HPC cluster: too many contigs

[Nonno Hasegawa]

Hello, I am a new user of plink2 and Im trying to use vcf with 190k contigs. I am working on our university HPC cluster, and installed plink2 via conda. 

So naturally I get the "too many contigs error":

--vcf: 65k variants scanned.

Error: Too many distinct nonstandard chromosome/contig names.

The usual limit is about 65k.  You can raise this to ~980k by uncommenting

"#define HIGH_CONTIG_BUILD" at the top of plink2_common.h and recompiling.  If

However I've looked through my conda directory (find . -name plink2_common.h) to locate plink2_common.h file but am unable to locate. I have also read on this google groups that you can find said file on github but i was unable to locate it. Also even after locating and changing the file, I do not know how to recompile (how does that work??). 

can you please give me pointers in solving this issue ? 

thanks so much,
Nonno

[Christopher Chang]

I have posted a precompiled Linux high-contig build to https://s3.amazonaws.com/plink2-assets/plink2_linux_avx2_high_contig_20240318.zip ; let me know if you have trouble using that.  (Posted a message with an incorrect "amd" link a minute ago, sorry about that.)

[Nonno Hasegawa]

Thank you so much! It is working now :)