# Canu FAQ¶

## What resources does Canu require for a bacterial genome assembly? A mammalian assembly?¶

Canu will detect available resources and configure itself to run efficiently using those resources. It will request resources, for example, the number of compute threads to use, Based on the genome size being assembled. It will fail to even start if it feels there are insufficient resources available.

A typical bacterial genome can be assembled with 8GB memory in a few CPU hours - around an hour on 8 cores. It is possible, but not allowed by default, to run with only 4GB memory.

A well-behaved large genome, such as human or other mammals, can be assembled in 10,000 to 25,000 CPU hours, depending on coverage. A grid environment is strongly recommended, with at least 16GB available on each compute node, and one node with at least 64GB memory. You should plan on having 3TB free disk space, much more for highly repetitive genomes.

Our compute nodes have 48 compute threads and 128GB memory, with a few larger nodes with up to 1TB memory. We develop and test (mostly bacteria, yeast and drosophila) on laptops and desktops with 4 to 12 compute threads and 16GB to 64GB memory.

## How do I run Canu on my SLURM / SGE / PBS / LSF / Torque system?¶

Canu will detect and configure itself to use on most grids. Canu will NOT request explicit time limits or queues/partitions. You can supply your own grid options, such as a partition on SLURM, an account code on SGE, and/or time limits with gridOptions="<your options list>" which will passed to every job submitted by Canu. Similar options exist for every stage of Canu, which could be used to, for example, restrict overlapping to a specific partition or queue.

To disable grid support and run only on the local machine, specify useGrid=false

It is possible to limit the number of grid jobs running at the same time, but this isn’t directly supported by Canu. The various gridOptions parameters can pass grid-specific parameters to the submit commands used; see Issue #756 for Slurm and SGE examples.

## My run stopped with the error 'Mhap precompute jobs failed'¶

Several package managers make a mess of the installation causing this error (conda and ubuntu in particular). Package managers don’t add much benefit to a tool like Canu which is distributed as pre-compiled binaries compatible with most systems so our recommended installation method is downloading a binary release. Try running the assembly from scratch using our release distribution and if you continue to encounter errors, submit an issue.

## My run stopped with the error 'Failed to submit batch jobs'¶

The grid you run on must allow compute nodes to submit jobs. This means that if you are on a compute host, qsub/bsub/sbatch/etc must be available and working. You can test this by starting an interactive compute session and running the submit command manually (e.g. qsub on SGE, bsub on LSF, sbatch on SLURM).

If this is not the case, Canu WILL NOT work on your grid. You must then set useGrid=false and run on a single machine. Alternatively, you can run Canu with useGrid=remote which will stop at every submit command, list what should be submitted. You then submit these jobs manually, wait for them to complete, and run the Canu command again. This is a manual process but currently the only workaround for grids without submit support on the compute nodes.

## My run of Canu was killed by the sysadmin; the power going out; my cat stepping on the power button; et cetera. Is it safe to restart? How do I restart?¶

Yes, perfectly safe! It’s actually how Canu runs normally: each time Canu starts, it examines the state of the assembly to decide what it should do next. For example, if six overlap tasks have no results, it’ll run just those six tasks.

This also means that if you want to redo some step, just remove those results from the assembly directory. Some care needs to be taken to make sure results computed after those are also removed.

Short answer: just rerun the _exact_ same command as before. It’ll do the right thing.

## My genome size and assembly size are different, help!¶

The difference could be due to a heterozygous genome where the assembly separated some loci. It could also be because the previous estimate is incorrect. We typically use two analyses to see what happened. First, a BUSCO analysis will indicate duplicated genes. For example this assembly:

INFO      C:98.5%[S:97.9%,D:0.6%],F:1.0%,M:0.5%,n:2799
INFO      2756 Complete BUSCOs (C)
INFO      2740 Complete and single-copy BUSCOs (S)
INFO      16 Complete and duplicated BUSCOs (D)


does not have much duplication but this assembly:

INFO      C:97.6%[S:15.8%,D:81.8%],F:0.9%,M:1.5%,n:2799
INFO      2732 Complete BUSCOs (C)
INFO      443 Complete and single-copy BUSCOs (S)
INFO      2289 Complete and duplicated BUSCOs (D)


does. We have had some success (in limited testing) using purge_haplotigs to remove duplication. Purge haplotigs will also generate a coverage plot which will usually have two peaks when assemblies have separated some loci.

## What parameters should I use for my reads?¶

Canu is designed to be universal on a large range of PacBio (C2, P4-C2, P5-C3, P6-C4) and Oxford Nanopore (R6 through R9) data. Assembly quality and/or efficiency can be enhanced for specific datatypes:

Nanopore R7 1D and Low Identity Reads

With R7 1D sequencing data, and generally for any raw reads lower than 80% identity, five to ten rounds of error correction are helpful:

canu -p r1 -d r1 -correct corOutCoverage=500 corMinCoverage=0 corMhapSensitivity=high -nanopore-raw your_reads.fasta
canu -p r2 -d r2 -correct corOutCoverage=500 corMinCoverage=0 corMhapSensitivity=high -nanopore-raw r1/r1.correctedReads.fasta.gz
canu -p r3 -d r3 -correct corOutCoverage=500 corMinCoverage=0 corMhapSensitivity=high -nanopore-raw r2/r2.correctedReads.fasta.gz
canu -p r4 -d r4 -correct corOutCoverage=500 corMinCoverage=0 corMhapSensitivity=high -nanopore-raw r3/r3.correctedReads.fasta.gz
canu -p r5 -d r5 -correct corOutCoverage=500 corMinCoverage=0 corMhapSensitivity=high -nanopore-raw r4/r4.correctedReads.fasta.gz


Then assemble the output of the last round, allowing up to 30% difference in overlaps:

canu -p asm -d asm correctedErrorRate=0.3 utgGraphDeviation=50 -nanopore-corrected r5/r5.correctedReads.fasta.gz

Nanopore R7 2D and Nanopore R9 1D
The defaults were designed with these datasets in mind so they should work. Having very high coverage or very long Nanopore reads can slow down the assembly significantly. You can try the overlapper=mhap utgReAlign=true option which is much faster but may produce less contiguous assemblies on large genomes.
Nanopore R9 2D and PacBio P6
Slightly decrease the maximum allowed difference in overlaps from the default of 12% to 10.5% with correctedErrorRate=0.105
PacBio Sequel V2
Based on an A. thaliana dataset, and a few more recent mammalian genomes, slightly increase the maximum allowed difference from the default of 4.5% to 8.5% with correctedErrorRate=0.085 corMhapSensitivity=normal.

Only add the second parameter (corMhapSensivity=normal) if you have >50x coverage.

PacBio Sequel V3
The defaults for PacBio should work on this data.
Nanopore R9 large genomes
Due to some systematic errors, the identity estimate used by Canu for correction can be an over-estimate of true error, inflating runtime and disk usage. The newest releases should automatically adjust for this but if you are using Canu 1.6 or older you can try 'corMhapOptions=--threshold 0.8 --ordered-sketch-size 1000 --ordered-kmer-size 14'.

## Can I assemble RNA sequence data?¶

Canu will likely mis-assemble, or completely fail to assemble, RNA data. It will do a reasonable job at generating corrected reads though. Reads are corrected using (local) best alignments to other reads, and alignments between different isoforms are usually obviously not ‘best’. Just like with DNA sequences, similar isoforms can get ‘mixed’ together. We’ve heard of reasonable success from users, but do not have any parameter suggestions to make.

Note that Canu will silently translate ‘U’ bases to ‘T’ bases on input, but NOT translate the output bases back to ‘U’.

## My assembly is running out of space, is too slow?¶

We don’t have a good way to estimate of disk space used for the assembly. It varies with genome size, repeat content, and sequencing depth. A human genome sequenced with PacBio or Nanopore at 40-50x typically requires 1-2TB of space at the peak. Plants, unfortunately, seem to want a lot of space. 10TB is a reasonable guess. We’ve seen it as bad as 20TB on some very repetitive genomes.

The most common cause of high disk usage is a very repetitive or large genome. There are some parameters you can tweak to both reduce disk space and speed up the run. Try adding the options corMhapFilterThreshold=0.0000000002 corMhapOptions="--threshold 0.80 --num-hashes 512 --num-min-matches 3 --ordered-sketch-size 1000 --ordered-kmer-size 14 --min-olap-length 2000 --repeat-idf-scale 50" mhapMemory=60g mhapBlockSize=500 ovlMerDistinct=0.975. This will suppress repeats more than the default settings and speed up both correction and assembly.

It is also possible to clean up some intermediate outputs before the assembly is complete to save space. If you already have a *.ovlStore.BUILDING/1-bucketize.successs file in your current step (e.g. correct), you can clean up the files under 1-overlapper/blocks. You can also remove the ovlStore for the previous step if you have its output (e.g. if you have asm.trimmedReads.fasta.gz, you can remove trimming/asm.ovlStore).

## My assembly continuity is not good, how can I improve it?¶

The most important determinant for assembly quality is sequence length, followed by the repeat complexity/heterozygosity of your sample. The first thing to check is the amount of corrected bases output by the correction step. This is logged in the stdout of Canu or in canu-scripts/canu.*.out if you are running in a grid environment. For example on a haploid H. sapiens sample:

-- BEGIN TRIMMING
--
...
-- In gatekeeper store 'chm1/trimming/asm.gkpStore':
--   Found 91697412754 bases (29.57 times coverage).
...


Canu tries to correct the longest 40X of data. Some loss is normal but having output coverage below 20-25X is a sign that correction did not work well (assuming you have more input coverage than that). If that is the case, re-running with corMhapSensitivity=normal if you have >50X or corMhapSensitivity=high corMinCoverage=0 otherwise can help. You can also increase the target coverage to correct corOutCoverage=100 to get more correct sequences for assembly. If there are sufficient corrected reads, the poor assembly is likely due to either repeats in the genome being greater than read lengths or a high heterozygosity in the sample. Stay tuned for mor information on tuning unitigging in those instances.

## What parameters can I tweak?¶

For all stages:

• rawErrorRate is the maximum expected difference in an alignment of two _uncorrected_ reads. It is a meta-parameter that sets other parameters.
• correctedErrorRate is the maximum expected difference in an alignment of two _corrected_ reads. It is a meta-parameter that sets other parameters. (If you’re used to the errorRate parameter, multiply that by 3 and use it here.)
• minReadLength and minOverlapLength. The defaults are to discard reads shorter than 1000bp and to not look for overlaps shorter than 500bp. Increasing minReadLength can improve run time, and increasing minOverlapLength can improve assembly quality by removing false overlaps. However, increasing either too much will quickly degrade assemblies by either omitting valuable reads or missing true overlaps.

For correction:

• corOutCoverage controls how much coverage in corrected reads is generated. The default is to target 40X, but, for various reasons, this results in 30X to 35X of reads being generated.
• corMinCoverage, loosely, controls the quality of the corrected reads. It is the coverage in evidence reads that is needed before a (portion of a) corrected read is reported. Corrected reads are generated as a consensus of other reads; this is just the minimum coverage needed for the consensus sequence to be reported. The default is based on input read coverage: 0x coverage for less than 30X input coverage, and 4x coverage for more than that.

For assembly:

• utgOvlErrorRate is essentially a speed optimization. Overlaps above this error rate are not computed. Setting it too high generally just wastes compute time, while setting it too low will degrade assemblies by missing true overlaps between lower quality reads.
• utgGraphDeviation and utgRepeatDeviation what quality of overlaps are used in contig construction or in breaking contigs at false repeat joins, respectively. Both are in terms of a deviation from the mean error rate in the longest overlaps.
• utgRepeatConfusedBP controls how similar a true overlap (between two reads in the same contig) and a false overlap (between two reads in different contigs) need to be before the contig is split. When this occurs, it isn’t clear which overlap is ‘true’ - the longer one or the slightly shorter one - and the contig is split to avoid misassemblies.

For polyploid genomes:

Generally, there’s a couple of ways of dealing with the ploidy.

1. Avoid collapsing the genome so you end up with double (assuming diploid) the genome size as long as your divergence is above about 2% (for PacBio data). Below this divergence, you’d end up collapsing the variations. We’ve used the following parameters for polyploid populations (PacBio data):

corOutCoverage=200 "batOptions=-dg 3 -db 3 -dr 1 -ca 500 -cp 50"

This will output more corrected reads (than the default 40x). The latter option will be more conservative at picking the error rate to use for the assembly to try to maintain haplotype separation. If it works, you’ll end up with an assembly >= 2x your haploid genome size. Post-processing using gene information or other synteny information is required to remove redundancy from this assembly.

2. Smash haplotypes together and then do phasing using another approach (like HapCUT2 or whatshap or others). In that case you want to do the opposite, increase the error rates used for finding overlaps:

corOutCoverage=200 correctedErrorRate=0.15

When trimming, reads will be trimmed using other reads in the same chromosome (and probably some reads from other chromosomes). When assembling, overlaps well outside the observed error rate distribution are discarded.

We typically prefer option 1 which will lead to a larger than expected genome size. We have had some success (in limited testing) using purge_haplotigs to remove this duplication.

For metagenomes:

The basic idea is to use all data for assembly rather than just the longest as default. The parameters we’ve used recently are:

corOutCoverage=10000 corMhapSensitivity=high corMinCoverage=0 redMemory=32 oeaMemory=32 batMemory=200

For low coverage:

• For less than 30X coverage, increase the alllowed difference in overlaps by a few percent (from 4.5% to 8.5% (or more) with correctedErrorRate=0.105 for PacBio and from 14.4% to 16% (or more) with correctedErrorRate=0.16 for Nanopore), to adjust for inferior read correction. Canu will automatically reduce corMinCoverage to zero to correct as many reads as possible.

For high coverage:

• For more than 60X coverage, decrease the allowed difference in overlaps (from 4.5% to 4.0% with correctedErrorRate=0.040 for PacBio, from 14.4% to 12% with correctedErrorRate=0.12 for Nanopore), so that only the better corrected reads are used. This is primarily an optimization for speed and generally does not change assembly continuity.

## My asm.contigs.fasta is empty, why?¶

Canu creates three assembled sequence output files: <prefix>.contigs.fasta, <prefix>.unitigs.fasta, and <prefix>.unassembled.fasta, where contigs are the primary output, unitigs are the primary output split at alternate paths, and unassembled are the leftover pieces.

The contigFilter parameter sets several parameters that control how small or low coverage initial contigs are handled. By default, initial contigs with more than 50% of the length at less than 3X coverage will be classified as ‘unassembled’ and removed from the assembly, that is, contigFilter="2 0 1.0 0.5 3". The filtering can be disabled by changing the last number from ‘3’ to ‘0’ (meaning, filter if 50% of the contig is less than 0X coverage).

## Why is my assembly is missing my favorite short plasmid?¶

In Canu v1.6 and earlier only the longest 40X of data (based on the specified genome size) is used for correction. Datasets with uneven coverage or small plasmids can fail to generate enough corrected reads to give enough coverage for assembly, resulting in gaps in the genome or even no reads for small plasmids. Set corOutCoverage=1000 (or any value greater than your total input coverage) to correct all input data.

An alternate approach is to correct all reads (-correct corOutCoverage=1000) then assemble 40X of reads picked at random from the <prefix>.correctedReads.fasta.gz output.

More recent Canu versions dynamically select poorly represented sequences to avoid missing short plasmids so this should no longer happen.

## Why do I get less corrected read data than I asked for?¶

Some reads are trimmed during correction due to being chimeric or because there wasn’t enough evidence to generate a quality corrected sequence. Typically, this results in a 25% loss. Setting corMinCoverage=0 will report all bases, even low those of low quality. Canu will trim these in its ‘trimming’ phase before assembly.

## What is the minimum coverage required to run Canu?¶

For eukaryotic genomes, coverage more than 20X is enough to outperform current hybrid methods. Below that, you will likely not assemble the full genome. The following two papers have several examples.

## Can I use Illumina data too?¶

No. We’ve seen that using short reads for correction will homogenize repeats and mix up haplotypes. Even though the short reads are very high quality, their length isn’t sufficient for the true alignment to be identified, and so reads from other repeat instances are used for correction, resulting in incorrect corrections.

## My circular element is duplicated/has overlap?¶

This is expected for any circular elements. They can overlap by up to a read length due to how Canu constructs contigs. Canu provides an alignment string in the GFA output which can be converted to an alignment to identify the trimming points.

An alternative is to run MUMmer to get self-alignments on the contig and use those trim points. For example, assuming the circular element is in tig00000099.fa. Run:

nucmer -maxmatch -nosimplify tig00000099.fa tig00000099.fa
show-coords -lrcTH out.delta


to find the end overlaps in the tig. The output would be something like:

1 1895    48502   50400   1895    1899    99.37   50400   50400   3.76    3.77    tig00000001     tig00000001
48502     50400   1       1895    1899    1895    99.37   50400   50400   3.77    3.76    tig00000001     tig00000001


means trim to 1 to 48502. There is also an alternate writeup.

## My genome is AT (or GC) rich, do I need to adjust parameters? What about highly repetitive genomes?¶

On bacterial genomes, no adjustment of parameters is (usually) needed. See the next question.

On repetitive genomes with with a significantly skewed AT/GC ratio, the Jaccard estimate used by MHAP is biased. Setting corMaxEvidenceErate=0.15 is sufficient to correct for the bias in our testing.

In general, with high coverage repetitive genomes (such as plants) it can be beneficial to set the above parameter anyway, as it will eliminate repetitive matches, speed up the assembly, and sometime improve unitigs.

## How can I send data to you?¶

FTP to ftp://ftp.cbcb.umd.edu/incoming/sergek. This is a write-only location that only the Canu developers can see.

Here is a quick walk-through using a command-line ftp client (should be available on most Linux and OSX installations). Say we want to transfer a file named reads.fastq. First, run ftp ftp.cbcb.umd.edu, specify anonymous as the user name and hit return for password (blank). Then cd incoming/sergek, put reads.fastq, and quit.

That’s it, you won’t be able to see the file but we can download it.