TypeError: AlignmentValidationError.__init__() missing 1 required positional argument: 'alns'

[olivertam]

Hi,

Thank you for the recent fix for the overflow error.
I have encountered another issue, and it's unclear if this is due to the program, or my input.
Here is my log:

2024-08-08 11:07:21 INFO     #-------------Stage 0: Initialize Stellarscope-----
--------# (from startrun in stages.py:34)
2024-08-08 11:07:24 INFO     
Version:                          1.4+3.g4ad3e7e-py3.12-linux-x86_64.egg
Input Options
    samfile:                      gencode.sortedByCB.bam
    gtffile:                      hg38_stellarscope_retroV1.gtf
    filtered_bc:                  Solo.out/GeneFull/filtered/barcodes.tsv
    celltype_tsv:                 None
    barcode_tag:                  CB
    umi_tag:                      UB
    attribute:                    locus
    feature_type:                 exon
    no_feature_key:               __no_feature
    nproc:                        10
    tempdir:                      Not set
Reporting Options
    outdir:                       output
    exp_tag:                      gencode_individual
    updated_sam:                  True
    use_every_reassign_mode:      False
    logfile:                      None
    quiet:                        False
    debug:                        False
    progress:                     1000000
Run Modes
    pooling_mode:                 individual
    reassign_mode:                best_exclude
    seed:                         1174263729
    conf_prob:                    0.9
    overlap_mode:                 threshold
    overlap_threshold:            0.2
    annotation_class:             intervaltree
    stranded_mode:                F
    ignore_umi:                   False
    umi_counts:                   False
Model Parameters
    pi_prior:                     0
    theta_prior:                  200000
    em_epsilon:                   1e-07
    max_iter:                     500
    use_likelihood:               False
    skip_em:                      False
 (from run in stages.py:65)
2024-08-08 11:07:24 INFO     #------Initialize Stellarscope complete in 3.270 secs------# (from endrun in stages.py:41)
2024-08-08 11:07:24 INFO                                                                  (from endrun in stages.py:42)
2024-08-08 11:07:24 INFO     #-----------------Stage 1: Load annotation-----------------# (from startrun in stages.py:34)
2024-08-08 11:07:30 INFO       Loaded 27812 loci                                          (from log in statistics.py:80)
2024-08-08 11:07:30 INFO     #----------Load annotation complete in 5.876 secs----------# (from endrun in stages.py:41)
2024-08-08 11:07:30 INFO                                                                  (from endrun in stages.py:42)
2024-08-08 11:07:30 INFO     #-----------------Stage 2: Load alignment------------------# (from startrun in stages.py:34)
2024-08-08 11:08:32 INFO         ...processed 1.0M fragments                              (from log_progress in statistics.py:144)
2024-08-08 11:09:34 INFO         ...processed 2.0M fragments                              (from log_progress in statistics.py:144)
2024-08-08 11:10:36 INFO         ...processed 3.0M fragments                              (from log_progress in statistics.py:144)
2024-08-08 11:11:37 INFO         ...processed 4.0M fragments                              (from log_progress in statistics.py:144)
...
2024-08-08 14:27:27 INFO         ...processed 192.0M fragments                            (from log_progress in statistics.py:144)
2024-08-08 14:28:30 INFO         ...processed 193.0M fragments                            (from log_progress in statistics.py:144)
2024-08-08 14:29:33 INFO         ...processed 194.0M fragments                            (from log_progress in statistics.py:144)
Traceback (most recent call last):
  File "/gpfs/bin/stellarscope", line 33, in <module>
    sys.exit(load_entry_point('stellarscope==1.4+3.g4ad3e7e', 'console_scripts', 'stellarscope')())
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/lib/python3.12/site-packages/stellarscope-1.4+3.g4ad3e7e-py3.12-linux-x86_64.egg/stellarscope/__main__.py", line 142, in stellarscope
    args.func(args)
  File "/gpfs/lib/python3.12/site-packages/stellarscope-1.4+3.g4ad3e7e-py3.12-linux-x86_64.egg/stellarscope/stellarscope_assign.py", line 137, in run
    alninfo = LoadAlignments(curstage).run(opts, st_obj, annot)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/lib/python3.12/site-packages/stellarscope-1.4+3.g4ad3e7e-py3.12-linux-x86_64.egg/stellarscope/stages.py", line 93, in run
    alninfo = st_obj.load_alignment(annot)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/lib/python3.12/site-packages/stellarscope-1.4+3.g4ad3e7e-py3.12-linux-x86_64.egg/stellarscope/utils/model.py", line 990, in load_alignment
    maps, alninfo = self._load_sequential(annotation)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/lib/python3.12/site-packages/stellarscope-1.4+3.g4ad3e7e-py3.12-linux-x86_64.egg/stellarscope/utils/model.py", line 1129, in _load_sequential
    store_read_info(_cur_qname, _cur_bcode, _cur_umi)
  File "/gpfs/lib/python3.12/site-packages/stellarscope-1.4+3.g4ad3e7e-py3.12-linux-x86_64.egg/stellarscope/utils/model.py", line 1049, in store_read_info
    raise AlignmentValidationError(
          ^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: AlignmentValidationError.__init__() missing 1 required positional argument: 'alns'

Is the error telling me that the BAM file is missing an alignment? Or is the error coming from the initialization step of the object?
Any suggestions on what to look for would be most welcome.

Thanks.