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Known Issues
============

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 and
https://github.com/ged-lab/khmer/issues/96 and
https://github.com/ged-lab/khmer/issues/246

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

annotate-partitions.py only outputs 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