Runing canu in conda environment in HPC, which one is the assembly contig file I that I should get?

[JWang52md]

I runing canu in conda environment in HPC (version 2.2), after running, it give me the output files seeing attached files, I just cannot find where are my assemblied contigs. This is my script: conda activate canu canu -d 2A -p 2A genomeSize=2.5m -nanopore cat_barcode12.fastq

[skoren]

I suspect it's running on the grid (https://canu.readthedocs.io/en/latest/faq.html#how-do-i-run-canu-on-my-slurm-sge-pbs-lsf-torque-system), what was the output of the command you ran? If it says submitted that is the case, you can turn off grid use with useGrid=false.

[alpapan]

@JWang52md when you run canu on a grid, without the use grid set to false, canu's command submits the scripts to the grid and then exits.

Assuming you submitted them correctly, you should check the job queue and wait for your jobs to finish.

[skoren]

Idle, answered above