kesiaeds

Hi I had to delete this part from the config file: ``` ''' Notes: 'no_check' is for switching off the user check at the start of the run. This enables...

It is rubra version 0.1.5 and I'm using SCG Informatics Cluster https://login.scg.stanford.edu/

Sorry, do you mean I have to ask them to install another version of rubra? This one? https://github.com/bjpop/rubra/tree/slurm

Hi We installed Rubra-0.1.5 from the slurm branch as you suggested and the pipeline started to run, however, we got another error message: `Starting pipeline... 70 jobs to be executed...

I have changed the modules in the config file for the local installation and I also removed the #'s from sequence names but I'm still getting the same error message....

These files were not created. The only files that were created in the log folder were: makeDir.sh makeRef.sh pipeline.log

Hi I had to add the following information to makeDir.sh file to run via batch outside the pipeline: #!/bin/bash #SBATCH --job-name=makedir #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=4 #SBATCH --partition=interactive #SBATCH...

Hi David, Thank you so much for your email. I changed my config file following your suggestions and I could run the pipeline in two samples to test and worked....

Hi David, I download all the RedDog files again and I used the https://github.com/katholt/RedDog/blob/master/RedDog_config_massive.py as the config file.... this time the pipeline started but failed at check bam stage. Here...

Hi David, Hope you are doing well. I download my dataset again and ran the pipeline. This time the pipeline successfully passed the check bam stage, however I am getting...