Submitting Sequences to NCBI by FTP - meyermicrobiolab/Meyer_Lab_Resources GitHub Wiki
Transferring files from HiperGator to GenBank
First, make sure you have a stable internet connection, wifi in the lab is not recommended for large datasets. You can use the Mac lab computer that has a physical ethernet connection to the internet.
Login to HiperGator. You can do this by entering in the following code into the terminal:
You will be prompted to enter your password and verify your identity by two-factor authentication. Once you have successfully logged in, you’re going to want to navigate to your directory that houses all of your sequences using the cd command.
cd /blue/juliemeyer/path/to/your/directory/
Once you’re in the directory with all of the sequencing files you want to upload, you are going to remotely connect to the NCBI submissions server. To do this, you will enter the following code:
lftp ftp-private.ncbi.nlm.nih.gov
You should get a confirmation that you have remotely connected to the server. Each new line of code that you enter will start with this: lftp ftp-private.ncbi.nlm.nih.gov:~>. Next, you will enter the username that NCBI assigns to you during the submission process - you find this by expanding the "FTP Instructions" section in the SRA submission portal.
user [ncbi username]
You will then be prompted to provide the password. Again, this is a unique password that NCBI provides you with in the submission portal. Note that it will not appear as you type it. Once you’ve entered the password, click enter. Again, you will get a confirmation that you’ve successfully logged into your individual submission portal. Each new line of code that you enter will start with: username @ftp-private.ncbi.nlm.nih.gov :~> You then need to navigate to your submission directory. The Submission portal provides a unique account folder pathway for all of your individual submissions(again, you find this by expanding the "FTP Instructions" section in the SRA submission portal). You will type the command from the instruction portal to navigate to your submission account folder, which will look something like this (with email and identifier that will change each time):
cd uploads/gatorlink_ufl.edu_uniqueid
You should get a line back that reads ‘cd ok, cwd=/uploads/gatorlink_ufl.edu_uniqueid’. This verifies you have remotely navigated into your unique account folder. You can kind of think of this as being the NCBI equivalent of your folder unique folder in the juliemeyer Hipergator directory. That being said, each project submission needs its own folder within your account folder. Make a new directory for this submission in your account folder:
mkdir new_folder
Navigate into the folder you just created.
cd new_folder
Now you are essentially operating within two folders: your folder on Hipergator that holds all of the sequencing files you want to deposit, and the remote folder on the NCBI server that you want to deposit your files in. Run the following code to copy all files from the HiperGator folder to the NCBI folder:
mput *
This will take some time depending on the number and size of your files, but it will let you know when they’re done and successfully uploaded. Once complete, you can exit out of the NCBI server by typing:
exit
Navigate back to your submission portal, and click on ‘select pre-loaded folder’. You should see the directory you created with all your uploaded files. Select that one, and hit ‘Continue’ on your submission. It will take you to the next submission page, where you can double check that all of the files uploaded properly and are assigned to the correct sample. If all of this looks good, you can click ‘Submit’!