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liu-congcong / MetaDecoder

An algorithm for clustering metagenomic sequences.
GNU General Public License v3.0
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Medaka compatibility #12

Closed alegarritano closed 1 year ago

alegarritano commented 1 year ago

Hello,

I am running MetaDecoder on some long-read datasets that I have and it seems that while it runs without any issues when using the assembly generated by Flye, but it fails to generate the seed for the polished assembly.

The polishing was done using Medaka. Is MetaDecoder not compatible with the polished assembly?

Thank you

This is the error message:

metadecoder seed --threads 24 -f /Paratimea_ONT/Medaka/consensus.fasta -o consensus.metadecoder.seed 2023-07-17 08:17:28 -> Identifying protein sequences. Traceback (most recent call last): File "/mypython3env_MetaDecoder/bin/metadecoder", line 220, in metadecoder_seed.main(parameters) File "/mypython3env_MetaDecoder/lib/python3.10/site-packages/metadecoder/metadecoder_seed.py", line 59, in main run_fraggenescan( File "/mypython3env_MetaDecoder/lib/python3.10/site-packages/metadecoder/run_subprocess.py", line 26, in run_fraggenescan worker( File "/mypython3env_MetaDecoder/lib/python3.10/site-packages/metadecoder/run_subprocess.py", line 11, in worker assert not run(command, stdout = DEVNULL, stderr = DEVNULL).returncode, message File "/apps/z_install_tree/linux-rocky8-ivybridge/gcc-12.2.0/python-3.10.8-pmtwsrrmcmrs6olvgx5xhepgh7gl5vro/lib/python3.10/subprocess.py", line 503, in run with Popen(*popenargs, **kwargs) as process: File "/apps/z_install_tree/linux-rocky8-ivybridge/gcc-12.2.0/python-3.10.8-pmtwsrrmcmrs6olvgx5xhepgh7gl5vro/lib/python3.10/subprocess.py", line 971, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/apps/z_install_tree/linux-rocky8-ivybridge/gcc-12.2.0/python-3.10.8-pmtwsrrmcmrs6olvgx5xhepgh7gl5vro/lib/python3.10/subprocess.py", line 1847, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) PermissionError: [Errno 13] Permission denied: '/mypython3env_MetaDecoder/lib/python3.10/site-packages/metadecoder/fraggenescan'

liu-congcong commented 1 year ago

Hi alegarritano,

Thank you for your feedback.

MetaDecoder can handle any FASTA format file. The logs show that you don't have enough permissions to run the built-in component fraggenescan, you can reinstall MetaDecoder and the program will fix all the permissions for you. pip3 install --force-reinstall https://github.com/liu-congcong/MetaDecoder/releases/download/v1.0.17/metadecoder-1.0.17-py3-none-any.whl

Additionally, you can manually change the permissions of the necessary files: chmod 755 /mypython3env_MetaDecoder/lib/python3.10/site-packages/metadecoder/fraggenescan chmod 755 /mypython3env_MetaDecoder/lib/python3.10/site-packages/metadecoder/hmmsearch

Best,

Cong-Cong

alegarritano commented 1 year ago

Hi Cong, Thanks for getting back to me. This is weird, because the software ran without any issues when using Flye's assembly. Regardless, we have decided not to use the polished assembly for the binning, so I will just close this thread. Thanks once again.