Confusing error when using "~" synonym for home directory in paths

[mikemc]

Using lemur 1.0.1 installed from conda on Mac OS (Apple Silicon).

If I run lemur on the example reads using the current database (from Zenodo) using fully-specified absolute paths,

lemur -i /Users/michael/Downloads/src/lemur/examples/example-data/example.fastq \
  -o example-lemur \
  -d /Users/michael/data/lemur-db/rv221bacarc-rv222fungi \
  --tax-path /Users/michael/data/lemur-db/rv221bacarc-rv222fungi/taxonomy.tsv \
  -r species \
  --num-threads 6

everything seems to work fine; but if I instead use "~" instead of /Users/michael in the database paths,

lemur -i /Users/michael/Downloads/src/lemur/examples/example-data/example.fastq \
  -o example-lemur \
  -d ~/data/lemur-db/rv221bacarc-rv222fungi \
  --tax-path ~/data/lemur-db/rv221bacarc-rv222fungi/taxonomy.tsv \
  -r species \
  --num-threads 6

initially everything seems to be working, but eventually lemur crashes, apparently due to an empty alignments (.sam) file (output below).

2025-09-29 01:30:03 PM INFO:    Starting run of minimap2 at 2025-09-29 13:30:03.509876
2025-09-29 01:30:40 PM INFO:    Finished running minimap2 in 36628.664 ms
2025-09-29 01:30:40 PM INFO:    Finished loading taxonomy in 85.817 ms
2025-09-29 01:30:40 PM INFO:    Finished initializing F in 3.708 ms
2025-09-29 01:30:40 PM INFO:    Finished building alignment model in 0.019 ms
Traceback (most recent call last):
  File "/opt/homebrew/Caskroom/miniconda/base/envs/lemur/bin/lemur", line 901, in <module>
    main()
    ~~~~^^
  File "/opt/homebrew/Caskroom/miniconda/base/envs/lemur/bin/lemur", line 883, in main
    run.build_P_rgs_df()
    ~~~~~~~~~~~~~~~~~~^^
  File "/opt/homebrew/Caskroom/miniconda/base/envs/lemur/bin/lemur", line 402, in build_P_rgs_df
    samfile = pysam.AlignmentFile(self.sam_path)
  File "pysam/libcalignmentfile.pyx", line 751, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 956, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file does not contain alignment data

[mikemc]

The same issue seems to occur when using $HOME instead of ~ if the paths are not enclosed in quotes, but things work fine with $HOME and quote-enclosed paths