The alignment file has no sequences. PASTA quits.

[TanHoa-DinhNguyen]

Hi,

I have a trouble when I'm running test run_pasta.py -i small.fasta

/usr/local/bin/run_pasta.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import('pkg_resources').require('PASTA==1.9.1') PASTA INFO: Reading input sequences from 'small.fasta'... PASTA INFO: Masking alignment sites with less than 1 sites before running the tree step PASTA INFO: Configuration written to "/home/tanhoa96/27ENA/pastajob_temp_pasta_config.txt".

PASTA INFO: Directory for temporary files created at /home/tanhoa96/.pasta/pastajob/tempp4r97pad PASTA INFO: Name translation information saved to /home/tanhoa96/27ENA/pastajob_temp_name_translation.txt as safe name, original name, blank line format. PASTA INFO: Creating a starting tree for the PASTA algorithm... PASTA INFO: Performing initial alignment of the entire data matrix... Exception in thread Thread-1: Traceback (most recent call last): File "/home/tanhoa96/pasta_code/pasta/pasta/scheduler.py", line 199, in call job.results = job.result_processor() File "/home/tanhoa96/pasta_code/pasta/pasta/tools.py", line 280, in rpc = lambda : read_internal_alignment(alignedfn, File "/home/tanhoa96/pasta_code/pasta/pasta/tools.py", line 79, in read_internal_alignment raise ValueError("The alignment file %s has no sequences. PASTA quits." % fn) ValueError: The alignment file /home/tanhoa96/.pasta/pastajob/tempp4r97pad/init_aln/tempmafftsm0mas61/input.aligned has no sequences. PASTA quits.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner self.run() File "/usr/lib/python3.10/threading.py", line 953, in run self._target(*self._args, **self._kwargs) File "/home/tanhoa96/pasta_code/pasta/pasta/scheduler.py", line 211, in call traceback.print_exc(file=err) File "/usr/lib/python3.10/traceback.py", line 179, in print_exc print_exception(*sys.exc_info(), limit=limit, file=file, chain=chain) File "/usr/lib/python3.10/traceback.py", line 121, in print_exception print(line, file=file, end="") TypeError: a bytes-like object is required, not 'str'

Any idea on how this can be fixed?

Any help would be appreciated. Thank you very much!