KeyError: '.:0'

[avdanurag]

Hi
I am getting KeyError: '.:0' when I run the program. Can you please suggest cause for this.

Command I am using :
python3 Compare_imputation_to_WGS.py --ga /storage/Anurag/INVITE/Imputation/MO-17-Ref/phasing/WGS_ARRAY_COMMON_600K_GENO.vcf.gz --wgs /storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/vcf/INVITE_160_maize_GenomicDB/VCFs/work/sorted_merged_new/snps/chr7_snp_filtered_2.vcf.gz --imputed /storage/Anurag/INVITE/Imputation/MO-17-Ref/phasing/Final_Imputed_WGS_ARRAY_COMMON_600K_GENO.vcf.gz

Error:
Namespace(disable_warnings='False', ga=['/storage/Anurag/INVITE/Imputation/MO-17-Ref/phasing/WGS_ARRAY_COMMON_600K_GENO.vcf.gz'], imputed=['/storage/Anurag/INVITE/Imputation/MO-17-Ref/phasing/Final_Imputed_WGS_ARRAY_COMMON_600K_GENO.vcf.gz'], max_per_core=1000, max_total_rows=10000, min_per_core=100, ref='', sout='', vout='', wgs=['/storage/Anurag/INVITE/pub_data/INVITE_DATA/160-INVITE-WGS/vcf/INVITE_160_maize_GenomicDB/VCFs/work/sorted_merged_new/snps/chr7_snp_filtered_2.vcf.gz'], xmode='False')
10000 1000 100
Processing 8 imputed samples
Processing chunk: 1 Max rows per chunk: 10000
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/avd/mambaforge/envs/imputation_accuracy_calculator/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/avd/mambaforge/envs/imputation_accuracy_calculator/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "Compare_imputation_to_WGS.py", line 625, in process_lines
pos_dosages_tmp, snp = extract_dose_from_line(line)
File "Compare_imputation_to_WGS.py", line 500, in extract_dose_from_line
result=convert_gt_to_int(column[0:3])
File "Compare_imputation_to_WGS.py", line 471, in convert_gt_to_int
result=genotype_to_int[gt[0:3]]
KeyError: '.:0'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "Compare_imputation_to_WGS.py", line 1254, in
main()
File "Compare_imputation_to_WGS.py", line 1245, in main
results = load_file_chunks(my_ncores)
File "Compare_imputation_to_WGS.py", line 745, in load_file_chunks
results_tmp = pool.map(process_lines,data)
File "/home/avd/mambaforge/envs/imputation_accuracy_calculator/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/avd/mambaforge/envs/imputation_accuracy_calculator/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
KeyError: '.:0'

Best Regards,

Anurag