I have downloaded docker and pymol as described by the ncbi..but i dont understand how to run them...if someone can guide me how to use pgap , I will be much appreciated. I have watched the tutorial by ncbi but I seem clueless
Syariffah Nuratiqah Syed Yaacob
As Zarrin Basharat
said, while submission, you can opt for PGAP, however, there are some instances where the genome have errors and the submission cannot be completed in this way.So, if you are trying to locally run PGAP, it is a good way to be sure that the submission will go smoothly.
To run PGAP locally, you just need to prepare your .yml file and proceed with the annotation. As you said you have installed docker, so you don't need any other software. First run the pipeline with the test data or exactly the same as shown in the webinar video. If you are successful, do similar with your genome.
https://www.youtube.com/watch?v=pNn_-_46lpI
https://github.com/ncbi/pgap/wiki/Quick-Start
Syariffah Nuratiqah Syed Yaacob
As Zarrin Basharat
said, while submission, you can opt for PGAP, however, there are some instances where the genome have errors and the submission cannot be completed in this way.So, if you are trying to locally run PGAP, it is a good way to be sure that the submission will go smoothly.
To run PGAP locally, you just need to prepare your .yml file and proceed with the annotation. As you said you have installed docker, so you don't need any other software. First run the pipeline with the test data or exactly the same as shown in the webinar video. If you are successful, do similar with your genome.
https://www.youtube.com/watch?v=pNn_-_46lpI
https://github.com/ncbi/pgap/wiki/Quick-Start
Dear Abhijeet Singh Thank You for your prompt reply. May I know did U need a super computer to do pgap? I mean do we need more than 8GB RAM and linux command to run the pgap? Can I run pgap locally using windows? Are the providing command from the server are only for linux?
Syariffah Nuratiqah Syed Yaacob
Please read the requirements for PGAP on https://github.com/ncbi/pgap/wiki/Quick-Start
It can be run on a standard laptop computers.
However, if you are not able to have a linux working platform, may be you need to look into Windows subsystem for linux, or use Docker.
But in my experience WSL and docker on windows do not work properly.
So, install linux on your computer as dual-boot and then install pipeline.
If you can not do all this, please submit fasta sequence of your genome to NCBI and ask PGAP annotation during the submission process.
Abhijeet Singh I ll try both..doing it manually on linux platform and also submit to NCBI..Thank You for your recommendation. I appreciate them much
Running PGAP is pretty simple. you need 100GB disk free space and 32 GB memory (8 core CPU, each CPU with minimum 12GB). Need to make a metadata in yaml format. Command to run PGAP is ./pgap.py -r (file link). Please check the link below to better understand how to run PGAP. Hope it helps
https://www.youtube.com/watch?v=pNn_-_46lpI&t=772s
Hi Syariffah Nuratiqah Syed Yaacob . Aside PGAP, You can also try PROKKA which is relatively easy to install and configure for use.
But you cannot submit prokka annotations in NCBI. PGAP is recommended for submission of complete genome annotations
PROKKA has an option that makes your annotations NCBI compliant.
Use the flag --compliant
I recently tried to submit genome using prokka the compliant one, but ncbi told us that specifically you need to use pgap, in order to submit your annotations or inform ncbi if they gonna do that on our behalf. I never got option for doing submissions using other pipelines.
You can have a look at their wiki here. https://github.com/ncbi/pgap/wiki
Also If you are using a linux platform you need to set the number of open files to about 8092.
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