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known bugs and fixes

Serious bugs
9.1 cluster_otus is broken in v9.0.2124.
9.9 unoise2 and uchime2_denovo are broken in v9.1.13.

  Bug First ver Fixed ver Description
  9.1 9.0 9.0.2130 Serious bug The cluster_otus chimera detection is badly broken in v9.0.2124. Do not use cluster_otus in v9.0.2124!
  9.2 9.0 9.0.2133 Labels generated by -relabel option of -cluster_otus had  gaps in the numbering, e.g. there might be Otu19 and Otu21 but no Otu20.
  9.3 9.0 9.0.2159 -annot failed to recognize some database hits that should be classified as "db_perfect", were identified as "other".
  9.4 9.0  9.0.2161 -unoise failed to include the abundance contribution of error-corrected input sequences with size < minampsize to the correct sequence abundance. The result is that the size= annotations in the output were systematically under-estimated. This should not usually matter much in practice.
  9.5 9.0 9.1 -cluster_agg command fatal error "Agg needs to be reimplemented".
  9.6 9.0  10.0 malloc.c:2372: sysmalloc: Assertion `(old_top == (((mbinptr) (((char *)... See Malloc bug in version 9 for workaround and discussion.
  9.7  9.1   unoise2 command produces empty -tabbout file.
  9.8 9.0    calc_distmx fatal error "SparseDistMx::ToFile not implemented". Workaround is to use v8.1.
  9.9 9.1.13   Serious bug uchime2_denovo does not work in v9.1.13, no chimeras are found. The chimera detection in unoise2 in v9.1.13 fails for the same reason. Work-around is to use unoise and uchime2_denovo in v9.0.
  9.10  8.1   search_pcr fails with -pcr_strip_primers. Work-around is to use -fastx_truncate to strip the primer sequences.
  9.11 9.0 no fix planned The otu_radius_pct option of cluster_otus has no effect, clustering is always performed at 97%. In future builds this option will be removed, see UPARSE OTU radius for discussion.
  9.12 9.0 9.2 -cluster_aggd gives fatal error "SparseMx::FromFile not implemented.
  9.13 9.0   The uniq=xxx annotations in the -otudbout output from the unoise2 command are wrong.
  9.14 9.0 9.2.118 The "XX uniques written" message from fastx_uniques reports an incorrect number of sequences.
  9.15 9.0 9.2.130 -fulldp option causes segfault or fatal error.
  9.16 9.0 9.2.152 -min_freq option of otutab_trim did not work.
  9.17 9.0 10.0 -cluster_agg fatal error "TreeToClusters not implemented". Work-around is to use v8.1.
  9.18 9.0 10.0 Fatal error " SampleIndex < m_SampleCount" with some otu commands.