IndexError: list index out of range

[MariusMathies]

Hello, I want to run dandelion on my 10X data (5') and already in the beginning I get the error message "IndexError: list index out of range"

Does anyone know how to deal with that?

Best,
Marius

(base) [mam8432@compute-a-16-83 Normal_01]$ singularity run -B /home/mam8432/Normal_01 /n/app/singularity/containers/mam8432/sc-dandelion-latest.sif dandelion-preprocess
Software versions:

dandelion==0.3.7 pandas==2.2.2 numpy==1.26.4 matplotlib==3.8.4 networkx==3.3 scipy==1.13.0

Begin preprocessing

command line parameters:
: --------------------------------------------------------------
--meta = None
--chain = ig
--org = human
--file_prefix = all
--db = imgt
--strain = None
--sep = _
--flavour = strict
--filter_to_high_confidence = False
--keep_trailing_hyphen_number = False
--skip_format_header = False
--skip_tigger = False
--skip_reassign_dj = False
--skip_correct_c = False
--clean_output = False
: --------------------------------------------------------------

Formatting fasta(s) : | | 0/0 [00:00<?, ?it/s]
Assigning genes : | | 0/0 [00:00<?, ?it/s]
Processing data file(s) : | | 0/0 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/share/dandelion_preprocess.py", line 378, in
main()
File "/share/dandelion_preprocess.py", line 309, in main
ddl.pp.reassign_alleles(
File "/opt/conda/envs/sc-dandelion-container/lib/python3.11/site-packages/dandelion/preprocessing/_preprocessing.py", line 1508, in reassign_alleles
Path(filepathlist_heavy[0]),
~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range

[zktuong]

hi @MariusMathies, it looks like it has failed at the very first step (formating fasta). can you check if there's any incorrect file names or weird hidden files in your folder?

[MariusMathies]

I sued the wrong prefix. Thank you for the help!