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Split mates in fastq-dump retry fallback - #11
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On retry, SRATOOLS_FASTERQDUMP falls back to fastq-dump, which does not split mates by default. Paired runs came back as a single file of concatenated mates: multi-run samples failed in mergeRuns with a paired/single mix, and single-run samples would silently pass as single-end with double-length reads. Use --split-3 so the fallback produces the same _1/_2/unpaired layout as fasterq-dump. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
jbrestel
self-requested a review
October 26, 2026 20:24
jbrestel
approved these changes
Oct 26, 2026
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Problem
SRATOOLS_FASTERQDUMPretries withfastq-dump, which, unlikefasterq-dump, does not split mates unless asked. A paired run that hits the retry comes back as one file of concatenated mates.mergeRuns:Sample Brazil15: runs must be all paired or all single-end; found a mix.(all three Brazil15 runs — SRR1568233, SRR1565062, SRR1564632 — are PAIRED per ENA; one hit the retry).Fix
fastq-dump --split-3on retry, matching the defaultfasterq-dump_1/_2/unpaired layout, so the existing third-file handling andnormalizeReadswork unchanged.Not in this PR
library_layoutmetadata, to catch any other paired-to-single-file path.groupKey(id, nRuns)inRETRIEVE_FROM_SRAso samples with many technical replicates proceed as soon as their own runs finish rather than after all downloads.🤖 Generated with Claude Code