Command output:

  Running EUKulele with command line arguments, as no valid configuration file was provided.

  The current EUKulele version is 2.1.2

 

  Setting things up...

  Could not successfully install all external dependent software.

  Check DIAMOND, BLAST, BUSCO, and TransDecoder installation.

  ['proteins']

  Specified reference directory, reference FASTA, and protein map/taxonomy table not found. Using database in location: eukulele/gtdb.

  Found database folder for eukulele/gtdb in current directory; will not re-download.

  Creating a diamond reference from database files...

  Diamond database file already created; will not re-create database.

  Aligning to reference database...

  Aligning sample proteins...

  Diamond process exited for sample proteins.

  Performing taxonomic estimation steps...

  Performing taxonomic visualization steps...

 



Command error:

  mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'

  Matplotlib created a temporary cache directory at /tmp/matplotlib-q__3vf7u because there was an issue with the default path (/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.

  Fontconfig error: No writable cache directories

  /usr/local/lib/python3.12/site-packages/EUKulele/manage_steps.py:29: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`

    MEM_AVAIL_GB = pd.read_csv("free.csv", sep = "\s+").free[0] / 10**3

  /usr/local/lib/python3.12/site-packages/EUKulele/busco_runner.py:19: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`

    MEM_AVAIL_GB = pd.read_csv("free.csv", sep = "\s+").free[0] / 10**3

  Running EUKulele with command line arguments, as no valid configuration file was provided.

  The current EUKulele version is 2.1.2

 

  Setting things up...

  Could not successfully install all external dependent software.

  Check DIAMOND, BLAST, BUSCO, and TransDecoder installation.

  ['proteins']

  Specified reference directory, reference FASTA, and protein map/taxonomy table not found. Using database in location: eukulele/gtdb.

  Found database folder for eukulele/gtdb in current directory; will not re-download.

  Creating a diamond reference from database files...

  Diamond database file already created; will not re-create database.

  Aligning to reference database...

  Aligning sample proteins...

  Diamond process exited for sample proteins.

  Performing taxonomic estimation steps...

  Performing taxonomic visualization steps...

  gzip: megahit.protein_consolidate_99.gtdb_gtdb/taxonomy_estimation/*.out: No such file or directory



Work dir:

  /home/evalopes/metadnovo23/work/a3/a8bdf174c51d0bff6e74af937117b7