What causes "iterate chunk while re-encoding" in thanos-io/thanos?

Inspect the inner error from currDelIter.Err() to identify the corrupt chunk/series

iterate chunk while re-encoding

Error message

iterate chunk while re-encoding

What it means

Inside the populateWithDelChunkSeriesIterator.Next, after advancing the deletion-filtered chunk iterator, any iterator error is wrapped as "iterate chunk while re-encoding". The chunk was being rewritten (e.g. with tombstones/time-window modifiers applied) and the source iterator failed mid-iteration.

Solutions

Inspect the inner error from currDelIter.Err() to identify the corrupt chunk/series
Validate or remove the source block containing the failing chunk
Check storage I/O health; retry compaction if transient
If a modifier (e.g. deleting a time range) triggers it, verify the deletion window against actual chunk boundaries

Defensive patterns

Strategy: try-catch

Validate before calling

// Pre-validate block chunk files before compaction with modifiers
if err := tsdb.CheckChunks(blockDir); err != nil {
    return err
}

Try / catch

if err := comp.WriteSeries(ctx, readers, sWriter, progress); err != nil {
    if strings.Contains(err.Error(), "iterate chunk while re-encoding") {
        logger.Error("chunk iteration failed during re-encode", "err", err)
    }
    return err
}

Prevention

Run block verification before destructive compactions with modifiers
Ensure deletion ranges are applied through the intended pre-filtering pipeline
Monitor storage for read errors during compaction

When it happens

Trigger: currDelIter.Next() returns ValNone and currDelIter.Err() is non-nil — a decoding error, corrupted chunk data, or I/O error while reading chunk samples during chunk rewriting with deletion modifiers.

Common situations: Corrupted source chunk data in a block being compacted with a deletion/time-range modifier; I/O errors reading chunk segments mid-compaction; incompatible chunk encoding discovered during re-encode.

Understand the failure class

Background: Database query failed: Internal Server Error 500s wrapping SQL, Prisma, and connection failures — what to check first — this error's family across 16 libraries.

Related errors

AI-assisted analysis of thanos-io/thanos@35b8b99117 (2026-09-07). Data as JSON: /api/errors/87c19cf0eea14cd2. Report an issue: GitHub.

Appendix: source

Thrown at pkg/compactv2/modifiers.go:329

		return false
	}

	p.curr = p.currChkMeta
	if p.currDelIter == nil {
		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")

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