# segmentation fault - make.contigs

**URL:** <https://forum.mothur.org/t/segmentation-fault-make-contigs/3523>\
**Category:** mothur bugs\
**Created:** [June 15, 2018, 11:25am UTC](https://forum.mothur.org/t/segmentation-fault-make-contigs/3523 "2018-06-15T11:25:19Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jopollock](https://avatars.discourse-cdn.com/v4/letter/j/74df32/32.png) [@jopollock](https://forum.mothur.org/u/jopollock)\
**Post date:** [June 15, 2018, 11:25am UTC](https://forum.mothur.org/t/segmentation-fault-make-contigs/3523/1 "2018-06-15T11:25:19Z")

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Hello,

I am using the 1.36.1 version of mothur and I am getting a segmentation fault when running make.contigs on fastq.gz files:

> > > > > Processing file pair trimmed\_2\_R1.fastq.gz - trimmed\_2\_R2.fastq.gz (files 2 of 374) \<\<\<\<\<  
> > > > > M03742\_14\_000000000-BNJ5K\_1\_1102\_16619\_1766 is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > Making contigs…  
> > > > > Segmentation fault

As far as I am aware, this version of mothur should be able to cope with missing sequences (which are as a result of removing sequences prior to inputting into mothur).

Many thanks in advance for your help on this issue,

Jo

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<div class="post-metadata">

**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:** [June 18, 2018, 8:18pm UTC](https://forum.mothur.org/t/segmentation-fault-make-contigs/3523/2 "2018-06-18T20:18:27Z")

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Can you update your version of mothur? That’s a few years old - we’re up to 1.40 now and I suspect these bugs may have been fixed in the mean time.

pat