Setting up a portable RNA-Seq pipeline for CBIO

04/25/2018

12:57 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Thanks Gerrit,
Will go through the results and see at which steps we might want to adjust parameters. Yes it's fin... Katie Lennard

11:55 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

HI Katie,
This is good news, thanks for testing a complete run from beginning to end.
Also , thanks for openin... Gerrit Botha

10:51 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

Test run completed successfully! Input and output at /researchdata/fhgfs/katie/NGI-RNAseq-test/ (permissions open to ... Katie Lennard

04/24/2018

03:18 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Andrew has enabled sendmail to send emails from the compute nodes. I tested
~~~
gerrit@srvslshpc602:~> echo "Subj... Gerrit Botha

04/23/2018

05:46 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

The run completed successfully.
Here was the rest of the screen logs.
~~~
....
[50/552125] NOTE: Process `m... Gerrit Botha

01:03 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

OK the MarkDuplicates process ran out of memory. I added a section here: https://github.com/uct-cbio/RNAseq/commit/71... Gerrit Botha

11:42 AM Support #25: Configure NGI-RNAseq pipeline to run on hex

STAR alignment on sample38 and 39 completed successfully. It now however failed on running Picard MarkDuplicates. Can... Gerrit Botha

05:29 PM Screenshot from 2018-04-23 17-29-13.png

RNAseq results output Gerrit Botha

04/20/2018

05:19 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

The core settings were stuck to ppn=16. This was because the default max core settings were set to 16. Added a defaul... Gerrit Botha

04:15 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

I've added STAR requirements to use 40 cores on the first run attempt. With 40 cores we will be able to access 80GB R... Gerrit Botha

12:53 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

The STAR job on sample38 failed again.
~~~
PBS Job Id: 1841542.srvslshpc001
Job Name: sample39
Exec host: sr... Gerrit Botha

04/19/2018

01:11 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

I've been looking a few things over the last 2 days. Just did not get time to record it.
The maxRetries setting di... Gerrit Botha

04/17/2018

02:26 PM Support #25: Configure NGI-RNAseq pipeline to run on hex

Hi Katie.
It seems like I found the issue why it was not submitting to PBS. The ```executer``` setting should have... Gerrit Botha