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This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.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

HTSeq through module rcbio/1.3.3

Owned by Lingsheng Dong
Last updated: Dec 11, 2023
2 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

Make alignment using: STAR through module rcbio/1.1 , bowtie2 through module rcbio/1.1 or bwa through module rcbio/1.1 

After alignment finishes, go to that folder, for example star

cd /n//users/a/abc123/star

Copy the example htseq bash script:

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

Now you can modify the options as needed. For example, if your file are huge, you may need increase mem and runtime -t for sbatch command. 

To edit the htseq bash script:

To test the pipeline run the following command if you did alignment by bwa as on this page. If you did alignment using bowtie2 following this page, please change -p bwaOut to -p bowtieOut, or if you used star following this page, please change -p bwaOut to -p starOut. 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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