IOError: [Errno 9] Bad file descriptor

[JiaB-He]

ERROR 2022-11-16 09:35:06,865 run_spades_single-<Process(PoolWorker-22, started daemon)> Caught exception in worker thread Traceback (most recent call last): File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/run_spades.py", line 75, in run_spades_single retcode = cmd.run(cmd_log_fd_out=spades_log_fd, timeout=timeout) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/external_cmd.py", line 20, in run self.p = subprocess.Popen(self.cmd, stderr=cmd_log_fd_err, stdout=cmd_log_fd_out) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory INFO 2022-11-16 09:35:07,116 extract_read_pairs-<Process(PoolWorker-16, started daemon)> Examined 829 pairs in 1.0125 seconds INFO 2022-11-16 09:35:07,116 extract_read_pairs-<Process(PoolWorker-16, started daemon)> Extraction counts [('all_pair_hq', 778), ('non_perfect_hq', 268)] INFO 2022-11-16 09:35:07,117 run_spades_single-<Process(PoolWorker-16, started daemon)> Running SPADES/SPADES.PY with arguments ['-1', 'work/spades/0/_all_pair_hq_1.fq', '-2', 'work/spades/0/_all_pair_hq_2.fq', '-o', 'work/spades/0/spades_all_pair_hq/', '-m', '4', '-t', '1', '--phred-offset', '33'] ERROR 2022-11-16 09:35:07,124 run_spades_single-<Process(PoolWorker-16, started daemon)> Caught exception in worker thread Traceback (most recent call last): File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/run_spades.py", line 75, in run_spades_single retcode = cmd.run(cmd_log_fd_out=spades_log_fd, timeout=timeout) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/external_cmd.py", line 20, in run self.p = subprocess.Popen(self.cmd, stderr=cmd_log_fd_err, stdout=cmd_log_fd_out) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory () () () () () () () () () () () () () () () INFO 2022-11-16 09:35:07,196 metasv.run_spades Merging the contigs from [] Traceback (most recent call last): File "/home/jbhe/software/anaconda3/envs/metasv/bin/run_metasv.py", line 143, in sys.exit(run_metasv(args)) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/main.py", line 306, in run_metasv assembly_max_tools=args.assembly_max_tools) File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/site-packages/metasv/run_spades.py", line 214, in run_spades_parallel for line in fileinput.input(assembly_fastas): File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/fileinput.py", line 237, in next line = self._readline() File "/home/jbhe/software/anaconda3/envs/metasv/lib/python2.7/fileinput.py", line 342, in _readline return self._readline() IOError: [Errno 9] Bad file descriptor