Error with alignment files?

[shesanIsland]

Hello,

Thank you for developing one of the few tools that computes strain abundance, this has been very helpful!

My team keep running into an error that suggests our client's .sam/ .bam files have issues.

Traceback (most recent call last):
  File "/opt/conda/envs/strainest/bin/strainest", line 11, in <module>
    load_entry_point('strainest==1.2.4', 'console_scripts', 'strainest')()
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/strainest/scripts/strainest_cmd.py", line 180, in est
    threads)
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/strainest/api/_est.py", line 138, in est
    counts = get_counts(align, positions, quality_thr)
  File "/opt/conda/envs/strainest/lib/python2.7/site-packages/strainest/api/_est.py", line 47, in get_counts
    quality_threshold=quality_threshold)
  File "pysam/libcalignmentfile.pyx", line 1536, in pysam.libcalignmentfile.AlignmentFile.count_coverage
ValueError: interval of size less than 0

We have checked the contents of the bam files and ran integrity checks on them (and the .fastq files) which all look fine.
We have tried realigning the reads to generate new bam files as well as using subset files to test it and no changes.

Any help would be much appreciated!

Regards,