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Bug |
First ver |
Fixed ver |
Description |
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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.
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10.2 |
10.0 |
10.0.248 |
Fatal error from fastx_demux "Cannot convert FASTA to
FASTQ".
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10.3 |
10.0 |
10.0.260 |
Fatal error "TreeToClusters not implemented" from cluster_tree and cluster_aggd
with -clusterout option.
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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.
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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.
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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.
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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.
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10.8 |
10.0 |
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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.
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10.9 |
10.0 |
10.0.278 |
fastx_demux fatal error "Cannot convert FASTA to FASTQ".
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10.10 |
? |
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The -sizeout option gives incorrect results with -dbmatched for the otutab
command and other search commands with -maxaccepts> 1.
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10.11 |
10.0 |
10.0.416 |
Some commands hang if a FASTQ or FASTA input file is empty.
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10.12 |
10.0 |
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Command tax_stats gives "unknown option" fatal error. Work-around is to use
v9.2.
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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
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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.
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