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known bugs and fixes
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  Bugs in previous versions
  Fixed versions
  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.
  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.
  8.0.7 8.0 8.0.1460 -top_hits_only sometimes reports non-top hits.
  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.
  8.0.12 8.0 8.0.1539 -fastqout option of -fastx_truncate did not work.
  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.
  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).
  8.0.17 8.0 8.0.1589 fastx_revcomp did not reverse the order of the Q scores in FASTQ output.
  8.0.18 8.0 8.0.1604 -sizeout option to -cluster_otus gave incorrect size values.
  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.
  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.
  8.0.22 8.0 8.0.1629 "Unknown option alpha" error if -alpha specified on command line.
  8.0.23 8.0 8.0.1638 -notmatchedfq option produces FASTA output, should be FASTQ.
  8.0.24 8.0 8.0.1465 segfault in allpairs_local.
  8.0.25 ? 8.0.1689 -fastx_truncate with -padlen gives
---Fatal error---
seqinfo.cpp(153) assert failed: m_Qual == m_QualBuffer
  8.0.26 8.0 8.0.1702 Labels in -msaout files may be in wrong order compared with the sequences.
  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.
  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.
  8.0.29   8.1.1748 -fastqout option generated FASTA output with -orient.
  8.1.30 8.1 8.1.1763 -derep commands segfault with -fastqout. Work-around is to use v8.0.1623.
  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.
  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.
  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).
  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).
  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

  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.
  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.
  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.
  8.1.40 8.0 8.1.2060 Fatal error Bin < BinCount from fastq_mergepairs. Workaround is to omit the -log and -report options.
  8.1.41 8.9    -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.