`start_time` in fastq file not available afterbasecalling

LooseLab / Icarust

A fully featured MinKNOW simulator for testing read until experiments.

Mozilla Public License 2.0

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`start_time` in fastq file not available afterbasecalling #20

Closed lborcard closed 4 months ago

lborcard commented 4 months ago

Dear Icarust,

I am testing your software and I just noticed that the fastq files that I obtained from Dorado (HAC) do not contain the start_time in the fastq header. Is this info available somewhere after the run ? I ran Icarust from the docker using -vvv flag.

thank you!

Loïc

Adoni5 commented 4 months ago

Hi @lborcard - sorry for the slow reply! Is this still an issue? I think the start time should be present, but it might not represent the actual read start time.

Cheers, Rory

lborcard commented 4 months ago

Hi @Adoni5 ,

At least using my version of dorado, the resulting fastqs do not have the start_time flag in their headers. I tried to use readfish to circumvent that as it outputs the time of the "decision" but this timing seems to be off .