SocketClient(address)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 614, in SocketClient
s.connect(address)
FileNotFoundError: [Errno 2] No such file or directory
Process Process-1003:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 749, in _callmethod
conn = self._tls.connection
AttributeError: 'ForkAwareLocal' object has no attribute 'connection'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 264, in check_if_pacbio_read_spans_vntr
self.check_if_flanking_regions_align_to_str(str(read.seq).upper(), length_distribution, spanning_reads)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 260, in check_if_flanking_regions_align_to_str
spanning_reads.append(read_str[left_align[3]:right_align[3]+flanking_region_size])
File "", line 2, in append
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 753, in _callmethod
self._connect()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/managers.py", line 740, in _connect
conn = self._Client(self._token.address, authkey=self._authkey)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 487, in Client
c = SocketClient(address)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/connection.py", line 614, in SocketClient
s.connect(address)
FileNotFoundError: [Errno 2] No such file or directory
Traceback (most recent call last):
File "/opt/miniconda3/envs/gene36/bin/advntr", line 11, in
sys.exit(main())
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/main.py", line 121, in main
genotype(args, genotype_parser)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/advntr_commands.py", line 101, in genotype
genome_analyzier.find_repeat_counts_from_pacbio_alignment_file(input_file)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/genome_analyzer.py", line 103, in find_repeat_counts_from_pacbio_alignment_file
copy_numbers = self.vntr_finder[vid].find_repeat_count_from_pacbio_alignment_file(alignment_file, reads)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/profiler.py", line 8, in wrapper
retval = func(*args, **kwargs)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 477, in find_repeat_count_from_pacbio_alignment_file
mapped_spanning_reads = self.get_spanning_reads_of_aligned_pacbio_reads(alignment_file)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/profiler.py", line 8, in wrapper
retval = func(*args, **kwargs)
File "/opt/miniconda3/envs/gene36/lib/python3.6/site-packages/advntr/vntr_finder.py", line 329, in get_spanning_reads_of_aligned_pacbio_reads
p.start()
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/process.py", line 105, in start
self._popen = self._Popen(self)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/context.py", line 223, in _Popen
return _default_context.get_context().Process._Popen(process_obj)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/context.py", line 277, in _Popen
return Popen(process_obj)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/opt/miniconda3/envs/gene36/lib/python3.6/multiprocessing/popen_fork.py", line 65, in _launch
parent_r, child_w = os.pipe()
OSError: [Errno 24] Too many open files