ERROR: File supplied on command line; use -s, -pacbio-raw, -pacbio-corrected, -nanopore-raw, or -nanopore-corrected

Question

[knudnornielsen]

Hi everyone, I have tried to run the tutorial on ecoli supplied on the CANU readthedocs http://canu.readthedocs.io/en/latest/quick-start.html. I downloaded 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 anyone experienced this before or have a explanation?

[Brian Bushnell]

I've never used CANU, but have you tried adding the flag "-pacbio-raw"?

[knudnornielsen]

I just tried it, and it didn't help.

[1234anjalianjali1234]

got answer? having same problem

Answer 1

[lagartija]

I use these flags for the inputs and it works. Are you sure that you have correctly downloaded the fastq or fasta file ? Can you copy your entire canu command so we can see ?