This File Contains Inconsistent Headers

Question

[gtasource]

Illumnia Base Space is giving me this error that my FASTQ files have inconsistent header information.

This file contains inconsistent header information. We expected all cluster headers to match '@Sample:116:FlowId:1:1101:19361:1047:N:0:AGTCAACA+TCTTTCCC#0/1' but we encountered the header '@Sample:116:FlowID:1:1101:23023:1063**:N:0:AGTCAACA+TCTTTCCC#0/1' at cluster 2.

I edited parts of the header sample names, but as you can see, the header differs at this position: 19361:1047 23023:1063

Are there any tools I can use to fix this header issue?

Cheers!

[Mensur Dlakic]

I think the part that is causing problems may be the asterisks [*] rather than what you indicated. It is normal that headers have different numbering, but asterisks are what to my eye is inconsistent.

[swbarnes2]

The last two numbers in the read name are xy coordinates on the flow cell tile...they absolutely are supposed to be different for every read.

Answer 1

[swbarnes2]

a sed command would probably fix things, but I'd worry where there's one error, there might be more. Where did you get this fastq? How was it generated?

[gtasource]

The FASTQ file that is giving the errors was generated from Kneaddata to remove human data from the dataset (we are doing a metagenomics analysis.) When uploading the original FASTQ file, no header issues are given.

I don't have to use Kneaddata for removal of the human contamination using a reference genome. But it seemed easier than using an aligner, removing the unmapped BAM and converting to a FASTQ file (I also feel like this would give FASTQ issues as well.)