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Bug |
First ver |
Fixed ver |
Description |
| |
8.0.1 |
8.0 |
8.0.1412 |
cluster_otus fails with ""Must sort by size for OTU clustering".
|
| |
8.0.2 |
8.0 |
8.0.1733 |
calc_distmx sometimes produces incorrect results.
|
| |
8.0.3 |
8.0 |
8.0.1416 |
-dbmatched and -dbnotmatched give "No such file or directory" error.
|
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8.0.4 |
8.0 |
8.0.1426 |
search_pcr bugs: diffs did not consider IUPAC codes, spurious "strand ignored"
warning, multithreading bug, crashed unless -threads 1.
|
| |
8.0.5 |
8.0 |
8.0.1429 |
search_oligodb failed to report some valid hits.
|
| |
8.0.6 |
8.0 |
8.0.1432 |
fasta_rarify crashed, e.g. with floating point exception.
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| |
8.0.7 |
8.0 |
8.0.1460 |
-top_hits_only sometimes reports non-top hits.
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8.0.8 |
8.0.1465 |
8.0.1473 |
-utax reported two records for each query sequence if -strand both is given, one
for each strand. Only the higher-confidence record should be reported.
|
| |
8.0.9 |
8.0 |
8.0.1478 |
derep_prefix does not write output.
|
| |
8.0.10 |
8.0.1512 |
8.0.1517 |
-sortbysize gives fatal error "seqdb.h(58) assert failed: m_Quals != 0" with
FASTA input file.
|
| |
8.0.11 |
8.0 |
(not fixed) |
See: Kernel too old error.
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8.0.12 |
8.0 |
8.0.1539 |
-fastqout option of -fastx_truncate did not work.
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8.0.13 |
8.0 |
(not fixed) |
Fatal error from utax command:
e:\r\src\usearch\taxtree.h(51) assert failed: TaxId <= m_MaxTaxId
This is caused by lower-case input sequences. Work-around is to convert to upper
case.
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| |
8.0.14 |
8.0 |
8.0.1564 |
-eeout option to -fastq_filter did not work. See also bug
|
| |
8.0.15 |
8.0 |
8.0.1574 |
-relabel option of -fastq_filter failed to create unique, sequential label.
Workaround: use -threads 1.
|
| |
8.0.16 |
8.0 |
8.0.1574 |
search_pcr and search_ologi fail intermittently with "nt sequences required" if
there are many IUPAC codes (automatic nt alphabet detection looks for {ACGTU}
only).
|
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8.0.17 |
8.0 |
8.0.1589 |
fastx_revcomp did not reverse the order of the Q scores in FASTQ output.
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8.0.18 |
8.0 |
8.0.1604 |
-sizeout option to -cluster_otus gave incorrect size values.
|
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8.0.19 |
8.0 |
8.0.1606 |
fastq_eestats command sometimes segfaulted if no log file specified. Workaround
is to specify -log logfile.txt.
|
| |
8.0.20 |
8.0.1606 |
8.0.1623 |
uchime_ref and uchime_denovo fatal error if -chimeras or -nonchimeras option used:
seqdb.h(58) assert failed: m_Quals != 0.
Work-round is to use -uchimeout file, get non-chimeric labels by grep "N$"
out.uchime | cut -f2 > labels.txt then use fastx_getseqs.
|
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8.0.21 |
8.0 |
8.0.1629 |
-sort other did not work in cluster_fast. Workaround is to use -threads 1 or
cluster_smallmem.
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8.0.22 |
8.0 |
8.0.1629 |
"Unknown option alpha" error if -alpha specified on command line.
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8.0.23 |
8.0 |
8.0.1638 |
-notmatchedfq option produces FASTA output, should be FASTQ.
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8.0.24 |
8.0 |
8.0.1465 |
segfault in allpairs_local.
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8.0.25 |
? |
8.0.1689 |
-fastx_truncate with -padlen gives
---Fatal error---
seqinfo.cpp(153) assert failed: m_Qual == m_QualBuffer
|
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8.0.26 |
8.0 |
8.0.1702 |
Labels in -msaout files may be in wrong order compared with the sequences.
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8.0.27 |
8.0 |
8.1.1727 |
Fatal error from cluster_otus or uparse_ref
uparsedp.cpp(219) assert failed: SumLengths == QL
Caused by gap character '-' or '.' in query sequence. Workaround is to delete
gaps.
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8.0.28 |
8.0 |
8.1.1723 |
-fastaout option causes -cluster_otus to hang. This option is not supported in
v8, fix is to delete the option.
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8.0.29 |
|
8.1.1748 |
-fastqout option generated FASTA output with -orient.
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8.1.30 |
8.1 |
8.1.1763 |
-derep commands segfault with -fastqout. Work-around is to use v8.0.1623.
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8.1.31 |
8.0 |
8.1.1791 |
-fastq_join did not reverse-complement the reverse reads. Workaround is to use
fastx_revcomp on the reverse reads using -threads 1 to preserve the order the
reads appear in the FASTQ file.
|
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8.1.32 |
8.1 |
8.1.1812 |
-fastq_mergepairs calculated incorrect posteriors. This bug was not present in
8.0; it was introduced by a typo in the "improvements" made in 8.1. (This bug is
especially embarrassing considering that I criticized other paired read
assemblers for calculating incorrect posteriors in
Edgar & Flyvbjerg 2015). |
| |
8.1.33 |
8.1.1800 |
8.1.1822 |
-relabel option of fastq_filter appends 0 instead of read number to the label.
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8.1.34 |
8.1.1800 |
8.1.1824 |
Some OTU table counts calculated incorrecly (-otutabout, -mothur_shared_out and
-biomout options of usearch_global).
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8.1.35 |
8.1.1824 |
8.1.1835 |
fastq_filter, fastq_mergepairs and fastq_join would change read labels as if the
-relabel @ option had been specified. Workaround is to use -relabel - (value of
the option is a minus sign).
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8.1.36 |
? |
8.1.1848 |
fastx_truncate fatal error when stripleft or
stripleft value is the same as an input sequence length.
---Fatal error---
seqinfo.cpp(380) assert failed: n < m_L
|
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8.1.37 |
? |
8.1.1856 |
fastq_maxdiffs default was not enforced so any number of differences was allowed
by default. Work-around is to set the option on the command line.
|
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8.1.38 |
? |
8.1.1898 |
-fastq_eeout did not work unless another relableing option was also specified.
Workaround is to use -relabel or -sample.
|
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8.1.39 |
8.1.1800 |
8.1.2044 |
Rules for recognizing OTU identifiers sometimes failed, e.g. if "otu" is all
lower-case. Work-around is to use at least one upper-case letter, e.g. Otu or
OTU.
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8.1.40 |
8.0 |
8.1.2060 |
Fatal error Bin < BinCount from fastq_mergepairs. Workaround is to omit the -log
and -report options.
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8.1.41 |
8.9 |
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-derep_fulllength fails to find rev-comp'd duplicates if there are Us in the
sequence and -strand both. Work-around is to replace Us by Ts.
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