Wrong abundance annotation in chimera.uchime

[lentendu]

The chimera.uchime command annotate sequence abundance with "/size=xx/" when uchime expect to find it in the format "/ab=xx/"

Error produced by the following command:
mothur "#chimera.uchime(fasta=A01_rhizo.trim.unique.good.filter.precluster.fasta, name=A01_rhizo.trim.unique.good.filter.precluster.names, reference=self)"

The standard error being:

00:00  29Mb    0.1% Reading A01_rhizo.trim.unique.good.filter.precluster.temp
WARNING: Ignoring gaps in FASTA file 'A01_rhizo.trim.unique.good.filter.precluster.temp'
00:01  33Mb  100.0% Reading A01_rhizo.trim.unique.good.filter.precluster.temp
00:01  33Mb 10.1k sequences                                                  

/global/apps/ecogen/mothur/1.37.3/bin/uchime --input A01_rhizo.trim.unique.good.filter.precluster.temp --uchimeout A01_rhizo.trim.unique.good.filter.precluster
.denovo.uchime.chimeras

---Fatal error---
Missing abundance /ab=xx/ in label >M03696_2_000000000-AH4JL_1_1101_22078_1905_1/size=2020/

and the mothur logfile contains:

Linux version

Running 64Bit Version

mothur v.1.37.1
Last updated: 4/18/2016

by
Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan
pschloss@umich.edu
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. 
Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

Type 'quit()' to exit program
Script Mode


mothur > chimera.uchime(fasta=A01_rhizo.trim.unique.good.filter.precluster.fasta, name=A01_rhizo.trim.unique.good.filter.precluster.names, reference=self)

Using 1 processors.

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from A01_rhizo.trim.unique.good.filter.precluster.fasta ...
[ERROR]: A01_rhizo.trim.unique.good.filter.precluster.denovo.uchime.chimeras is blank. Please correct.

It took 3 secs to check 0 sequences. 0 chimeras were found.

Output File Names: 
A01_rhizo.trim.unique.good.filter.precluster.denovo.uchime.chimeras
A01_rhizo.trim.unique.good.filter.precluster.denovo.uchime.accnos


mothur > quit()


************************************************************
************************************************************
************************************************************
Detected 1 [ERROR] messages, please review.
************************************************************
************************************************************
************************************************************

I tested it with version 1.37.2 and 1.37.3, and also after removing gaps from the sequences, the error remains.
By the way, in all logfiles of mothur v.1.37.2 and v.1.37.3, the version is wrong ('v.1.37.1').

[mothur-westcott]

Thanks for reporting this bug. I have released version 1.37.4 to fix it, https://github.com/mothur/mothur/releases/tag/v1.37.4.