TypeError: value expected to be scalar, given len=2

[gyuanh]

I encountered the following error while running multigrmpy.py, I can't find where the problem is? May I ask if everyone can answer this? Thank you!
2025-01-07 23:05:08,118 ERROR Traceback (most recent call last):
2025-01-07 23:05:08,458 ERROR File "/public/home/04034/guoyuanhao/12/bin/multigrmpy.py", line 340, in run vcfupdate.update_vcf_from_grmpy(vcf_input_path, grmpyOutput, result_vcf_path, sample_names)
2025-01-07 23:05:08,459 ERROR File "/public/home/04034/guoyuanhao/12/lib/python3/grm/vcfgraph/vcfupdate.py", line 218, in update_vcf_from_grmpy record.samples[sample][k] = v
2025-01-07 23:05:08,459 ERROR File "pysam/libcbcf.pyx", line 3544, in pysam.libcbcf.VariantRecordSample.setitem
2025-01-07 23:05:08,459 ERROR File "pysam/libcbcf.pyx", line 876, in pysam.libcbcf.bcf_format_set_value
2025-01-07 23:05:08,459 ERROR File "pysam/libcbcf.pyx", line 598, in pysam.libcbcf.bcf_check_values
2025-01-07 23:05:08,459 ERROR TypeError: value expected to be scalar, given len=2
Traceback (most recent call last):
File "/public/home/04034/guoyuanhao/12/bin/multigrmpy.py", line 353, in
main()
File "/public/home/04034/guoyuanhao/12/bin/multigrmpy.py", line 349, in main
run(args)
File "/public/home/04034/guoyuanhao/12/bin/multigrmpy.py", line 340, in run
vcfupdate.update_vcf_from_grmpy(vcf_input_path, grmpyOutput, result_vcf_path, sample_names)
File "/public/home/04034/guoyuanhao/12/lib/python3/grm/vcfgraph/vcfupdate.py", line 218, in update_vcf_from_grmpy
record.samples[sample][k] = v
File "pysam/libcbcf.pyx", line 3544, in pysam.libcbcf.VariantRecordSample.setitem
File "pysam/libcbcf.pyx", line 876, in pysam.libcbcf.bcf_format_set_value
File "pysam/libcbcf.pyx", line 598, in pysam.libcbcf.bcf_check_values
TypeError: value expected to be scalar, given len=2

[hechaolei]

Hello, I’m experiencing the same problem and was wondering if you’ve managed to resolve it. I’d greatly appreciate any insights. Thank you!

[tkn132]

Got the same error. Removing all the genotypes and FORMAT worked. bcftools view -G