# Gz make contigs error

**URL:** <https://forum.mothur.org/t/gz-make-contigs-error/22294>\
**Category:** mothur bugs\
**Created:** [February 14, 2025, 6:33am UTC](https://forum.mothur.org/t/gz-make-contigs-error/22294 "2025-02-14T06:33:50Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Arkio](https://avatars.discourse-cdn.com/v4/letter/a/a87d85/32.png) [@Arkio](https://forum.mothur.org/u/Arkio)\
**Post date:** [February 14, 2025, 6:33am UTC](https://forum.mothur.org/t/gz-make-contigs-error/22294/1 "2025-02-14T06:33:50Z")

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mothur \> make.contigs(file=stability.files)  
When I use with gz type fastq, it happens

Using 16 processors.

> > > > > Processing file pair SRR28485495\_1.fastq.gz - SRR28485495\_2.fastq.gz (files 1 of 13) \<\<\<\<\<  
> > > > > Making contigs…  
> > > > > [WARNING]: readingp▒▒fSRR28485495\_1.fastq▒▒ݎ▒▒▒O1▒▒▒▒J▒▒$ expected a name with @ as a leading character, ignoring read.  
> > > > > [WARNING]: reading 0▒▒+ expected a name with + as a leading character, ignoring.[WARNING]: names do not match. readp▒▒fSRR28485495\_1.fastq▒▒ݎ▒▒▒O1▒▒▒▒J▒▒$ for fasta and 0▒▒+ for quality, ignoring.[WARNING]: Lengths do not match for sequencep▒▒fSRR28485495\_1.fastq▒▒ݎ▒▒▒O1▒▒▒▒J▒▒$. Read 1 characters for fasta and 35 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? [FASTQ format - Wikipedia](http://en.wikipedia.org/wiki/FASTQ_format#Encoding)  
> > > > > [WARNING]: readingp▒▒fSRR28485495\_2.fastq▒▒ے▒8▒▒ expected a name with @ as a leading character, ignoring read.  
> > > > > [WARNING]: reading ▒?▒▒▒▒t;▒▒s▒▒o expected a name with + as a leading character, ignoring.[WARNING]: names do not match. readp▒▒fSRR28485495\_2.fastq▒▒ے▒8▒▒ for fasta and ▒?▒▒▒▒t;▒▒s▒▒o for quality, ignoring.[WARNING]: Lengths do not match for sequencep▒▒fSRR28485495\_2.fastq▒▒ے▒8▒▒. Read 56 characters for fasta and 12 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? [FASTQ format - Wikipedia](http://en.wikipedia.org/wiki/FASTQ_format#Encoding)  
> > > > > ]M▒▒▒▒ƌ▒5Z▒^▒P▒▒▒y▒i])▒L"▒@ek▒fi[▒c is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > )▒▒oVhpB▒y̛▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > \<▒▒&▒\*u\_▒p▒KU▒z▒▒?▒?▒▒▒▒▒+▒qB▒V▒qpW▒ObI~▒▒X\_f.▒͠▒w is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > S+f▒e▒▒▒▒▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > Vo▒7-▒[d▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒▒#8▒8k=▒1▒$▒▒P▒ɜ9▒▒▒ڣ▒▒,▒▒|▒dͩNS▒▒▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding. p▒▒fSRR28485495\_1.fastq▒▒ݎ▒▒▒O1▒▒▒▒J▒▒$ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒n▒8?Ke|5K▒gmj▒▒▒▒`▒loo?▒▒▒#▒▒;▒D▒▒▒53▒ʣǻ▒a▒61▒▒▒N▒q?▒j▒<"▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding. ▒B▒Sွ▒▒p▒|R0▒N@l▒,wk▒▒▒▒s▒▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding. ▒Of▒`\>4V▒▒AVN\_▒Yƈ▒]▒,2▒+A▒▒▒JmVY▒▒▒}▒▒=▒▒▒▒▒1z▒▒▒ed▒(▒.i▒r\>▒/v▒▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒▒▒▒Bz▒k▒▒eװ▒~U▒▒A▒▒p)▒Z▒Y▒▒▒▒y/▒d▒M▒\▒#▒▒▒\_▒▒, is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒▒▒dd.A▒▒fa▒▒b䧋▒bd▒u▒▒ʻ▒▒▒tV▒F=▒0y▒Gl▒Z▒|V▒▒▒▒f^▒▒▒m6p▒▒▒▒▒U]Y%▒▒mof▒▒▒z▒F▒&▒(O=▒▒Qң▒▒,bݷ▒%▒▒}▒٬▒▒0▒|!▒aLl is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒▒▒b-▒X▒▒▒Y5▒+▒▒▒▒qx䝬▒|▒ϧ▒~|▒▒▒▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒v▒M’]cĔ7Y▒▒▒Ͳ▒z▒▒▒▒`BX▒w▒d!$▒▒▒իG▒G▒▒kU▒(▒N6▒zkS▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒2▒.▒▒▒#▒▒-r▒▒s▒9▒▒s▒J/5▒Y▒W▒b▒▒▒8▒▒▒▒▒ͰxcN▒▒xZm▒UK is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ▒▒▒▒ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > xterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256colorSegmentation fault (core dumped)  
> > > > > xterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256colorxterm-256color

Why did it happen?

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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:** [February 17, 2025, 1:55pm UTC](https://forum.mothur.org/t/gz-make-contigs-error/22294/2 "2025-02-17T13:55:47Z")

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It looks like you have some read mismatches between the paired fastq files, or mothur is not reading the gz file correctly. Could you send the SRR28485495\_1.fastq.gz and SRR28485495\_2.fastq.gz files to [mothur.westcott@gmail.com](mailto:mothur.westcott@gmail.com) so I can troubleshoot the issue for you?

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<div class="post-metadata">

**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:** [February 27, 2025, 1:56pm UTC](https://forum.mothur.org/t/gz-make-contigs-error/22294/3 "2025-02-27T13:56:09Z")

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