The path is wrong, the file is unreadable, or its index is missing
htslib reports the same message for a missing path, a permissions problem, and a file whose companion index is absent. Inside a container or on a cluster node, a path that exists for you may simply not be mounted there.
Check the exact path from the same context the tool runs in — inside the container, on the compute node — not from your login shell. Then confirm the index exists next to the file (.bai, .tbi, .fai) and is newer than the file itself.