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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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how to use the example files #116

Open wonaya opened 5 years ago

wonaya commented 5 years ago

Hi, I am testing racons with the test files you have on repository. I was wondering if you could help.

Currently getting error like this: $ racon -u --threads 48 sample_reads.fastq sample_overlaps.paf sample_reference.fasta WARNING: Not mounting /var/tmp (already mounted in container) [racon::Polisher::initialize] loaded target sequences [racon::Polisher::initialize] loaded sequences [racon::Polisher::initialize] error: empty overlap set! $ racon --version 1.3.2

rvaser commented 5 years ago

Hello, you have to run racon on sample data either with:

racon -u --threads 48 sample_reads.fastq sample_overlaps.paf sample_layout.fasta

or

racon -u --threads 48 -f sample_reads.fastq sample_ava_overlaps.paf sample_reads.fastq

sample_reference.fasta is used to calculate the edit distance between the consensus and the actual reference. You can also build racon_test which will run racon automatically on the test data. To obtain it add -Dracon_build_tests=ON while running cmake (run make afterwards).

Best regards, Robert

wonaya commented 5 years ago

Thank you!