I'm very new to MIDAS and also Linux. Can you please help me with this error?
When I run test_midas.py -vf, RunSNPs always fail. What's the problem here?
FAIL: test_class (main._07_RunSNPs)
Traceback (most recent call last):
File "/home/daisy/MIDAS/test/test_midas.py", line 102, in test_class
self.assertTrue(code==0, msg=err)
AssertionError: False is not true : b'Traceback (most recent call last):\n File "/home/daisy/MIDAS/scripts/run_midas.py", line 757, in \n run_program(program, args)\n File "/home/daisy/MIDAS/scripts/run_midas.py", line 82, in run_program\n snps.run_pipeline(args)\n File "/home/daisy/MIDAS/midas/run/snps.py", line 301, in run_pipeline\n pysam_pileup(args, species, contigs)\n File "/home/daisy/MIDAS/midas/run/snps.py", line 228, in pysam_pileup\n aln_stats = utility.parallel(species_pileup, argument_list, args[\'threads\'])\n File "/home/daisy/MIDAS/midas/utility.py", line 101, in parallel\n return [r.get() for r in results]\n File "/home/daisy/MIDAS/midas/utility.py", line 101, in \n return [r.get() for r in results]\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/pool.py", line 771, in get\n raise self._value\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/pool.py", line 537, in _handle_tasks\n put(task)\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/connection.py", line 211, in send\n self._send_bytes(_ForkingPickler.dumps(obj))\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/reduction.py", line 51, in dumps\n cls(buf, protocol).dump(obj)\nTypeError: cannot pickle \'_io.TextIOWrapper\' object\n'
Hello,
I'm very new to MIDAS and also Linux. Can you please help me with this error? When I run
test_midas.py -vf, RunSNPs always fail. What's the problem here?FAIL: test_class (main._07_RunSNPs)
Traceback (most recent call last): File "/home/daisy/MIDAS/test/test_midas.py", line 102, in test_class self.assertTrue(code==0, msg=err) AssertionError: False is not true : b'Traceback (most recent call last):\n File "/home/daisy/MIDAS/scripts/run_midas.py", line 757, in\n run_program(program, args)\n File "/home/daisy/MIDAS/scripts/run_midas.py", line 82, in run_program\n snps.run_pipeline(args)\n File "/home/daisy/MIDAS/midas/run/snps.py", line 301, in run_pipeline\n pysam_pileup(args, species, contigs)\n File "/home/daisy/MIDAS/midas/run/snps.py", line 228, in pysam_pileup\n aln_stats = utility.parallel(species_pileup, argument_list, args[\'threads\'])\n File "/home/daisy/MIDAS/midas/utility.py", line 101, in parallel\n return [r.get() for r in results]\n File "/home/daisy/MIDAS/midas/utility.py", line 101, in \n return [r.get() for r in results]\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/pool.py", line 771, in get\n raise self._value\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/pool.py", line 537, in _handle_tasks\n put(task)\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/connection.py", line 211, in send\n self._send_bytes(_ForkingPickler.dumps(obj))\n File "/home/daisy/anaconda3/lib/python3.9/multiprocessing/reduction.py", line 51, in dumps\n cls(buf, protocol).dump(obj)\nTypeError: cannot pickle \'_io.TextIOWrapper\' object\n'
Thank you.
Daisy