gtdbtk.exceptions.MSAMaskLengthMismatch: Mask (41084) and alignment (284596) length do not match

[gortey]

EXCEPTION: MSAMaskLengthMismatch
MESSAGE: Mask (41084) and alignment (284596) length do not match.

---

Traceback (most recent call last):
File "/mnt/lustre/users/sanger/app/bioinfo/metaGenomic/miniconda3/envs/gtdbtk_2.4.1/lib/python3.13/site-packages/gtdbtk/main.py", line 102, in main
gt_parser.parse_options(args)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
File "/mnt/lustre/users/sanger/app/bioinfo/metaGenomic/miniconda3/envs/gtdbtk_2.4.1/lib/python3.13/site-packages/gtdbtk/main.py", line 1176, in parse_options
all_failed_prodigal = self.align(options)
File "/mnt/lustre/users/sanger/app/bioinfo/metaGenomic/miniconda3/envs/gtdbtk_2.4.1/lib/python3.13/site-packages/gtdbtk/main.py", line 367, in align
reports,all_failed_prodigal = markers.align(options.identify_dir,
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
options.skip_gtdb_refs,
^^^^^^^^^^^^^^^^^^^^^^^
...<11 lines>...
options.outgroup_taxon if hasattr(options, 'outgroup_taxon') else None,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
self.genomes_to_process)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/lustre/users/sanger/app/bioinfo/metaGenomic/miniconda3/envs/gtdbtk_2.4.1/lib/python3.13/site-packages/gtdbtk/markers.py", line 661, in align
trimmed_seqs, pruned_seqs = self._apply_mask(gtdb_msa,
~~~~~~~~~~~~~~~~^^^^^^^^^^
user_msa,
^^^^^^^^^
gtdb_msa_mask,
^^^^^^^^^^^^^^
min_perc_aa / 100.0)
^^^^^^^^^^^^^^^^^^^^
File "/mnt/lustre/users/sanger/app/bioinfo/metaGenomic/miniconda3/envs/gtdbtk_2.4.1/lib/python3.13/site-packages/gtdbtk/markers.py", line 356, in _apply_mask
raise MSAMaskLengthMismatch(
f'Mask ({list_mask.shape[0]}) and alignment ({list_seq.shape[0]}) length do not match.')
gtdbtk.exceptions.MSAMaskLengthMismatch: Mask (41084) and alignment (284596) length do not match.

[pchaumeil]

Hi,

I need a bit more information to help debug the GTDB-Tk issue.
I can see that you are using GTDB-Tk v2.4.1, but which GTDB-Tk reference package are you using? Could you also provide the exact command(s) you are running?

In addition, which MSA are you providing that results in an alignment length of 284k+ amino acids?