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but the adapterLen set by user is: 0 #780

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MartinSchmitz95 opened this issue Feb 14, 2025 · 0 comments
Open

but the adapterLen set by user is: 0 #780

MartinSchmitz95 opened this issue Feb 14, 2025 · 0 comments

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@MartinSchmitz95
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Hello,
I encounter an issue using Hifiasm ONT. I use synthetic reads sampled from PBSim3 like this:

pbsim --strategy wgs --method qshmm --qshmm data/QSHMM-ONT.model --depth {depth} --genome {ref_path}

This gives me ONT reads in fastq format using the PBSim default simulated model. The reads fastq file looks normal.

Then running Hifiasm don't like this:

./hifiasm --ont -o asm -t32 ont_reads.fastq.gz

I am getting the following error message:

the adapterLen of index is: 32766, but the adapterLen set by user is: 0
When running it multiple times on the same dataset the number '32766' changes slightly.

I would like to understand what this error message wants to tell me and what is the problem exactly with the reads?

Since it says something about adapters I also tried chopping adapters from the reads with PoreChop, but it didn't help.

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