IndexError : too many indices for array when run ecole_call.sh

[sonder-mei]

(ecole_env) source ecole_call.sh
Creation of the directory failed
[ 2025-02-10 11:25:50 ] ECOLÉ: Using GPU!
[ 2025-02-10 11:25:54 ] ECOLÉ: Calling for CNV regions...
0%| | 0/1 [00:00<?, ?it/s][ 2025-02-10 11:25:54 ] ECOLÉ: calling sample: SRR645579_chr9
0%| | 0/1 [00:00<?, ?it/s]
Traceback (most recent call last):
File "./scripts/ECOLE_call.py", line 279, in
temp_sampnames = sampledata[:,0]
IndexError: too many indices for array

(ecole_env) cat ecole_call.sh
python ./scripts/ECOLE_call.py --model ecole-ft-somatic --input ./processed_samples --output ./ecole_calls_output --cnv merged --batch_size 16 --normalize ecole_stats.txt --gpu 0

[Thanujay]

@sonder-mei Im not sure if this would be helpful but I faced the same issue. I recreated the index file for the BAM and retried with model == "ecole". It worked! Mine was a germline sample so went with "ecole" by default.

Edit - Just saw the error message and that you're trying for the example data which is germline too. Just for safety please recreate the index and run with "ecole". It should work! :)