AssertionError: Expect col to appear in data only once.

[Tingwei1021]

I am using the command popcorn compute --bfile PATH_TO_PLINK_FILESET OUTPUT_RESULT
But I keep getting this error:
Traceback (most recent call last): File "/mnt/data_schen_1/anaconda3/envs/Popcorn/bin/popcorn", line 8, in <module> sys.exit(main()) File "/mnt/data_schen_1/anaconda3/envs/Popcorn/lib/python3.7/site-packages/popcorn/__main__.py", line 227, in main scores = compute.covariance_scores_1_pop(args) File "/mnt/data_schen_1/anaconda3/envs/Popcorn/lib/python3.7/site-packages/popcorn/compute.py", line 62, in __init__ bed_1_index = np.sort(bed_1.sid_to_index(snps_to_use)) # File "/mnt/data_schen_1/anaconda3/envs/Popcorn/lib/python3.7/site-packages/pysnptools/snpreader/snpreader.py", line 520, in sid_to_index return self.col_to_index(list) File "/mnt/data_schen_1/anaconda3/envs/Popcorn/lib/python3.7/site-packages/pysnptools/pstreader/pstreader.py", line 574, in col_to_index ), "Expect col to appear in data only once." AssertionError: Expect col to appear in data only once.

I found out that the input was read incorrectly. This issue causes variants to be same(let's say 12:000012 reads as 12:00001, which duplicates with actual 12:00001)

[chirrie]

How did you solve the issue? I am also stuck there