Make.contigs with gz not working

[leocadio]

Hello all,

I just got the 1.48.0 installed last week in the server at ASU (Agave; SLURM queue manager).

I had a problem with make.contigs. I pass make.file with gz with no problem, but then make.contigs crashes the system.

outfile:

Linux version

Using ReadLine
mothur v.1.48.0
Last updated: 5/20/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan

mothur website

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

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

Type ‘quit()’ to exit program

[NOTE]: Setting random seed to 19760620.

Batch Mode

mothur > make.file(inputdir=./, type=gz)
Setting input directories to:
/scratch/lblancob/phyto/

Output File Names:
/scratch/lblancob/phyto/stability.files

Error file:
/var/spool/slurmd/job17740685/slurm_script: line 14: 29838 Segmentation fault mothur phyto.sh

Code run:

make.file(inputdir=./, type=gz)
make.contigs(file=current, deltaq=10, insert=30, trimoverlap=T, processors=10)

If I decompress all gz files to fastq (and removing that part in make.file), it runs like a charm. So, something is going on (I think) with the gz step. Tried also forcing to 1 processor only (just in case) and same result. Also tried running it in interactive mode (just in case was something with the batch file) and same - gz files crash the make.contigs.

Best,

Leo

[pschloss]

Hi Leo- You will need to have the Boost libraries installed to use type=gz. It doesn’t look like your version of mothur was compiled with Boost.

Pat

[leocadio]

Thanks Pat!

I will pass the message to the ASU team. Since this is a Uni resource, I am not in charge of compiling/updates, etc. I had a previous problem with vsearch (it was not there), but that one I was able to identify the problem myself (and they corrected it with no problem).

Leo

[pschloss]

Hi Leo,

You could always use conda to install the latest version of mothur to install it within your account or grab the binary from our github release page.

Pat

[leocadio]

Well, my idea was (is) starting to use mothur when teaching in class (now that I have teaching duties) so I would prefer if it is up and running in the server for the student to use, instead of making them install it in their partition.