Username: $denisel0
Cluster: $Yggdrasil
I am trying to use ipyrad Welcome to ipyrad — ipyrad documentation but I get the following error. Prior to the Yggdrasil update, it worked well.
ipyrad [v.0.9.105]
Interactive assembly and analysis of RAD-seq data
Parallel connection |
Step 1: Demultiplexing fastq data to Samples
Encountered an Error.
Message: This operation requires engines. Try client.wait_for_engines(n) to wait for engines to register.
I also tried to debug as mentionned on the ipyrad FAQ with the following commands but the error remains the same.
$ echo “# Prevent ipyparallel engines from dying in a headless environment” >> ~/.bashrc
$ echo “export QT_QPA_PLATFORM=offscreen” >> ~/.bashrc
$ echo “export QT_QPA_PLATFORM=offscreen” >> ~/.profile
$ source ~/.bashrc
$ source ~/.profile
$ env | grep QT
These are the parameters I am using in my script:
#SBATCH --job-name ipyrad
#SBATCH --error %j.e.
#SBATCH --output %j.o.
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 12
#SBATCH --partition shared-bigmem
#SBATCH --time 10:00:00
Did anyone had similar issues with engines?
Many thanks
Elisa