populateWithDelChunkSeriesIterator: unexpected empty chunk…

Error message

populateWithDelChunkSeriesIterator: unexpected empty chunk found while rewriting chunk

What it means

While re-encoding a chunk under deletion modifiers, the iterator reached ValNone with no iterator error and an empty chunk was produced. The code explicitly treats this as an invariant violation: fully-deleted chunks should have been filtered out before this iterator, so an empty rewritten chunk means internal state is wrong.

Solutions

Ensure fully-deleted chunks are filtered before populating (run vertical compaction/tombstone cleanup, or check the deletion filtering in the modifier pipeline)
Check the modifier's deletion ranges — make sure minTime/maxTime handling drops chunks fully covered by deletions
Report/inspect as a bug if it reproduces with a specific modifier range; work around by adjusting the deletion window
Rerun compaction after tombstone cleanup (e.g. after a clean compaction level removes tombstones)

Defensive patterns

Strategy: validation

Validate before calling

// Drop chunks fully covered by the deletion range before rewriting
chunks = filterOutFullyDeleted(chunks, delMinTime, delMaxTime)

Prevention

Always filter fully tombstoned chunks before the rewriting iterator
Run tombstone cleanup compaction before applying deletion modifiers
Test modifiers with deletion windows exactly covering whole chunks

When it happens

Trigger: currDelIter.Next() == ValNone, currDelIter.Err() == nil, and err happens to be nil when wrapped — i.e. a chunk whose samples were all deleted (fully tombstoned) still reached the rewriting iterator instead of being dropped earlier.

Common situations: Deletion/time-range modifier selecting a window covering an entire chunk but the pre-filter not removing that chunk; block with tombstones not previously cleaned; edge-case chunk boundary conditions with modifiers.

Understand the failure class

Background: "This is a bug, please report it": internal invariant violations, unreachable panics, and SNH errors explained — this error's family across 47 libraries.

Related errors

AI-assisted analysis of thanos-io/thanos@35b8b99117 (2026-09-07). Data as JSON: /api/errors/8d2f5996a9b349f0. Report an issue: GitHub.

Appendix: source

Thrown at pkg/compactv2/modifiers.go:334

		return true
	}

	// Re-encode the chunk if iterator is provider. This means that it has some samples to be deleted or chunk is opened.
	newChunk := chunkenc.NewXORChunk()
	app, err := newChunk.Appender()
	if err != nil {
		p.err = err
		return false
	}

	if p.currDelIter.Next() == chunkenc.ValNone {
		if err := p.currDelIter.Err(); err != nil {
			p.err = errors.Wrap(err, "iterate chunk while re-encoding")
			return false
		}

		// Empty chunk, this should not happen, as we assume full deletions being filtered before this iterator.
		p.err = errors.Wrap(err, "populateWithDelChunkSeriesIterator: unexpected empty chunk found while rewriting chunk")
		return false
	}

	t, v := p.currDelIter.At()
	p.curr.MinTime = t
	app.Append(t, v)

	for p.currDelIter.Next() != chunkenc.ValNone {
		t, v = p.currDelIter.At()
		app.Append(t, v)
	}
	if err := p.currDelIter.Err(); err != nil {
		p.err = errors.Wrap(err, "iterate chunk while re-encoding")
		return false
	}

	p.curr.Chunk = newChunk
	p.curr.MaxTime = t

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