Hi, I wish to run align_seqs.py using MUSCLE de novo methods on Virtual Box. It works well on small test dataset but the process halted when I run the actual dataset which is ~27,000 sequences. I ran a simple one as below:
Traceback (most recent call last):
File "/usr/local/bin/align_seqs.py", line 211, in <module>
main()
File "/usr/local/bin/align_seqs.py", line 208, in main
log_path=log_path)
File "/usr/local/lib/python2.7/dist-packages/qiime/align_seqs.py", line 123, in __call__
log_path=log_path, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/qiime/util.py", line 259, in __call__
result = self.getResult(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/qiime/align_seqs.py", line 117, in getResult
result = module.align_unaligned_seqs(seqs, params=params)
File "/usr/local/lib/python2.7/dist-packages/bfillings/muscle_v38.py", line 556, in align_unaligned_seqs
res = app(int_map.toFasta())
File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 303, in __call__
result_paths)
File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 325, in _handle_app_result_build_failure
raise ApplicationError("Error constructing CommandLineAppResult.")
burrito.util.ApplicationError: Error constructing CommandLineAppResult.
Could that be memory issue? How do I solve the problem? Would it helps if I increase --muscle_max_memory? Thank you.