Activity

From 04/10/2018 to 05/09/2018

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

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

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

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

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

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

05:05 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: For now I do not think we will make changes on the main code. So yes, all that we would need to do is merge the main ... Gerrit Botha
04:50 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: Aha, yes you're right - if we specify -r dev with the run (using our repo fork) it does pick up the uct_hex profile. ... Katie Lennard
04:44 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: Hi Katie,
Everything is on the ```dev``` branch: https://github.com/uct-cbio/RNAseq/tree/dev . So should things no... Gerrit Botha
04:31 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: Gerrit I see even though you noticed that the uct_hex.conf was only on the dev branch it looks like the master branch... Katie Lennard
03:55 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: I've tested the custom build singularity image described above. This specific repository (https://github.com/nf-core/... Katie Lennard

05:28 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: Thanks Gerrit, much appreciated - I'll go through this and do some testing on the new image. Katie Lennard
05:04 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: Hi Katie,
I did the following.
1. Made a fork of the stable RNASeq pipeline to here: https://github.com/uct-cbi... Gerrit Botha

11:41 AM Support #25: Configure NGI-RNAseq pipeline to run on hex: Katie if this is the Docker file you are using https://github.com/ewels/nf-core-RNAseq/blob/master/Dockerfile you wou... Gerrit Botha
11:28 AM Support #25: Configure NGI-RNAseq pipeline to run on hex: Katie Lennard wrote:
> Oh dear..Ok we'll have to get rebuild the image then I guess..See latest response from Phil o... Katie Lennard
11:23 AM Support #25: Configure NGI-RNAseq pipeline to run on hex: Oh dear..Ok we'll have to get rebuild the image then I guess..See latest response from Phil on this https://github.co... Katie Lennard
11:18 AM Support #25: Configure NGI-RNAseq pipeline to run on hex: OK that is fine Katie.
Just on the overlay issue. Overlayfs is only available for kernel 3.18 or higher: https://w... Gerrit Botha
11:11 AM Support #25: Configure NGI-RNAseq pipeline to run on hex: Hi Gerrit,
At the moment the main problem is that I can't download the development version of the Singularity imag... Katie Lennard
10:55 AM Support #25: Configure NGI-RNAseq pipeline to run on hex: Hi Katie,
1. Can you please point me to the Docker / Singularity file on GitHub which you have an issue with?
2... Gerrit Botha

05:33 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: Gerrit Botha wrote:
> So what happens if you do use the ```--size``` flag with a rough estimate of the container siz... Katie Lennard
02:22 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: So what happens if you do use the ```--size``` flag with a rough estimate of the container size?
Ok, try running t... Gerrit Botha
01:41 PM Support #25: Configure NGI-RNAseq pipeline to run on hex: Development branch with custom 'uct_hex' profile up and running but having issues with the singularity image specifie... Katie Lennard

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Setting up a portable RNA-Seq pipeline for CBIO