Error: EOF marker is absent. The input is probably truncated
From Array Suite Wiki
Tabix may generate this warning when indexing a bgzip-compressed file written by OmicSoft products
tabix -p vcf OS.created.output.vcf.gz [W::bgzf_read_block] EOF marker is absent. The input is probably truncated
This is generally a false error because tabix is expecting the file to have been compressed with a version of bgzip more recent than the one implemented within OmicSoft products. As long as a .tbi file is written, it should be a valid index file.