Activity
From 04/03/2018 to 05/02/2018
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...
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...
- 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... - 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 ...
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...
- 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.
- 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... - 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... - 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 ...
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...
04/23/2018
- 06:08 PM Testing Redmine project features Bug #41 (Resolved): Testing adding image inline
- 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 ...
- 05:53 PM Testing Redmine project features Bug #41: Testing adding image inline
- Adding image inline
: Testing adding image inline
- Testing adding image inline
- 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... - 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...
- 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...
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...
- 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...
- 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... - 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...
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... - 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... - 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> ...
04/17/2018
- 04:51 PM Setting up the BST helpdesk Feature #33 (In Progress): Adding time tracking to the tickets
- A potential option is to have a keyword in the ticket comment that can be picked up and parsed by a function. This me...
- 04:45 PM Setting up the BST helpdesk Feature #33 (Resolved): Adding time tracking to the tickets
- In order to be able to repost the time we responding on different tasks, we need to be able to log time spent on tick...
- 04:42 PM Setting up the BST helpdesk Feature #29 (Closed): Create list of research groups to appear for ticket submission.
- 04:42 PM Setting up the BST helpdesk Feature #11 (Closed): Add email system
- 02:26 PM Setting up a portable RNA-Seq pipeline for CBIO 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...
04/16/2018
- 05:05 PM Setting up a portable RNA-Seq pipeline for CBIO 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 ...
- 04:50 PM Setting up a portable RNA-Seq pipeline for CBIO 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. ...
- 04:44 PM Setting up a portable RNA-Seq pipeline for CBIO 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... - 04:31 PM Setting up a portable RNA-Seq pipeline for CBIO 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...
- 03:55 PM Setting up a portable RNA-Seq pipeline for CBIO 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/...
04/12/2018
- 05:28 PM Setting up a portable RNA-Seq pipeline for CBIO 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.
- 05:04 PM Setting up a portable RNA-Seq pipeline for CBIO 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...
04/11/2018
- 02:26 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup
- Ok
- 02:25 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup
- No problem Gerrit. No, Jai only got as far as asking Andrew to install the necessary software.
- 02:22 PM Setting up a portable metagenome assembly pipeline for CBIO Support #27: What we already know and have setup
- Hi Katie,
I picked up this message from you on the bst-redmine@cbio.uct.ac.za account.
*"Gerrit this was wit... - 01:26 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample
- Jon this message is from Nicky.
"Ok so the evaluation is done already. We need to decide if we need to make use of... - 12:56 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample
- I found out that they have already compared Dragen to GATK and BWA using the Platinum genomes trio, the accuracy and ...
- 11:41 AM Setting up a portable RNA-Seq pipeline for CBIO 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...
- 11:28 AM Setting up a portable RNA-Seq pipeline for CBIO 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... - 11:23 AM Setting up a portable RNA-Seq pipeline for CBIO 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...
- 11:18 AM Setting up a portable RNA-Seq pipeline for CBIO 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... - 11:11 AM Setting up a portable RNA-Seq pipeline for CBIO 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... - 10:55 AM Setting up a portable RNA-Seq pipeline for CBIO 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...
04/10/2018
- 05:33 PM Setting up a portable RNA-Seq pipeline for CBIO 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... - 02:22 PM Setting up a portable RNA-Seq pipeline for CBIO 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... - 01:41 PM Setting up a portable RNA-Seq pipeline for CBIO 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...
04/09/2018
- 04:37 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample
- We had a BST meeting. Seems like there is a slight diversion from the original plan and suggestions made. Maybe bette...
- 12:56 PM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Katie Lennard wrote:
> Gerrit Botha wrote:
> > Try again. I opened up read permissions to the binary.
>
> Hmmm, ... - 12:54 PM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Gerrit Botha wrote:
> Try again. I opened up read permissions to the binary.
Hmmm, kry nou:
Downloading nextflow... - 11:43 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Try again. I opened up read permissions to the binary.
- 11:38 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Have added lines to .bashrc but can't test nextflow (version -v):
/bin/bash: /opt/exp_soft/cbio/nextflow/nextflow:... - 11:13 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Gerrit Botha wrote:
> Ok it is setup in ```/opt/exp_soft/cbio/nextflow```
>
> Add the following lines in your ```... - 10:59 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30: Update Nextflow to version 0.27.6
- Ok it is setup in ```/opt/exp_soft/cbio/nextflow```
Add the following lines in your ```.bashrc```
~~~
JAVA_C... - 10:09 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30 (In Progress): Update Nextflow to version 0.27.6
- Ok Katie, will do it in the next hour or so. Will get back to you.
- 09:51 AM Setting up a portable RNA-Seq pipeline for CBIO Support #30 (In Progress): Update Nextflow to version 0.27.6
- The RNAseq pipeline requires an updated version of Nextflow (currently 0.26.3, need 0.27.6)
- 12:32 PM Setting up the BST helpdesk Feature #29 (Resolved): Create list of research groups to appear for ticket submission.
- The research group menu has been updated with the group found in the link above.
- 11:14 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Gerrit Botha wrote:
> Hi Katie,
>
> Initially asked me if the info you are planning to share in this ticket shoul... - 11:08 AM Setting up a portable RNA-Seq pipeline for CBIO Support #25: Configure NGI-RNAseq pipeline to run on hex
- Hi Katie,
Initially asked me if the info you are planning to share in this ticket should go in the ticket or on th...
04/06/2018
- 03:38 PM Setting up a portable RNA-Seq pipeline for CBIO Support #25 (In Progress): Configure NGI-RNAseq pipeline to run on hex
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