Some users have reported that normalize-by-median.py will utilize more memory than it was configured for. This is being investigated in https://github.com/ged-lab/khmer/issues/266
Some FASTQ files confuse our parser when running with more than one thread. For example, while using load-into-counting.py. If you experience this then add “–threads=1” to your command line. This issue is being tracked in https://github.com/ged-lab/khmer/issues/249
If your hashfile gets truncated, perhaps from a full filesystem, then our tools currently will get stuck. This is being tracked in https://github.com/ged-lab/khmer/issues/247
Paired-end reads from Casava 1.8 currently require renaming for use in normalize-by-median and abund-filter when used in paired mode. The integration of a fix for this is being tracked in https://github.com/ged-lab/khmer/issues/23
A user has reported a floating point exception when running count-overlap.py. There is no workaround at this time. https://github.com/ged-lab/khmer/issues/282
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