Redmine

05/18/2018

01:41 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #52: Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Thank you Samson, I will have a look and get back to you.
Gerrit Gerrit Botha

05/17/2018

03:14 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Thank you Samson, I will have a look and get back to you. Gerrit Botha

02:12 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Reply from Samson on email
-----
*I am finalizing a README file, giving details of steps done for everyone to ... Gerrit Botha

01:59 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Hi Samson,
Please send me an example of the files you currently use to manually calculate the OTU adjustments and ... Gerrit Botha

01:56 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53 (New): Setup a decontamination pipeline for Mark's project

All 16S analysis from Mark's project follows an additional QC protocol that was originally suggested by guys from JCV... Gerrit Botha

02:54 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex

Katie I've renamed the repos to https://github.com/uct-cbio/RNAseq-pipeline . In your Git config you just need to mod... Gerrit Botha

02:52 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Hi Katie,
I've forked the HPCBIo repos to here: https://github.com/uct-cbio/16S-rDNA-dada2-pipeline . I've given y... Gerrit Botha

02:09 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Katie and Samson,
Chris has made their DADA2 Nextflow pipeline available here: https://github.com/HPCBio/dada2-Nex... Gerrit Botha

02:05 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54 (New): DADA2 workflow as an additional option for processing 16S data

As mentioned in the description of this project non OTU picking methods such as DADA2 seems to be the choice of many ... Gerrit Botha

01:43 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #52: Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Hi Samson,
I've uploaded the document Sugnet has shared with me regarding the issues that she is currently experie... Gerrit Botha

01:37 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #52 (New): Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Gerrit Botha, Nicki Tiffin and Ray Moholisa had a discussion with Mark Nicol and Sugnet Lubbe regarding their needs i... Gerrit Botha

04/26/2018

01:13 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup

Hi Katie,
Regarding metabat.
1. Yes it is dockerised but Hex does not support that so we would need to convert... Gerrit Botha

04/25/2018

03:24 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup

I met the developer of this workflow: https://github.com/alesssia/YAMP at the Nextflow workshop last year. I do not t... Gerrit Botha

02:46 PM Testing Redmine project features Bug #44 (New): Testing category assignment

Testing category assignment / so that we can distinguish between parts of the project. Gerrit Botha

11:55 AM Setting up a portable RNA-Seq pipeline for CBIO 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

04/24/2018

03:18 PM Setting up a portable RNA-Seq pipeline for CBIO 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

06:08 PM Testing Redmine project features Bug #41 (Resolved): Testing adding image inline

Gerrit Botha

06:07 PM Testing Redmine project features Bug #41: Testing adding image inline

OK seems like you need to attach an image to the ticket. I removed spacing and replaced with underscore, not sure if ... Gerrit Botha

05:53 PM Testing Redmine project features Bug #41: Testing adding image inline

Adding image inline
![](http://bst.cbio.uct.ac.za/redmine/attachme... Gerrit Botha

05:52 PM Testing Redmine project features Bug #41 (Resolved): Testing adding image inline

Testing adding image inline Gerrit Botha

05:46 PM Setting up a portable RNA-Seq pipeline for CBIO 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 Setting up a portable RNA-Seq pipeline for CBIO 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 Setting up a portable RNA-Seq pipeline for CBIO 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

04/20/2018

05:19 PM Setting up a portable RNA-Seq pipeline for CBIO 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 Setting up a portable RNA-Seq pipeline for CBIO 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 Setting up a portable RNA-Seq pipeline for CBIO 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 Setting up a portable RNA-Seq pipeline for CBIO 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