error: overlap is not transmuted!

[aliexclusive]

Dear Team,

I'm using Racon 1.4.0 and trying to polish the assembly using Illumina reads.

racon -t 64 NP_trim.fq assembly_minimap_il.paf assembly_raconNP_medaka2x.fa > assembly_raconNP_medaka2x_raconILM.fa

Here is my jobscript.

#SBATCH -N 1
#SBATCH --ntasks-per-node=64
#SBATCH --partition=batch
#SBATCH -J medaka
#SBATCH -o racon.%J.out
#SBATCH -e racom.%J.err
#SBATCH --time=24:00:00
#SBATCH --mem=200G

I'm getting the following error.

[racon::Polisher::initialize] loaded target sequences 1.513 s
[racon::Polisher::initialize] loaded sequences 85.565 s
[racon::Polisher::initialize] loaded overlaps 42.113 s
[racon::Overlap::find_breaking_points] error: overlap is not transmuted!

Any suggestion, how can I solve this issue.

[rvaser]

Hello, can you please paste the command that produced assembly_minimap_il.paf?

Best regards, Robert

[aliexclusive]

Here it is

minimap2 -x sr assembly_raconNP_medaka2x.fa IL_trim.fq > assembly_minimap_il.paf

[rvaser]

I guess you misplaced the read file in your racon command, i.e. instead of IL_trim.fq you used NP_trim.fq. The valid command should look like this:

racon -t 64 IL_trim.fq assembly_minimap_il.paf assembly_raconNP_medaka2x.fa > assembly_raconNP_medaka2x_raconILM.fa

The errors overlap is not transmuted or empty overlap set indicate that the overlap file does not contain both the sequence headers and contig headers.

Best regards, Robert

[aliexclusive]

It worked fine. Thanks for your kind guidance.