# fastq.info

**URL:** <https://forum.mothur.org/t/fastq-info/2417>\
**Category:** Commands in mothur\
**Created:** [June 23, 2015, 1:46pm UTC](https://forum.mothur.org/t/fastq-info/2417 "2015-06-23T13:46:09Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![zhangyu](https://avatars.discourse-cdn.com/v4/letter/z/a183cd/32.png) [@zhangyu](https://forum.mothur.org/u/zhangyu)\
**Post date:** [June 23, 2015, 1:46pm UTC](https://forum.mothur.org/t/fastq-info/2417/1 "2015-06-23T13:46:09Z")

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Hi all,  
I recently got some Bacteria sequence using HiSeq2500.It gives me segfault when I try to run fastq.info.

mothur\>fastq.info(fastq=Hiseq\_raw1.fq,format=illumina)

[ERROR]: finding negative quality scores, do you have the right format selected?

> **[FASTQ format](https://en.wikipedia.org/wiki/FASTQ_format)**
>
> FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.
> It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA formatted sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illum...

  
[WARNING]: your sequence names contained ‘:’. I changed them to ‘\_’ to avoid pr  
oblems in your downstream analysis.

mothur \> fastq.info(fastq=Hiseq\_raw1.fq,format=illumina1.8+)

Output File Names:  
Hiseq\_raw1.fasta  
Hiseq\_raw1.qual

[WARNING]: your sequence names contained ‘:’. I changed them to ‘\_’ to avoid pr  
oblems in your downstream analysis.  
My question(s) are :  
(1)I am wondering the differents between illumina and illumina1.8+.  
(2) how to how to select suitable format for my 16S rRNA gene sequences that are generated using Illumina’s HiSeq2500 platform.  
(3)If the WARNING[] have a pernicious effect ondata analysis.  
I look forward to your advice.

Regards,  
Zhangyu.

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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:** [June 23, 2015, 3:58pm UTC](https://forum.mothur.org/t/fastq-info/2417/2 "2015-06-23T15:58:09Z")

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Illumina has had 3 versions of its format. Mothur allows for 2 format options for illumina data.

Illumina 1.3+ Phred+64, raw reads typically (0, 40) - format in mothur = illumina  
Illumina 1.5+ Phred+64, raw reads typically (3, 40) - format in mothur = illumina  
Illumina 1.8+ Phred+33, raw reads typically (0, 41) - format in mothur = illumina1.8+

Most likely all your fastq data is illumina1.8+, which is mothur’s default, and you do not need to provide the format option. We have included other formats to make mothur flexible.

About the warning:  
Mothur converts the ‘:’ characters to ‘\_’ characters because the ‘:’ is a special character is trees. When you have sequence names that include ':'s, the tree files created will be unable to be read by any tree software. You can ignore the warning.