ValueError: X needs to be 2-dimensional, not 1-dimensional.

[Jinloong-dream]

I used scTE to analyze raw data from public database. here is my code:

scTE \
        -i /home/zhaoyang/hjl/project/LiuGH/cellranger/Lung_scRNA_Young/outs/CB_clean.bam \
        -o Young \
        -x /home/zhaoyang/hjl/database/mm10.exclusive.idx \
        --hdf5 True \
        -CB CB \
        -UMI UB \
        -p 13

here is the log:

/home/zhaoyang/miniforge3/envs/scte/bin/scTE:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').run_script('scTE==1.0', 'scTE')
DEBUG   : Creating converter from 7 to 5
DEBUG   : Creating converter from 5 to 7
DEBUG   : Creating converter from 7 to 5
DEBUG   : Creating converter from 5 to 7
DEBUG   : Registering codec 'zlib'
DEBUG   : Registering codec 'gzip'
DEBUG   : Registering codec 'bz2'
DEBUG   : Registering codec 'lzma'
DEBUG   : Registering codec 'blosc'
DEBUG   : Registering codec 'zstd'
DEBUG   : Registering codec 'lz4'
DEBUG   : Registering codec 'astype'
DEBUG   : Registering codec 'delta'
DEBUG   : Registering codec 'quantize'
DEBUG   : Registering codec 'fixedscaleoffset'
DEBUG   : Registering codec 'packbits'
DEBUG   : Registering codec 'categorize'
DEBUG   : Registering codec 'pickle'
DEBUG   : Registering codec 'base64'
DEBUG   : Registering codec 'shuffle'
DEBUG   : Registering codec 'bitround'
DEBUG   : Registering codec 'crc32'
DEBUG   : Registering codec 'adler32'
DEBUG   : Registering codec 'jenkins_lookup3'
DEBUG   : Registering codec 'json2'
DEBUG   : Registering codec 'vlen-utf8'
DEBUG   : Registering codec 'vlen-bytes'
DEBUG   : Registering codec 'vlen-array'
DEBUG   : Registering codec 'fletcher32'
DEBUG   : Registering codec 'crc32c'
INFO    : Parameter list:
Sample = Young
Reference annotation index = /home/zhaoyang/hjl/database/mm10.exclusive.idx
Minimum number of genes required = 200
Minimum number of counts required = None
Number of threads = 13

INFO    : Loading the genome annotation index... 2025-04-21 16:15:10
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Finished loading the genome annotation index... 2025-04-21 16:15:31

INFO    : Processing BAM/SAM files ...2025-04-21 16:15:31
INFO    : Input SAM/BAM file appears to be valid
INFO    : Done BAM/SAM files processing ...2025-04-21 16:52:22

INFO    : Splitting ...2025-04-21 16:52:22
INFO    : Executing multiple thread path with 13 threads
['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '3', '4', '5', '6', '7', '8', '9', 'M', 'X', 'Y']
CB UB good

INFO    : Reading Young.chr1.count.gz
INFO    : Reading Young.chr10.count.gz
INFO    : Reading Young.chr11.count.gz
INFO    : Reading Young.chr12.count.gz
INFO    : Reading Young.chr13.count.gz
INFO    : Reading Young.chr14.count.gz
INFO    : Reading Young.chr15.count.gz
INFO    : Reading Young.chr16.count.gz
INFO    : Reading Young.chr17.count.gz
INFO    : Reading Young.chr18.count.gz
INFO    : Reading Young.chr19.count.gz
INFO    : Reading Young.chr2.count.gz
INFO    : Reading Young.chr3.count.gz
INFO    : Reading Young.chr4.count.gz
INFO    : Reading Young.chr5.count.gz
INFO    : Reading Young.chr6.count.gz
INFO    : Reading Young.chr7.count.gz
INFO    : Reading Young.chr8.count.gz
INFO    : Reading Young.chr9.count.gz
INFO    : Reading Young.chrM.count.gz
INFO    : Reading Young.chrX.count.gz
INFO    : Reading Young.chrY.count.gz
INFO    : Before filter 0
INFO    : Aefore filter 0
INFO    : Finished processing sample files 2025-04-21 16:53:29

INFO    : Fetching from the annotation index... 2025-04-21 16:53:29
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Loaded '/home/zhaoyang/hjl/database/mm10.exclusive.idx' binary file with 3900779 items
INFO    : Done fetching... 2025-04-21 16:55:04

INFO    : Calculating expression... 2025-04-21 16:55:04
Traceback (most recent call last):
  File "/home/zhaoyang/miniforge3/envs/scte/bin/scTE", line 4, in <module>
    __import__('pkg_resources').run_script('scTE==1.0', 'scTE')
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/pkg_resources/__init__.py", line 752, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/pkg_resources/__init__.py", line 1739, in run_script
    exec(code, namespace, namespace)
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/scTE-1.0-py3.11.egg/EGG-INFO/scripts/scTE", line 173, in <module>
    main()
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/scTE-1.0-py3.11.egg/EGG-INFO/scripts/scTE", line 155, in main
    len_res, genenumber, filename = Countexpression(filename=args.out, allelement=allelement, genenumber=args.genenumber, cellnumber=args.cellnumber, hdf5=args.hdf5)
                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/scTE-1.0-py3.11.egg/scTE/base.py", line 493, in Countexpression
    adata = ad.AnnData(np.asarray(data).astype(int),var = var,obs = obs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/legacy_api_wrap-1.4.1-py3.11.egg/legacy_api_wrap/__init__.py", line 82, in fn_compatible
    return fn(*args_all, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/anndata-0.12.0rc1-py3.11.egg/anndata/_core/anndata.py", line 241, in __init__
    self._init_as_actual(
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/anndata-0.12.0rc1-py3.11.egg/anndata/_core/anndata.py", line 390, in _init_as_actual
    _check_2d_shape(X)
  File "/home/zhaoyang/miniforge3/envs/scte/lib/python3.11/site-packages/anndata-0.12.0rc1-py3.11.egg/anndata/_core/anndata.py", line 2102, in _check_2d_shape
    raise ValueError(msg)
ValueError: X needs to be 2-dimensional, not 1-dimensional.

And I tried set --hdf5 to False, but the output .csv is 0 object of 56422 variables, in other words, it is empty.
Could you please give me some suggestion?

[Jinloong-dream]

here is part of bam file:

CB:Z:TTCTAACCACTATCGA-1 UR:Z:CTGATACAAGAG       UY:Z:FFFFFFFFFFFF       UB:Z:CTGATACAAGAG
:FFFFF,,FFF   CB:Z:CCCTCTCTCGGTCTAA-1 UR:Z:AAGTTCACTCTG       UY:Z:F:FFFFF:FFFF       UB:Z:AAGTTCACTCTG
FFF   CB:Z:TTCAGGATCATGAGAA-1 UR:Z:ATTATCCAAAGA       UY:Z:FFFFFFFFFFFF       UB:Z:ATTATCCAAAGA
FFF   CB:Z:TTCAGGATCATGAGAA-1 UR:Z:ATTATCCAAAGA       UY:Z:FFFFFFFFFFFF       UB:Z:ATTATCCAAAGA
FFF   CB:Z:TTCAGGATCATGAGAA-1 UR:Z:ATTATCCAAAGA       UY:Z:FFFFFFFFFFFF       UB:Z:ATTATCCAAAGA
FFF   CB:Z:CTGTATTTCCATCTAT-1 UR:Z:ACAAAAGTGAGT       UY:Z:FFFFFFFFFFFF       UB:Z:ACAAAAGTGAGT
:FFFFFFF,FF   CB:Z:ATGAGGGGTAATGCTC-1 UR:Z:GGTGCAAAGAAG       UY:Z:,FF:FFF::FFF       UB:Z:GGTGCAAAGAAG
FFF   CB:Z:ATGACCAGTGCCTGAC-1 UR:Z:ATCGGCCAAACT       UY:Z:FFFFFFFFFFFF       UB:Z:ATCGGCCAAACT
FFF   CB:Z:ATGACCAGTGCCTGAC-1 UR:Z:ATCGGCCAAACT       UY:Z:FFFFFFFFFFFF       UB:Z:ATCGGCCAAACT
FFF   CB:Z:TGTACAGTCAATCAGC-1 UR:Z:GAACCCCATATG       UY:Z:FFFFFFFFFFFF       UB:Z:GAACCCCATATG