phyluce_align_get_only_loci_with_min_taxa not giving the correct number of taxa in output

[GabrielaFJacintho]

Hi, I'm having this issue: my matrix of 90% would have 167 alignments but only 1 is being copied with phyluce_align_get_only_loci_with_min_taxa. Any idea what might be going on here?

#2025-06-03 16:49:34,909 - phyluce_align_get_align_summary_data - INFO - ---------------- Data matrix completeness summary ---------------
#2025-06-03 16:49:34,909 - phyluce_align_get_align_summary_data - INFO - [Matrix 50%] 1653 alignments
#2025-06-03 16:49:34,909 - phyluce_align_get_align_summary_data - INFO - [Matrix 55%] 1394 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 60%] 1152 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 65%] 935 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 70%] 753 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 75%] 612 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 80%] 451 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 85%] 312 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 90%] 167 alignments
#2025-06-03 16:49:34,910 - phyluce_align_get_align_summary_data - INFO - [Matrix 95%] 38 alignments

#phyluce_align_get_only_loci_with_min_taxa --alignments maff-edge-trimmed2 --taxa 129 --percent 0.9 --output maff-edge-trimmed2-90p --cores 32 --input-format fasta --log-path log
2025-06-03 16:52:28,269 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --percent: 0.9
2025-06-03 16:52:28,269 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --taxa: 129
2025-06-03 16:52:28,269 - phyluce_align_get_only_loci_with_min_taxa - INFO - Argument --verbosity: INFO
2025-06-03 16:52:28,269 - phyluce_align_get_only_loci_with_min_taxa - INFO - Getting alignment files
2025-06-03 16:52:28,855 - phyluce_align_get_only_loci_with_min_taxa - INFO - Copied 1 alignments of 2504 total containing ≥ 0.9 proportion of taxa (n = 116)
2025-06-03 16:52:28,855 - phyluce_align_get_only_loci_with_min_taxa - INFO - ====== Completed phyluce_align_get_only_loci_with_min_taxa ======