racon: error: overlap is not transmuted!

Hi, I am trying to polish a PacBio assembly with illumina reads. After one round of polishing using the pacbio reads, I mapped the illumina reads to the the polished assembly with minimap2 and used the sam output as overlap information for polishing using the following commands:

minimap2 -t 64 -ax sr consensus1.fasta ${reads} > illumina.sam
racon -t 64 ${reads} illumina.sam consensus1.fasta > consensus2.fasta

The mapping works quite well, but after a few hours running I hit the following error:

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

I am not sure what does it mean or how to fix this. Any suggestions are more than welcome! Kind regards,

About this issue

Original URL
State: open
Created 6 years ago
Comments: 87

Most upvoted comments

Thanks a lot, I just need the second(correct reads) and try it now. I’ll let you know if it worked.

Best regards Fabian

Colorstorm on Nov 4, 2019

Dear Robert, Thank you very much for your help! Now all is working 😃 Best regards, Sara

SDA16 on Mar 18, 2019

No problem 😃 Thanks a lot for helping me out with the pesky not transmuted error!

rvaser on Dec 8, 2018

A quick fix is to replace line https://github.com/isovic/racon/blob/master/src/polisher.cpp#L314 with

l = c < n ? 0 : c - n;

This will lead us to the real error which is ... empty overlap set! Can you please verify that?

rvaser on Dec 7, 2018

Now I get this:

[racon::Polisher::initialize] loaded target sequences
[racon::Polisher::initialize] loaded sequences
Processing overlaps from 0 to 269501
Overlap 0/269501 is not valid, deleting
Overlap 1/269501 is not valid, deleting
Overlap 2/269501 is not valid, deleting
Overlap 3/269501 is not valid, deleting
--
Overlap 269497/269501 is not valid, deleting
Overlap 269498/269501 is not valid, deleting
Overlap 269499/269501 is not valid, deleting
Overlap 269500/269501 is not valid, deleting
Processing overlaps from 4294697795 to 22247
[racon::Polisher::initialize] loaded overlaps
Not transmuted at 0/22247
Not transmuted at 1/22247
Not transmuted at 2/22247
Not transmuted at 3/22247
Not transmuted at 4/22247
--
Not transmuted at 22241/22247
Not transmuted at 22242/22247
Not transmuted at 22243/22247
Not transmuted at 22244/22247
Not transmuted at 22245/22247
Not transmuted at 22246/22247
[racon::Overlap::find_breaking_points] error: overlap is not transmuted!
[racon::Overlap::find_breaking_points] error: overlap is not transmuted!
[racon::Overlap::find_breaking_points] error: overlap is not transmuted!
[racon::Overlap::find_breaking_points] error: overlap is not transmuted!

AntoineHo on Dec 7, 2018

Hi Robert, I just remembered that I changed the names of the illumina reads and added a /1 and /2 before shuffling the reads. But the /1 and /2 were removed from the read names after mapping. I’ll fix the same file manually and try again. I’ll keep you updated.

Cheers,

jdmontenegro on Jun 28, 2018