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Canu

A single molecule sequence assembler for large and small geonomes.

Usage

To use the default version of canu:

$ module load canu
$ canu

usage: canu [-correct | -trim | -assemble | -trim-assemble] \
            [-s <assembly-specifications-file>] \
            -p <assembly-prefix> \
            -d <assembly-directory> \
            genomeSize=<number>[g|m|k] \
            [other-options] \
            [-pacbio-raw | -pacbio-corrected | -nanopore-raw | -nanopore-corrected] \
            <files.fastq>

  The assembly is computed in the (created) -d <assembly-directory>, with most
  files named using the -p <assembly-prefix>.

  The genome size is your best guess of the genome size of what is being assembled.
  It is used mostly to compute coverage in reads.  Fractional values are
  allowed: '4.7m' is the same as '4700k' and '4700000'.

For full usage documentation, run canu --help.

Error message - Gatekeeper detected problems in your input reads

To resolve this error message, supplement each dataset with Illumina reads. Renaming the files in <assembly-directory>/correction or using the stopOnReadQuality=false option will produce an undesirable assembly.

When executing a canu command just like the one above, an Apocrita submission script is created and submitted. This script is available under: <assembly-directory>/canu-scripts/canu.N.sh where N is an incremented number used internally by canu to distinguish between Apocrita submissions.

This script contains the canu parameters passed via the first command and is submitted as a new job on Apocrita to start the canu sequence assembler. The output of this second script is written to: <assembly-directory>/canu-scripts/canu.N.out.

Example job

canu is unusual compared to other applications on Apocrita. Typically we expect users to prepare submissions scripts and use the qsub command to submit them.

canu creates the script and submits it automatically.

Serial job

Here is an example canu command which will submit an Apocrita job running with 4 cores and 8GB total memory (default is 1 core and 4G memory), using the gnuplot and java binaries loaded via the modulefile:

$ canu gridOptions='-l h_vmem=8G -pe smp 4' -p 'Ppal' -d 'output' \
       -nanopore-raw data.fq 'genomeSize=300M' gnuplot=$(which gnuplot) \
       java=$(which java)

When you run this command it will generate a script that should look something like this:

qsub \
      -l h_vmem=4g \
      -pe smp 1 \
      -l h_vmem=8G \
      -pe smp 4  \
      -cwd \
      -N 'canu_Ppal' \
      -j y \
      -o /data/home/abc/canu/output/canu-scripts/canu.01.out \
      /data/home/abc/canu/output/canu-scripts/canu.01.sh

You can see above that canu has duplicated the h_vmem and smp arguments, which may be confusing for experienced users but you shouldn't need to worry about that.

The qsub command will automatically be executed, so a new Apocrita job will be launched. The output of the second job is written to: /data/home/abc/canu/output/canu-scripts/canu.01.out which is symlinked in the parent directory.

References