error: overlap is not transmuted!

[Valentin-Bio-zz]

Hello I installed racon via conda conda install racon

I made my SAM file using bwa.

then I run racon: racon -t 20 joined_reads.fastq UlvaAlignContIlu.sam ulvacomp.contigs.fasta > polished_contigs.fasta

I got this error message:

error: overlap is not transmuted!

why im getting this? I took a look into this: https://github.com/isovic/racon/issues/77 but after 3-4 years idk if this still being a solution

THanks for your time :)

[rvaser]

Hello, can you please verify which version you are using with racon --version? Also, please paste commands which produced the .sam file.

Best regards, Robert

[gettl008]

I had this issue come up with 4 out of >200 assemblies that I've run through Racon. I'm using v1.4.20. The one thing that I'm noticing is that they all contain a number of smaller contigs with abnormal coverage. I removed contigs smaller than 50kb from the assembly which seems to do the trick. It'd be nice though to be able to pass these through without getting the cryptic error.