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Bugs and fixes in v10

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  Fixed versions
  Bug First ver Fixed ver Description
  10.1  10.0 10.0.241 Zotu labels not recognized by otutab command, causing an empty OTU table. Work-around is to change "Zotu" to "Otu" in the FASTA file with the ZOTUs.
  10.2 10.0 10.0.248 Fatal error from fastx_demux "Cannot convert FASTA to FASTQ".
  10.3 10.0 10.0.260 Fatal error "TreeToClusters not implemented" from cluster_tree and cluster_aggd with -clusterout option.
  10.4 10.0 10.0.261 BIOM file formatting errors. Work-around is to generate QIIME classic OTU table and use usearch v9.2 to convert to BIOM format.
  10.5 10.0 10.0.272 Fatal error from sintax_summary "line xx has 3 fields, need 4". Happens if prediction is empty (due to no rank exceeding threshold). Workaround is  insert a placeholder prediction e.g. d:__unknown__ as the fourth field in lines with < 4 fields.
  10.6 10.0 10.0.278 The -uchime3_denovo command fails with "Missing input file name". Workaround is to use uchime2_denovo in usearch v9 with the -abskew 16 option.
  10.7 10.0 10.0.285 Masking for a protein database defaulted to fastnucleo instead of fastamino. Work-around is to specify -dbmask fastamino on the command line. This bug is relatively benign as the fastnucleo algorithm successfully masks low-complexity regions in amino acid sequences.
  10.8 10.0   Field 6 (new label) not written to the uparseout file when the -relabel option is used for cluster_otus. Work-around is to run cluster_otus without -relabel and write your own script to relabel the FASTA output file.
  10.9 10.0 10.0.278 fastx_demux fatal error "Cannot convert FASTA to FASTQ".
  10.10 ?   The -sizeout option gives incorrect results with -dbmatched for the otutab command and other search commands with -maxaccepts> 1.
  10.11 10.0 10.0.416 Some commands hang if a FASTQ or FASTA input file is empty.
  10.12 10.0   Command tax_stats gives "unknown option" fatal error. Work-around is to use v9.2.
  10.13 10.0 10.0.423 Missing tabs in output from alpha_div_rare command. Work-around is to search and replace on a minus sign followed by a tab, replace by tab, minus sign, tab everywhere, e.g.:

sed "-es/-\t/\t-\t/g" < output.txt > fixed.txt