*** Error in `hisat2-build': double free or corruption (!prev): 0x00002b5724374370 ***

[rvarki]

Hi,

I am getting the above error when I try to run this command: hisat2-build -p 32 --large-index --snp Chr21.10.snp --haplotype Chr21.10.haplotype Homo_sapiens.GRCh38.dna.chromosome.21.fa Chr21.10 &> log.txt

I created the snp and haplotype files by running this command (created empty files without the --non-rs flag): ./hisat2_extract_snps_haplotypes_VCF.py --non-rs Homo_sapiens.GRCh38.dna.chromosome.21.fa Chr21.10.vcf.gz Chr21.10

For reference, I am using hisat2 version 2.2.1 and running the commands on a 200 GB node.

Thank you, Rahul

Chr21.10.vcf.gz Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz log.txt

[rvarki]

I was able to resolve this issue. The --haplotype option in the build command was causing the error, although I do not know why. Removing the --haplotype option allowed me to build the index successfully.