Home Software Services About Contact usearch manual
Bugs and fixes in v10

See also
  Fixed versions
  Bug First ver Fixed ver Description
  10.1  10.0 10.0.241 A label containing "otu" (all lower case) but not "otu=" is not correctly processed by the otutab command, causing an empty OTU table. This is most common when using labels like >Zotu123. Work-around is to change "otu" to something else, e.g. "Otu", in the FASTA file with the OTU or ZOTU sequences.
  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. Work-around is to delete the -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
  10.14 n/a n/a Fatal error from sintax:  sintaxsearcher.cpp(148) assert failed: m_U.Size == SeqCount. This is caused by  lower-case sequences in the input file whch is interpreted as soft-masking. Actually not a bug, but reported here because the error message is obscure. Fix is to convert to upper case using  fastx_mask with this option: -qmask none.
  10.15 10.0 10.0.537 The -fastq_merge_maxee option of fastq_mergepairs did not work. Workaround is to use fastq_filter after merging.
  10.16 9.0 10.0.553 Incorrect value of Chao1 reported by alpha_div command.
  10.17 10.0 10.0.605 Fatal error "uparsepretty.cpp(120) assert failed: SumLength == m_Query->m_L" with -uparsealnout option of cluster_otus. Work-around is to delete the uparsealnout option.