make.contigs creates an empty groups file

make.contigs creates an empty groups file when using compressed fastq.gz files as input.

Thank you for reporting this bug. It effects the file format when the fastq files are compressed in .gz format. I will fix the issue for the next release. In the meantime you can workaround the issue by decompressing the fastq files and rerunning the make.contigs command or by running it with allfiles=t. Sorry for the inconvenience and thanks for helping find this bug.

Hi, I am having a similar problem.
I am attempting to use make.contigs using just the stability file and it seems to work well but i end up with an empty groups file that causes problems downstream…

If i use allfiles=t do i then need to supply an oligos file? as when i ran this without one i got a segmentation fault…

As usual thanks for all your help

Kind regards

You should be seeing the error message “You can only use the allfiles option with an oligos file” on version 1.36. Can you check the log file for me? As a workaround you can always decompress the files until the next release.

Interestingly there doesnt seem to be anything in my logfile. Ill try extracting the files first.
Thanks for your help.



Linux version

Using ReadLine

Running 64Bit Version

mothur v.1.36.1
Last updated: 7/27/2015

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