Read at offset 59230953264 does not begin with "@".

Question

[Justine]

I have been trying to assemble a human genome that has been sequenced on Nanopore-PromethION, basecalled on the latest version of bonito, and am now trying to run an assembly using shasta. The basecalling had no issues, but now when I try to run shasta, I get this error message:

> Read rate: 2.46759e+09 bytes/s. 
> Found 12964000 lines in this file.
> 2021-Oct-13 16:56:18.278195 A runtime error occurred in thread 75:
> Read at offset 59230953264 does not begin with "@".

I have been trying to look up this 'read at offset' issue for fastq files but so far no luck. Also, I am not quite sure how to look up specifically which read it is referring to that 'does not begin with "@"'. Any help would be much appreciated!

Answer 1

[GenoMax]

Sounds like you have a corrupt read. Since you have only 12 million reads that error message is not pointing to the read number but something else. You can try a fastq validation program to see if you can identify/delete the culprit: Checking fastq is valid

[Justine]

Apologies for the late update but I managed to use FastQValidator and identified the corrupt read. Removed the corrupt read and got shasta to work normally! Thank you GenoMax for your help!