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Sketch store: trim a broken ENA stream to whole read pairs; retry partial downloads - #319
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…n under half the target arrived
Six PRJEB1497 runs (3 GB FASTQ files from 2013) streamed from ENA over HTTPS stopped at about a third of the 30x target, leaving a
truncated record that singlesketch rejects ("Failed to read a record"). take_pairs now keeps only whole records in whole pairs, and
an ENA subsample under half the target (or half the run, for smaller runs) exits as ena_partial so the planner retries it.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Follow-up to #315, found in the running A. fumigatus build.
Six PRJEB1497 runs fail at sketching with "Failed to read a record". These are 3 GB FASTQ files from 2013 that NCBI never loaded, so they come through the ENA HTTPS fallback. Their streams stopped at about a third of the 30x target (9.6-12.6x) and left a truncated last record, which
singlesketchrejects.take_pairsnow keeps only whole records (4 lines,@header, sequence and quality of equal length), in whole pairs for paired runs.ena_partial. The planner then retries it (up to 3 tries) instead of keeping a thin sketch.The fix is already deployed in the store's
bin/, and the planner will retry the 6 samples with it. The trimmer was checked on truncated test input: both a short quality line and a missing quality line keep only the complete pair.🤖 Generated with Claude Code