Question: Canu ERROR: File supplied on command line; use -s, -pacbio-raw, -pacbio-corrected, -nanopore-raw, or -nanopore-corrected.
1
gravatar for lbrutscher
7 months ago by
lbrutscher10
lbrutscher10 wrote:

Hi everyone,

I am trying to assemble a bacterial genome using PacBio reads and short illumina reads from a metagenomic pool of both eurkaryotic host and bacterial sequences.

In an ideal world, I would have been able to culture the bacteria and obtain pure DNA to sequence and assemble from, but its cultivation has proved challenging. So, instead we have a ton of metagenomic data sequenced obtained from whole host DNA. We have roughly ~70 million Illumina MiSeq paired end reads (2x150) and ~120,000 PacBio reads (5-20 KB). I suspect that I have roughly 3x coverage of the bacterial genome with the PacBio reads and ~20-30x coverage with the illumina reads (with 80-90% of the reads likely being host). This project is further complicated by the fact that the host genome is not fully sequenced, so I cannot remove known host sequence to simplify analysis and de novo assembly.

I have been trying to use Canu 1.4 to correct my PacBio reads using fastq as input and the following code:

./canu -correct -pacbio-raw m170212_104155_42146_c101160022550000001823267305221711_s1_p0.3.subreads.fastq -d subreads3-auto -p subreads3 genomeSize=1.5m gnuplotTested=true  corMinCoverage=0 errorRate=0.035 corMaxEvidenceErate=0.15

But I keep getting this error: ERROR: File supplied on command line; use -s, -pacbio-raw, -pacbio-corrected, -nanopore-raw, or -nanopore-corrected.

It appears that Canu is not recognizing my input fastq file "m170212_104155_42146_c101160022550000001823267305221711_s1_p0.3.subreads.fastq". Has anyone else received this error and know what to do about it?

Thanks for any help you can provide!

canu pacbio assembly • 470 views
ADD COMMENTlink modified 11 weeks ago by knudnornielsen0 • written 7 months ago by lbrutscher10

Have you tried moving -pacbio-raw m170212_104155_42146_c101160022550000001823267305221711_s1_p0.3.subreads.fastq to the end of the command-line? Some programs are finicky about the order of input options. Also all those - are hyphens (i.e. not smart hyphens etc).

ADD REPLYlink written 7 months ago by genomax37k

Thanks for the response. Moving -pacbio-raw m170212_104155_42146_c101160022550000001823267305221711_s1_p0.3.subreads.fastq to the end does not help.

ADD REPLYlink written 7 months ago by lbrutscher10

Check your java version. Use full path to canu /Full/Path/to/bin/Canu

It will be better to show all your error log

ADD REPLYlink modified 7 months ago • written 7 months ago by xiachongjing10

Hi, I am experiencing exactly the same problem, when I try to run the tutorial on ecoli supplied on the CANU readthedocs http://canu.readthedocs.io/en/latest/quick-start.html. I download the supplied pacbio file and run the script, and then: ERROR: File supplied on command line; use -s, -pacbio-raw, -pacbio-corrected, -nanopore-raw, or -nanopore-corrected. Have you cracked this problem?

ADD REPLYlink written 11 weeks ago by knudnornielsen0

Any particular reason for using 1.4 instead of the latest release (1.6)?

edit. just realized OP posted quite a long time ago

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by 5heikki6.9k

When I'm experiencing the same problem now, it is with v1.6.

ADD REPLYlink written 11 weeks ago by knudnornielsen0
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