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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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error: overlap is not transmuted! #203

Open Valentin-Bio-zz opened 2 years ago

Valentin-Bio-zz commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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.