Flye duplicated reads error with autocycler (v2.6.0)

[lborcard]

Description of the bug

I am currently using v2.6.0 of bacass with longreads and --assembler autocycler, I am getting an error at the flye step where the sub sampling (I assume but tbd) creates identical reads with the same ID but different complete headers. It seems that flye does compare the entire header but only the id of the reads since the subsampling of autocycler probably samples the same reads. Has anyone dealt with the issue?

best,

Loïc

Command used and terminal output

Relevant files

No response

System information

nextflow version 25.04.6
local
Singularity
bacass v2.6.0

[Daniel-VM]

Thanks for notifying!! 🙌🏾 I'll check it

[Daniel-VM]

Hi!

This looks more like an input issue than a pipeline issue.
The duplicated read IDs seem to already be present in Flye’s input FASTQ, rather than being introduced by Autocycler.

I couldn’t reproduce the issue, but I hope this helps with troubleshooting.