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malonge / RagTag

Tools for fast and flexible genome assembly scaffolding and improvement
MIT License
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Scaffold doesn't run #154

Closed aebaci closed 1 year ago

aebaci commented 1 year ago

Hi:

I have tried to run the scaffold option of ragtag, but I get an error message (below). It says it doesn't have the ragtag_scaffold.py, but I go to the folder and it was installed there (same folder as ragtag.py), so I'm not sure what to do. I tried the other commands and they give the same error, changing the executable file that is not found (and they are all there). I really hope to use this tool for my assemblies, so if you could help me out it would be great. Thanks! Software version is v2.1.0 /opt/mambaforge/bin/ragtag.py scaffold RprolixusVB.fasta racon1Rprol2.fasta Traceback (most recent call last): File "/opt/mambaforge/bin/ragtag.py", line 133, in main() File "/opt/mambaforge/bin/ragtag.py", line 89, in main subprocess.call(subcmd) File "/opt/mambaforge/lib/python3.8/subprocess.py", line 340, in call with Popen(*popenargs, **kwargs) as p: File "/opt/mambaforge/lib/python3.8/subprocess.py", line 858, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/opt/mambaforge/lib/python3.8/subprocess.py", line 1704, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'ragtag_scaffold.py'

malonge commented 1 year ago

There is just some sort of installation issue. I recommend just using conda or pypi if you are having difficulty installing from source. Also consider virtual environments to make things easier to interpret.