Hello, recently i am using automlsa2 for alignment and construction of iq tree file generation. For pracitce, i downloaded Salmonella genomes, and made a query file of amino acid (based on recA, 16s rRNA and DnaA) in fasta format. Everything was working fine while i provided the instruction-

automlsa2 --query ref_faa --dir /home/irfan/assembly/selected/spades_outputs/all_contigs -t 8 --allow_missing 4 --missing_check salmonella_paper

i got a iqtree file. But when i included an outgroup (Salmonella enterica) i have found some error- Command:

automlsa2 \
  --query ref_faa.txt \
  --dir all_contigs \
  --outgroup  Salmonella_DQ644934.1_recA.fasta \
  -t 8 \
  --allow_missing 20 \
  --missing_check \
  test_salmonella_final_try
Output: WARNING: No parsimony-informative sites in partition WP_308987050.1
6               6       466     0       465     MFP     WP_436591635.1
WARNING: No parsimony-informative sites in partition WP_436591635.1
Degree of missing data: 0.102
Info: multi-threading strategy over alignment sites

ERROR: Alignment does not have specified outgroup taxon Salmonella_DQ644934.1_recA.fasta
                    CRITICAL iqtree2 seems to have failed.                                                                                   phylogeny.py:86
                    CRITICAL Check the log files for error messages to see if they can be resolved.                                          phylogeny.py:91
                    INFO     Program exiting with code (73) indicating failure.                                                       helper_functions.py:95
                    INFO     Check error messages to resolve the problem.                                                             helper_functions.py:97

i changed outgroup many times but found same types of error every times!