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

01:28 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 Gerrit,
I have finished commenting on the google document you have shared.
Samson Samson Kilaza

05/17/2018

03:37 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Yeah, I have tried to run the tutorial dataset online (https://benjjneb.github.io/dada2/tutorial.html) using R on my ... Samson Kilaza

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

02:20 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #54: DADA2 workflow as an additional option for processing 16S data

Hi Gerrit,
Yes I'm keen to help with this and test on the WISH dataset.
Katie Lennard

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

03:21 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

Thanks Samson Kilaza

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

03:13 PM Setting up a portable 16S rDNA pipeline for CBIO Feature #53: Setup a decontamination pipeline for Mark's project

I have attached some files and steps to be done.
Still, I may clarify if this is not enough
Thanks Samson Kilaza

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

02:13 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,
I am working on the shared document.
Samson Samson Kilaza

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

05/16/2018

02:41 PM Setting up a portable metagenome assembly pipeline for CBIO Support #50: Validate binning using single copy core genes

checkM successfully run on hex. Example outputs listed under the 'Files' tab (checkm.e1851691.txt and checkm.o1851691... Katie Lennard

05/11/2018

11:37 AM Setting up a portable metagenome assembly pipeline for CBIO Support #50 (New): Validate binning using single copy core genes

The quality of the binning results from CONCOCT can be examined by looking at single copy core genes (i.e. genes that... Katie Lennard

05/08/2018

04:03 PM Testing Redmine project features Support #7: Support ticket 1

Just testing adding update as another user (non admin privileges). Want to see if I can edit afterwords.
Ok enable... Gerrit Botha2

04/30/2018

11:42 AM Setting up a portable metagenome assembly pipeline for CBIO Bug #46 (New): Read binning with CONCOCT

CONCOCT “bins” metagenomic contigs. Metagenomic binning is the process of clustering sequences into clusters correspo... Katie Lennard

04/26/2018

04:39 PM Setting up a portable metagenome assembly pipeline for CBIO Support #45 (New): Quality trimming with Trimmomatic

In short after a bit of a struggle to optimize parameters for quality trimming with Trimmomatic I recommend rather us... Katie Lennard

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

09:51 AM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup

Thanks Gerrit,
This workflow https://bitbucket.org/berkeleylab/metabat is also an option - it is dockerised, uses ... Katie Lennard

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

12:57 PM Setting up a portable RNA-Seq pipeline for CBIO 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 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

10:51 AM Setting up a portable RNA-Seq pipeline for CBIO 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 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

03:35 PM Setting up a portable metagenome assembly pipeline for CBIO Support #38 (New): How to download SRA files to hex

How to download input files (testdata) from SRA to hex:
Use sra-tools installed on hex (activate by doing ‘load modu... Katie Lennard

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

12:49 PM Setting up the BST helpdesk Feature #34 (New): Add ticket type

Add a new field to the tickets, their "Type"
The type can be:
* Query (or something else)
* Support request
* P... Jon Ambler

12:34 PM Setting up the BST helpdesk Feature #33 (Resolved): Adding time tracking to the tickets

Time tracking has now been added.
To log time, just add the time in the comment in the format:
Time: <number> ... Jon Ambler