check read errors in fastqreader - #533
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Sep 6, 2026
Use error_exit instead of returning NULL when a FASTQ record has an invalid separator or unequal sequence and quality lengths. Returning NULL made these detected errors indistinguishable from normal EOF, allowing incomplete processing to finish with exit status 0. Preserve existing record diagnostics and include the input filename in the fatal error message. This is separate from filesystem read-error handling proposed in PR OpenGene#533.
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It turns out, if there is a read error while reading a fastq, fastp will loop infinitely.
Per cpp fread docs, it looks like the caller should check both
feofandferror. Becauseferrorwasn't checked, fastp went right back toreadToBufand looped infinitely.The issue is really hard to reproduce because you need an unreliable filesystem. While complicated, thankfully I could rerun in our own environment and reliably reproduce, but not in a way I can easily post here.
Anyway, here are the logs I saw after fixing:
And I saw:
So we do see the process actually exit instead of hang.