I was able to reproduce this issue after running the same query for about 4 hours. This is related to roll ups in alpha.
These are the alpha logs when the first query failed at 22:57:31 and it has been failing since then.
One important observation is that roll ups were running in alpha at 22:57:31
I0416 22:19:23.103866 23073 log.go:34] Compaction for level: 0 DONE
I0416 22:54:29.544599 23073 groups.go:604] No healthy Zero leader found. Trying to find a Zero leader...
I0416 22:54:29.551467 23073 groups.go:897] Zero leadership changed. Renewing oracle delta stream.
E0416 22:54:29.552915 23073 groups.go:873] Error in oracle delta stream. Error: rpc error: code = Canceled desc = context canceled
I0416 22:54:29.645984 23073 groups.go:641] Found connection to leader: localhost:5080
I0416 22:54:29.696129 23073 groups.go:833] Leader idx=0x1 of group=1 is connecting to Zero for txn updates
I0416 22:54:29.696150 23073 groups.go:842] Got Zero leader: localhost:5080
I0416 22:55:30.942289 23073 draft.go:678] [0x1] Set Raft progress to index: 562031.
I0416 22:55:32.108007 23073 draft.go:383] Creating snapshot at index: 562083. ReadTs: 6160730.
I0416 22:55:32.108031 23073 storage.go:589] CreateSnapshot i=562083, cs=nodes:1
I0416 22:55:34.090251 23073 log.go:34] Got compaction priority: {level:0 score:1 dropPrefix:[]}
I0416 22:55:34.090315 23073 log.go:34] Running for level: 0
I0416 22:55:41.604493 23073 log.go:34] LOG Compact 0->1, del 6 tables, add 1 tables, took 7.514154308s
I0416 22:55:41.604526 23073 log.go:34] Compaction for level: 0 DONE
I0416 22:56:29.701271 23073 draft.go:678] [0x1] Set Raft progress to index: 564962.
I0416 22:57:29.710277 23073 draft.go:678] [0x1] Set Raft progress to index: 567688.
I0416 22:57:30.696727 23073 log.go:34] Rolling up Time elapsed: 01s, bytes sent: 0 B, speed: 0 B/sec
I0416 22:57:31.450630 23073 log.go:34] Rolling up Created batch of size: 1.5 MB in 4.53621ms.
I0416 22:57:31.450650 23073 log.go:34] Rolling up Sent 668 keys
I0416 22:57:31.454309 23073 draft.go:1076] Rolled up 665 keys. Done
I0416 22:57:31.454331 23073 draft.go:425] List rollup at Ts 6160730: OK.
I0416 22:57:31.456136 23073 draft.go:1109] Sent tablet size update to Zero. Total size: 279 MB
I0416 22:58:29.699431 23073 draft.go:678] [0x1] Set Raft progress to index: 567775.
I don’t see any activity in zero at the time of failure
I0416 19:01:02.070633 22755 log.go:34] 1 is starting a new election at term 15
I0416 19:01:02.070731 22755 log.go:34] 1 became pre-candidate at term 15
I0416 19:01:02.070779 22755 log.go:34] 1 received MsgPreVoteResp from 1 at term 15
I0416 19:01:02.070940 22755 log.go:34] 1 became candidate at term 16
I0416 19:01:02.070969 22755 log.go:34] 1 received MsgVoteResp from 1 at term 16
I0416 19:01:02.071167 22755 log.go:34] 1 became leader at term 16
I0416 19:01:02.071204 22755 log.go:34] raft.node: 1 elected leader 1 at term 16
I0416 19:01:02.071292 22755 raft.go:663] I've become the leader, updating leases.
I0416 19:01:02.071343 22755 assign.go:41] Updated Lease id: 690001. Txn Ts: 6170001
W0416 19:01:03.971531 22755 node.go:669] [0x1] Read index context timed out
I0416 19:01:18.607681 22755 zero.go:415] Got connection request: cluster_info_only:true
I0416 19:01:18.609582 22755 zero.go:433] Connected: cluster_info_only:true
I0416 19:01:18.612966 22755 zero.go:415] Got connection request: addr:"localhost:7080"
I0416 19:01:18.615132 22755 zero.go:452] Found a member with the same address. Returning: id:1 group_id:1 addr:"localhost:7080" leader:true last_update:1582009811
I0416 19:01:18.615213 22755 zero.go:454] Connected: addr:"localhost:7080"
I0416 22:54:29.645034 22755 zero.go:415] Got connection request: cluster_info_only:true
I0416 22:54:29.645551 22755 zero.go:433] Connected: cluster_info_only:true
I0416 22:55:34.697404 22755 oracle.go:107] Purged below ts:6160730, len(o.commits):0, len(o.rowCommit):0