Unable to cluster loci sequences

[mpgriesh]

It's unclear why clustering might fail given very similar input plasmid sequences which makes it very difficult to troubleshoot. Can you help me understand why this might happen?

lovis4u -gff plasmid_gffs/ -o plasmid_lovis/ -hl --reorient_loci ⦿ 85 loci were loaded from extended gff files folder ○ Running mmseqs for protein clustering... ⦿ 449 clusters for 3267 proteins were found with mmseqs mmseqs clustering results were saved to plasmid_lovis/mmseqs/mmseqs_clustering.tsv lovis4uError 💔: Unable to cluster loci sequences.

[art-egorov]

Could you please provide the error message you get with added '-debug' parameter? I'll have a look tomorrow morning

Best

[mpgriesh]

Thanks for the fast response and tool. Absolutely love it!

With a smaller example, it runs without error because the contig headers in the gffs were unique. Non-unique headers in the bigger set cause this error:

Traceback (most recent call last): File "/labs/asbhatt/mpgriesh/tools/miniconda3/lib/python3.12/site-packages/lovis4u/DataProcessing.py", line 735, in cluster_sequences self.locus_annotation.loc[locus.seq_id, "group"] = locus.group

  File "/labs/asbhatt/mpgriesh/tools/miniconda3/lib/python3.12/site-packages/pandas/core/indexing.py", line 911, in __setitem__
    iloc._setitem_with_indexer(indexer, value, self.name)
  File "/labs/asbhatt/mpgriesh/tools/miniconda3/lib/python3.12/site-packages/pandas/core/indexing.py", line 1944, in _setitem_with_indexer
    self._setitem_single_block(indexer, value, name)
  File "/labs/asbhatt/mpgriesh/tools/miniconda3/lib/python3.12/site-packages/pandas/core/indexing.py", line 2189, in _setitem_single_block
    value = self._align_series(indexer, Series(value))
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/labs/asbhatt/mpgriesh/tools/miniconda3/lib/python3.12/site-packages/pandas/core/indexing.py", line 2455, in _align_series
    raise ValueError("Incompatible indexer with Series")
ValueError: Incompatible indexer with Series

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/labs/asbhatt/mpgriesh/tools/miniconda3/bin/lovis4u", line 26, in <module>
    loci.cluster_sequences(mmseqs_clustering_results, one_cluster= parameters.args["one_cluster"])
  File "/labs/asbhatt/mpgriesh/tools/miniconda3/lib/python3.12/site-packages/lovis4u/DataProcessing.py", line 762, in cluster_sequences
    raise lovis4u.Manager.lovis4uError("Unable to cluster loci sequences.") from error
lovis4u.Manager.lovis4uError: Unable to cluster loci sequences.

I expected the track names to be dependent on the file name rather than the contig headers. Updating the contig headers fixed that issue.

For a small test set of plasmids, I see homologous sequences are rotated relative to each other based on the assembler arbitrarily setting the coordinates. Is there a way within this tool to rotate tracks to best align homologous sequences? Sorry if I missed that...