Nanopore data assembly with CANU

galaxy-local
assembly
ngs
tool-error
#1

Hello,

I’m trying to run an assembly on Nanopore raw reads (fastq) with the Canu 1.7.1 assembler. I tried on different servers, with my data and with public nanopore data from EMBL-EBI. I’m getting an error message from the tool every time : “Fatal error: Exit code 1 ()”.

Can someone tell me if the tool works or if it’s coming from me.

Thank you

1 Like
#2

Hi - Not sure if you worked the usage out or not yet, but I just tested the tool with some sample data from the tool author and everything processed fine at Galaxy EU https://usegalaxy.eu.

Shared history: https://usegalaxy.eu:/u/jenj/h/test-canu-nanopore-fastq

Expand the history annotation to see where I got the datasets and example command-line options. For the test jobs, I mapped over the command-line options to the tool form options without any other changes.

Hope that helps!