Hi, first of all, Gemini is a wonderful easy-to-use tool and works perfectly for my Varscan vcf 4.1 (reference is hg19). Then, I tried to load MuTect2 vcf 4.2 (reference is b37) and came across an error like: ValueError: Processing failed on GEMINI chunk load. Gemini was built on Python/2.7. So, I reinstalled Gemini by using Python/3.7.4. This time, the error message became: if isinstance(h, (cyvcf2.Variant, pysam.VariantRecord)): AttributeError: 'module' object has no attribute 'VariantRecord'. I then updated cyvcf2 and pysam. The error message turned to be: from backports.functools_lru_cache import lru_cache ImportError: No module named functools_lru_cache. I've checked the difference between vcf 4.1 and 4.2. I didn't find much discrepancy. Then, I was wondering if it is due to something else, e.g., reference being b37 instead of hg19? But there's no contig error so far. This project is very important to me and I definitely need your help. Thanks advance! Regards, Vic
Hi, first of all, Gemini is a wonderful easy-to-use tool and works perfectly for my Varscan vcf 4.1 (reference is hg19). Then, I tried to load MuTect2 vcf 4.2 (reference is b37) and came across an error like: ValueError: Processing failed on GEMINI chunk load. Gemini was built on Python/2.7. So, I reinstalled Gemini by using Python/3.7.4. This time, the error message became: if isinstance(h, (cyvcf2.Variant, pysam.VariantRecord)): AttributeError: 'module' object has no attribute 'VariantRecord'. I then updated cyvcf2 and pysam. The error message turned to be: from backports.functools_lru_cache import lru_cache ImportError: No module named functools_lru_cache. I've checked the difference between vcf 4.1 and 4.2. I didn't find much discrepancy. Then, I was wondering if it is due to something else, e.g., reference being b37 instead of hg19? But there's no contig error so far. This project is very important to me and I definitely need your help. Thanks advance! Regards, Vic