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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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[RaconWrapper::run] error: unable to find split target sequences! #182

Closed carolhsb closed 3 years ago

carolhsb commented 3 years ago

Hi,

I'm running racon_wrapper to polish an assembly (that I had previously corrected with PacBio reads) with Illumina reads.

This is the command I'm using:

python3 /home/carol/racon/build/bin/racon_wrapper -t 30 --split 28048207 /home/carol/short_reads_mma/concat.clean.fq.gz ./dbg.illumina.sam ./dbg.corrected.pb.fasta > dbg.corrected.illumina.fasta

I keep getting this error: [RaconWrapper::run] total number of splits: 0 [RaconWrapper::run] error: unable to find split target sequences!

In the split flag, I used the largest contig value.

How can I work it out?

Thanks in advance,

Carol

rvaser commented 3 years ago

Hi Carol, which Racon version are you using? How big is the assembly? The command you used seems fine to me at first glance.

Best regards, Robert

carolhsb commented 3 years ago

Hi Robert,

Thank you for your answer!

I'm using version 1.4.21. The assembly has 1.37 GB.

Cheers,

Carol

rvaser commented 3 years ago

Please run the below command from the racon root folder and check if anything is created: build/vendor/rampler/bin/rampler split dbg.corrected.pb.fasta 28048207

rvaser commented 3 years ago

Scratch that, I found the bug.

carolhsb commented 3 years ago

Hi Robert,

I've tried and it works...it splits the contigs

rvaser commented 3 years ago

You can pull the new commit and recompile. It should work now.

carolhsb commented 3 years ago

You can pull the new commit and recompile. It should work now.

Ok. I will do it.

Thank you so much!!

rvaser commented 3 years ago

Don't forget to run git submodule --update --recursive.

carolhsb commented 3 years ago

It's working now! :) thank you