problems with cluster(method=agc)

Classify (using vsearch via method=agc) creates the fasta.temp file with counts appended to each sequence name, but then fails with the message “Could not open”

I can manually run the two vsearch commands and the R procedure given in the hack outlined on issue #169 of the Github pages. Looking at the output with debug mode switched on gives:

"/gpfs/home/e130/hussein/mothur/vsearch" --maxaccepts=16--usersort--id=0.97--minseqlength=30--wordlength=8--uc=""--cluster_smallmem=""--maxrejects=64--strand=both--log=""--sizeorder

[DEBUG]: vsearch cluster command = “/gpfs/home/e130/hussein/mothur/vsearch” --maxaccepts=16 --usersort --id=0.97 --minseqlength=30 --wordlength=8 --uc=“” --cluster_smallmem=“” --maxrejects=64 --strand=both --log=“” --sizeorder .

[ERROR]: Could not open

Doing a bit of playing, the problem seems to be that my computer system doesn’t like having the full path to the vsearch executable - if I edit out the path, and paste this back to the command prompt that step works fine. So I assume that within mothur the vsearch command is not successfully running, but the error message to tell me this isn’t displaying, so then the error message that does display comes from the next line in the script.

If mothur simply invoked vsearch by name and relied on the path variable to find it, it looks like it would work OK.

Apologies if I’m missing something that would be obvious to a unix expert.



Linux version

Running 64Bit Version

mothur v.1.38.1
Last updated: 8/9/2016

Patrick D. Schloss

Department of Microbiology & Immunology
University of Michigan

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
Interactive Mode

mothur >

mothur > cluster(,count=singles.count_table,method=agc) You did not set a cutoff, using 0.03. [ERROR]: Could not open

mothur > quitting mothur