IndexError: list assignment index out of range in Mapper.py

It looks like something weird is happening with Mapper.py. I'm running read2tree through conda with Python=3.10.8, following the installation instructions in the documentation.

I think if bases in line 513 is not properly checking empty lists, or something funky is happening - this occurs for some datasets and not others.

                if bases:
                    seq[pileup_column.pos] = self._most_common(bases)

Resulting in the error message:

Loading alignments : 0 Alignment [00:00, ? Alignment/s]
--- Mapping of reads to reference sequences ---
--- Splitting reads from genomes/4_D_D6_S293_L004.fq ---
2023-10-16 16:11:18,904 - read2tree.Reads - INFO - 4DD6S293L004: --- Splitting reads from genomes/4_D_D6_S293_L004.fq ---
Splitting reads: 1693283 reads [00:03, 464240.82 reads/s]
2023-10-16 16:11:22,552 - read2tree.Reads - INFO - 4DD6S293L004: Reads larger than 20000 were split into 20000 bp long fragments with an overlap of 1000 bp.
2023-10-16 16:11:22,553 - read2tree.Reads - INFO - 4DD6S293L004: 1693283 reads were split into 1693283 reads.
2023-10-16 16:11:22,553 - read2tree.Reads - INFO - 4DD6S293L004: Splitting of reads took 3.6483232975006104.
Mapping reads to species:   0%|                                                                                     | 0/13 [00:00<?, ? species/s]2023-10-16 16:11:22,553 - read2tree.Mapper - INFO - 4DD6S293L004: --- Mapping of reads to DROBP reference species ---
2023-10-16 16:11:55,262 - read2tree.Mapper - INFO - 4DD6S293L004: Mapped 306991.0 / 418262.0 reads to DROBP_OGs.fa
2023-10-16 16:11:55,315 - read2tree.Mapper - INFO - 4DD6S293L004: Mapping to DROBP_OGs.fa references took 32.75954222679138.
Mapping reads to species:   0%|                                                                                     | 0/13 [00:47<?, ? species/s]
Traceback (most recent call last):
  File "/home/groups/dpetrov/bernard/miniconda3/envs/r2t/bin/read2tree", line 16, in <module>
    main(sys.argv[1:], exe_name=exe_name(), desc=desc)
  File "/home/groups/dpetrov/bernard/miniconda3/envs/r2t/lib/python3.10/site-packages/read2tree/main.py", line 357, in main
    mapper = Mapper(args, og_set=ogset.ogs, ref_set=reference.ref, progress=progress)  # Run the mapping
  File "/home/groups/dpetrov/bernard/miniconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 80, in __init__
    self._map_reads_to_references(ref_set)
  File "/home/groups/dpetrov/bernard/miniconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 289, in _map_reads_to_references
    processed_reads = self._call_wrapper(ref_tmp_file_handle, reads,
  File "/home/groups/dpetrov/bernard/miniconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 138, in _call_wrapper
    return self._post_process_read_mapping(ref_file_handle, bam_file)
  File "/home/groups/dpetrov/bernard/miniconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 570, in _post_process_read_mapping
    consensus = self._build_consensus_seq_v2(ref_file, outfile_name +
  File "/home/groups/dpetrov/bernard/miniconda3/envs/r2t/lib/python3.10/site-packages/read2tree/Mapper.py", line 514, in _build_consensus_seq_v2
    seq[pileup_column.pos-1] = self._most_common(bases)
IndexError: list assignment index out of range

DessimozLab / read2tree

IndexError: list assignment index out of range in Mapper.py #46