NOTICE: FULL O2 Cluster Outage, January 3 - January 10th

O2 will be completely offline for a planned HMS IT data center relocation from Friday, Jan 3, 6:00 PM, through Friday, Jan 10

  • on Jan 3 (5:30-6:00 PM): O2 login access will be turned off.
  • on Jan 3 (6:00 PM): O2 systems will start being powered off.

This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.

Specifically:

  • The O2 Cluster will be completely offline, including O2 Portal.
  • All data on O2 will be inaccessible.
  • Any jobs still pending when the outage begins will need to be resubmitted after O2 is back online.
  • Websites on O2 will be completely offline, including all web content.

More details at: https://harvardmed.atlassian.net/l/cp/1BVpyGqm & https://it.hms.harvard.edu/news/upcoming-data-center-relocation

Bwa through module rcbio/1.3.3

Owned by Lingsheng Dong
Last updated: Dec 11, 2023
1 min read

Start an interactive job, with a walltime of 2 hours, 2000MB of memory. 

srun --pty -p interactive -t 0-02:0:0 --mem 2000MB -n 1 /bin/bash

Create a working directory on scratch and change into the newly-created directory. For example, for user abc123, the working directory will be

mkdir /n/scratch/users/a/abc123/bwa cd /n/scratch/users/a/abc123/bwa


Copy some test data following this page: Build Folder Structures From Sample Sheet for rcbio NGS Workflows page.

Copy the example bwa bash script:

module load gcc/6.2.0 python/2.7.12 rcbio/1.3.3 cp /n/app/rcbio/1.1/bin/bwa.sh .



Now you can modify the options as needed. Please reference the bwa user manual if you have any questions.

To edit the bwa script:

To test the pipeline run the following command. Jobs will not be submitted to the scheduler.

To run the pipeline:

To understand how 'runAsPipeline' works, how to check output, how to re-run the pipeline, please visit: Run Bash Script As Slurm Pipeline

Now you are ready to run an rcbio workflow

To instead run the workflow on your own data, transfer the sample sheet to your local machine following this wiki page and modify the sample sheet. Then you can transfer it back to O2 under your account, then go to the build folder structure step.

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