maximum recursion depth exceeded while calling a Python object
pangao1990 opened this issue · comments
/share/Work/pangao/software/miniconda/envs/picrust2/bin/picrust2_pipeline.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import('pkg_resources').require('PICRUSt2==2.5.2')
Error running this command:
place_seqs.py --study_fasta /share/Work/pangao/16S/shell/1.2_feature_table/dada2-rep-seqs.fasta --ref_dir /share/Work/pangao/software/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref --out_tree /share/Work/pangao/16S/shell/7.1_picrust2/picrust2_output/out.tre --processes 20 --intermediate /share/Work/pangao/16S/shell/7.1_picrust2/picrust2_output/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng
Standard error of the above failed command:
/share/Work/pangao/software/miniconda/envs/picrust2/bin/place_seqs.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import('pkg_resources').require('PICRUSt2==2.5.2')
Traceback (most recent call last):
File "/share/Work/pangao/software/miniconda/envs/picrust2/bin/place_seqs.py", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/share/Work/pangao/software/picrust2-2.5.2/scripts/place_seqs.py", line 109, in
main()
File "/share/Work/pangao/software/picrust2-2.5.2/scripts/place_seqs.py", line 85, in main
place_seqs_pipeline(study_fasta=args.study_fasta,
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/place_seqs.py", line 45, in place_seqs_pipeline
system_call_check("hmmalign --trim --dna --mapali " +
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/util.py", line 265, in system_call_check
print(stderr_log, file=sys.stderr)
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/util.py", line 842, in exit
self.cleanup()
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/util.py", line 851, in cleanup
_shutil.rmtree(self.name)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 721, in rmtree
shutil.rmtree(path)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 721, in rmtree
shutil.rmtree(path)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 721, in rmtree
shutil.rmtree(path)
[Previous line repeated 986 more times]
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 719, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 629, in _rmtree_safe_fd
entries = list(scandir_it)
RecursionError: maximum recursion depth exceeded while calling a Python object
Traceback (most recent call last):
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/util.py", line 258, in system_call_check
sys.exit(1)
SystemExit: 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/share/Work/pangao/software/miniconda/envs/picrust2/bin/picrust2_pipeline.py", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/share/Work/pangao/software/picrust2-2.5.2/scripts/picrust2_pipeline.py", line 277, in
main()
File "/share/Work/pangao/software/picrust2-2.5.2/scripts/picrust2_pipeline.py", line 239, in main
func_outfiles, pathway_outfiles = full_pipeline(study_fasta=args.study_fasta,
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/pipeline.py", line 152, in full_pipeline
system_call_check(place_seqs_cmd, print_command=verbose,
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/util.py", line 265, in system_call_check
print(stderr_log, file=sys.stderr)
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/util.py", line 842, in exit
self.cleanup()
File "/share/Work/pangao/software/picrust2-2.5.2/picrust2/util.py", line 851, in cleanup
_shutil.rmtree(self.name)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 721, in rmtree
shutil.rmtree(path)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 721, in rmtree
shutil.rmtree(path)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 721, in rmtree
shutil.rmtree(path)
[Previous line repeated 986 more times]
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 719, in rmtree
_rmtree_safe_fd(fd, path, onerror)
File "/share/Work/pangao/software/miniconda/envs/picrust2/lib/python3.8/shutil.py", line 629, in _rmtree_safe_fd
entries = list(scandir_it)
RecursionError: maximum recursion depth exceeded while calling a Python object