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 k-mer table is truncated on write, an error may not be reported; this is being tracked in https://github.com/ged-lab/khmer/issues/443. However, khmer will now (correctly) fail when trying to read a truncated file (See #333).
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
Some scripts only output FASTA even if given a FASTQ file. This issue is being tracked in https://github.com/ged-lab/khmer/issues/46
A user reported that abundance-dist-single.py fails with small files and many threads. This issue is being tracked in https://github.com/ged-lab/khmer/issues/75