I have access to a cluster with 60GB RAM and 12 processors. I’ve been asked to not use the cluster in interactive mode. I never used mothur in batch mode, and less I used slurm or a cluster.
-I have my home folder in the main node, with 100Gb store for my files (/home/svazquez)
-I have to run mothur from anaconda3, they have the last version so I’m fine.
-The administrator placed mothur databases in a separate storage node (/share/databases/references/mothur)
-To have enough storage capacity during running, I should use a third compute node copying the files from my home folder into the /scratch forlder in this compute-0-1 node
- The files with the raw reads should be stored in the storage node, in a different folder than the databases are (/rawdata/reads)
I don´t know how I should write the script for slurm and the batch file for mothur following the MiSeq SOP (or any pipeline working with 2x300 bp Miseq amplicon reads), to work with the different files stored in the different paths.
Can anyone help me with this? Please?