# Make.contigs with gz not working **URL:** \ **Category:** mothur bugs\ **Created:** [October 7, 2022, 7:07pm UTC](https://forum.mothur.org/t/make-contigs-with-gz-not-working/21574 "2022-10-07T19:07:21Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![leocadio](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/leocadio/32/203_2.png) [@leocadio](https://forum.mothur.org/u/leocadio)\ **Post date:** [October 7, 2022, 7:07pm UTC](https://forum.mothur.org/t/make-contigs-with-gz-not-working/21574/1 "2022-10-07T19:07:21Z")
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](http://mothur.org/)** > > The website that supports the mothur software program - one of the most widely used tools for analyzing 16S rRNA gene sequence data. Step inside to learn how to use the software, get help, and join our community! 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](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 ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [October 11, 2022, 4:22pm UTC](https://forum.mothur.org/t/make-contigs-with-gz-not-working/21574/2 "2022-10-11T16:22:46Z")
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 ---
**Author:** ![leocadio](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/leocadio/32/203_2.png) [@leocadio](https://forum.mothur.org/u/leocadio)\ **Post date:** [October 11, 2022, 4:35pm UTC](https://forum.mothur.org/t/make-contigs-with-gz-not-working/21574/3 "2022-10-11T16:35:43Z")
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 ---
**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\ **Post date:** [October 14, 2022, 3:15pm UTC](https://forum.mothur.org/t/make-contigs-with-gz-not-working/21574/4 "2022-10-14T15:15:22Z")
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 ---
**Author:** ![leocadio](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/leocadio/32/203_2.png) [@leocadio](https://forum.mothur.org/u/leocadio)\ **Post date:** [October 14, 2022, 5:17pm UTC](https://forum.mothur.org/t/make-contigs-with-gz-not-working/21574/5 "2022-10-14T17:17:10Z")
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. ---
**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\ **Post date:** [October 24, 2022, 5:17pm UTC](https://forum.mothur.org/t/make-contigs-with-gz-not-working/21574/6 "2022-10-24T17:17:43Z")
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