Error with samtools index during TALON run

[jadedavis5]

Hi,
I am getting the following error when running TALON using a large plant reference genome:

Command output:
  [ 2024-08-28 02:47:36 ] Started talon_label_reads run.
  [ 2024-08-28 02:47:36 ] Splitting SAM by chromosome...
  [ 2024-08-28 02:47:36 ] -----Sorting and indexing...

Command error:
  [E::hts_idx_check_range] Region 548287349..548289692 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
  [E::sam_index] Read '5edb22b3-d236-4b8e-b51f-d110eca41670' with ref_name='chr2H', ref_length=675310294, flags=16, pos=548287350 cannot be indexed
  Traceback (most recent call last):
    File "/usr/local/bin/talon_label_reads", line 10, in <module>
      sys.exit(main())
    File "/usr/local/lib/python3.7/site-packages/talon/talon_label_reads.py", line 287, in main
      read_files = split_reads_by_chrom(options.sam_file, tmp_dir=options.tmp_dir, n_threads=options.threads)
    File "/usr/local/lib/python3.7/site-packages/talon/talon_label_reads.py", line 177, in split_reads_by_chrom
      pysam.index(bam_file)
    File "/usr/local/lib/python3.7/site-packages/pysam/utils.py", line 75, in __call__
      stderr))
  pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools index: failed to create index for "tmp_label_reads/raw/all_reads.sorted.bam": Numerical result out of range\n'

I am wondering if there is a way to store as a csi index instead?