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()
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Detected 1 [ERROR] messages, please review.
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I tested it with version 1.37.2 and 1.37.3, and also after removing gaps from the sequences, the error remains.
I also verified that the UCHIME executable used was the one provided with the corresponding mothur version.
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’).
I posted it first as an issue on GitHub, but I just realize that most bugs were reported here.