B1 Ocean project

NBIS project id #6005

Log

• 2022-01-21

Workflow will be restarted on Rackham using the config/myconfig_R-samples.yaml configfile. However, the time limit should be updated on the pfam_scan rule as it seems to be taking longer than expected for a few assemblies.

The config/cluster.yaml file should be updated to contain:

pfam_scan:
  time: 14400

The work directory should probably be unlocked as well. Then the workflow can be restarted with (remember to remove the -n flag):

snakemake --profile slurm --use-conda --configfile config/myconfig_R-samples.yaml -j 100 -rpk -n annotate

• November - December 2021

Project was set up on Rackham under /crex/proj/snic2020-6-126/nobackup/nbis-meta-2.3.2.

The nbis-meta workflow (v. 2.3.2) was downloaded from GitHub. The conda environment was installed under /crex/proj/snic2020-6-126/nobackup/envs/nbis-meta using command:

mkdir envs
conda env create -f environment.yml -p envs/nbis-meta

Config and sample files were set up as config/myconfig.yaml and sample_list_user-ids.tsv, respectively.

Preprocessing

Preprocessing was run with cutadapt as:

snakemake --profile slurm --use-conda --configfile config/myconfig.yaml -j 100 -rpk -n qc

Assembly

Assembly was run with megahit as:

snakemake --profile slurm --use-conda --configfile config/myconfig.yaml -j 100 -rpk -n assemble

Annotation

After this, an attempt at annotating the 'R' samples was made using a configfile config/myconfig_R-samples.yaml:

snakemake --profile slurm --use-conda --configfile config/myconfig_R-samples.yaml -j 100 -rpk -n annotate

However, the *.bam files generated by the workflow used up ~7TB of disk space causing the project to hit the uquota limit around Dec 28, 2021. This also caused the workflow to fail as files could no longer be moved from local node storage to the project directory.