# make.contigs error with .gz file

**URL:** <https://forum.mothur.org/t/make-contigs-error-with-gz-file/2809>\
**Category:** mothur bugs\
**Created:** [April 13, 2016, 10:55pm UTC](https://forum.mothur.org/t/make-contigs-error-with-gz-file/2809 "2016-04-13T22:55:16Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ldiao](https://avatars.discourse-cdn.com/v4/letter/l/45deac/32.png) [@ldiao](https://forum.mothur.org/u/ldiao)\
**Post date:** [April 13, 2016, 10:55pm UTC](https://forum.mothur.org/t/make-contigs-error-with-gz-file/2809/1 "2016-04-13T22:55:16Z")

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Hi, I downloaded mothur v.1.37.0 today and had issues with running make.contigs with a stability file when my files were in .gz format. However, when I decompressed the files and changed the names in the stability file accordingly to .fastq instead of .gz, everything seems to be working just fine.

Not sure if this is helpful, but here are some lines from mothur’s logfile for when the files were in .gz format:

mothur \> make.contigs(file=stability.file.small)

Using 1 processors.

> > > > > Processing file pair 1\_R1\_001.fastq.gz - 1\_R2\_001.fastq.gz (files 1 of 1) \<\<\<\<\<  
> > > > > [ERROR]: Could not open 1\_R2\_001.fastq.gz  
> > > > > [WARNING]: Blank fasta name, ignoring read.  
> > > > > [WARNING]: missing sequence for , ignoring.[WARNING]: expected a name with + as a leading character, ignoring.[WARNING]: missing quality for , ignoring.Making contigs…  
> > > > > [WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704\_9\_000000000-AA2CM\_1\_1101\_15239\_1353.  
> > > > > [WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704\_9\_000000000-AA2CM\_1\_1101\_16354\_1491.  
> > > > > [WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704\_9\_000000000-AA2CM\_1\_1101\_13888\_1599.  
> > > > > [WARNING]: name mismatch in forward and reverse fastq file. Ignoring, M00704\_9\_000000000-AA2CM\_1\_1101\_18599\_1656.  
> > > > > …  
> > > > > and so on for all sequences.

  
And then when they were decompressed (I changed the file names in stability.file.small accordingly):

mothur \> make.contigs(file=stability.file.small)

Using 1 processors.

> > > > > Processing file pair 1\_R1\_001.fastq - 1\_R2\_001.fastq (files 1 of 1) \<\<\<\<\<  
> > > > > Making contigs…

and it works just fine.

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**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [April 18, 2016, 5:53pm UTC](https://forum.mothur.org/t/make-contigs-error-with-gz-file/2809/2 "2016-04-18T17:53:03Z")

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Sorry for the inconvenience and thanks for reporting this bug. We will be releasing an updated version with a fix later today. In the meantime, decompressing your files will allow you to work around the bug.

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [April 18, 2016, 7:32pm UTC](https://forum.mothur.org/t/make-contigs-error-with-gz-file/2809/3 "2016-04-18T19:32:02Z")

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> **[mothur/mothur](https://github.com/mothur/mothur/releases/tag/v1.37.2)**
>
> Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seek...