Hi there I am working on a bioinformatics assignment and i am new to using mothur and have almost 0 experience using it, i have encountered an error and have absolutely 0 idea how to fix it. Anyways here it is, when i try to run the command fastq.info(fastq=HUMAN_MICROBIOME.fastq, qfile=F) i get an error saying -bash: syntax error near unexpected token `fastq=HUMAN_MICROBIOME.fastq,’ I read somewhere that this has something to do with the parenthesis but thing is i have been copying this command and pasting it into mothur and it worked once before as is, but it refuses to work now and i have no idea why! Any help would be greatly appreciated.
Hi,
That error is from the bash shell not mothur.
Bash command prompt:
$ fastq.info(fastq=HUMAN_MICROBIOME.fastq, qfile=F)
-bash: syntax error near unexpected token `fastq=HUMAN_MICROBIOME.fastq,’
Start mothur first then run the command
$ mothur
mothur v.1.36.1
Last updated: 7/27/2015
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
mothur > fastq.info()
You must provide a file or fastq option.
[ERROR]: did not complete fastq.info.
Alternative ways to call mothur:
http://www.mothur.org/wiki/General_operations
Regards
Ian