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Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
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Problem with chimera.uchime #366

Closed vtardy closed 5 years ago

vtardy commented 7 years ago

Hi, the chimera.uchime function does not work. the mothur logfile contains :

`mothur v.1.39.5 Last updated: 3/20/2017

by Patrick D. Schloss

Department of Microbiology & Immunology University of Michigan http://www.mothur.org

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

Distributed under the GNU General Public License

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

For questions and analysis support, please visit our forum at https://www.mothur .org/forum

Type 'quit()' to exit program

mothur > chimera.uchime(fasta=Run123.good.unique.good.filter.unique.precluster.f asta, name=Run123.good.unique.good.filter.unique.precluster.names, dereplicate=t)

Using 1 processors.

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

Checking sequences from Run123.good.unique.good.filter.unique.precluster.fasta . .. uchime v4.2.40 by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.

E:[Irstea 02] - Analyse Mothur\03 - Analyse Run Texas\03 - Alignement\uchime.exe --input Run123.good.unique.good.filter.unique.precluster.temp --uchimeout Run 123.good.unique.good.filter.unique.precluster.denovo.uchime.chimeras

---Fatal error--- ftello in GetFileSize [ERROR]: Run123.good.unique.good.filter.unique.precluster.denovo.uchime.chimeras is blank. Please correct.

It took 114 secs to check 0 sequences. 0 chimeras were found.

Output File Names: Run123.good.unique.good.filter.unique.precluster.denovo.uchime.chimeras Run123.good.unique.good.filter.unique.precluster.denovo.uchime.accnos`

mothur-westcott commented 7 years ago

That's an error from the uchime program. Have you tried the chimera.vsearch command?Vsearch is a open source 64bit version of uchime.

vtardy commented 7 years ago

Ok, thank for this solution. With vsearch program, it works correctly.