Support Level

Primary Support

Software Access Level

Open Access

Home Page

https://www.pacb.com/products-and-services/analytical-software/devnet/

Software Description

The PacBio Single Molecule Real Time (SMRT) analysis portal is an easy-to-use web-based platform for analyzing 3rd generation sequencing data generated from the PacBio SMRT platform.  Currently, workflows for microbial whole genome assembly, resequencing analysis, transcriptome analysis and various data processing steps are available through the portal.  For more information on the analysis portal itself, see http://www.pacb.com/devnet/ and the tutorial materials . The software must be run from a browser in the MSI network.  This can be achieved via connection through the NICE interface , or by working directly in one of the MSI laboratories. Genomes up to 100 Mbp in size can be successfully run on Mesabi.

General Linux

Instructions for SMRT Link version 3

Initial setup (only needed once unless re-installing)

1. Get a MSI account (https://www.msi.umn.edu/content/eligibility-getting-access)
2. Setup your NICE client. (https://www.msi.umn.edu/support/faq/how-do-i-obtain-graphical-connection-using-nice-system). You will need to download the DCV client first. You must use NICE to access the PacBio analysis portal at MSI remotely or you can come use the computer lab in Walter 575 or Cargill 138.
3. SSH to MSI, then in the Terminal type: "/home/support/public/smrtlink311/install.sh" then hit return. This will set up the pacbio portal files in your home directory under the folder name "smrtlink".

Running the PacBio portal (Mesabi queue for genomes < 100 Mbp)

Note: you must request a service unit (SU) allocation on Mesabi before proceeding with these instructions.

1. Open an NICE session (non-GPU session, with more RAM and time for larger genomes).
2. Within the NICE session open a terminal
3. In the Terminal: Type: "ssh -Y login" then enter your MSI account password and hit return to enter the gateway login node. Type: "ssh -Y mesabi" then enter your MSI account password and hit return to enter the HPC system. Type: "qsub -I -l nodes=1:ppn=8,walltime=24:00:00 -X" then hit return. [NOTE: the first -I is a capitol i and the second -l is a lowercase L.] [NOTE2: if you have a larger genome, e.g., > ~30 Mbp, see advanced user tips below] When prompted enter your MSI account password then hit return Wait for job to start Type: "/home/support/public/smrtlink311/start.sh" then hit return. This will start the portal server going. Copy down the URL for use in the next step.
4. In the same Terminal window and isub session: Type: "firefox &" then hit return When Firefox opens, enter the URL you copied down in the previous step into the browser address bar. It will look something like this "http://cn0575:9090/".
5. Note: If you receive an error message about needing to use Chrome, please follow these steps:
6. In the address bar type "about:config" and hit return.
7. In the list that appears, right-click, and select New -> String from the pop-up menu.
8. For "Enter the preference name", enter "general.useragent.override" (without quotes) and click "OK".
9. For the string value, paste "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_0) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/56.0.2895.0 Safari/537.36" (without quotes) and click "OK".
10. Do not exit the browser until the job is complete. You can always close out the NICE server and Save your session, reconnecting later as you please. The job will run in the background.
11. When you are all complete be sure to clean up the session by running the following script: Type: "/home/support/public/smrtlink311/stop.sh" then hit return. Then type "exit" to exit your isub session.

Changing from local jobs to PBS

Edit userdata/config/preset.xml, change "False" to "True" for pbsmrtpipe.options.distributed_mode.

<!-- Enable Distributed Mode -->
<option id="pbsmrtpipe.options.distributed_mode">
    <value>True</value>
</option>

Edit userdata/config/smrtlink.config, change "NONE" to "PBS" for jmsselect__jmstype.

jmsselect__jmstype='PBS';

Instructions for SMRT Link version 2

Initial setup (only needed once unless re-installing)

1. Get a MSI account (https://www.msi.umn.edu/content/eligibility-getting-access)
2. Setup your NICE client. (https://www.msi.umn.edu/support/faq/how-do-i-obtain-graphical-connection-using-nice-system). You will need to download the DCV client first. You must use NICE to access the PacBio analysis portal at MSI remotely or you can come use the computer lab in Walter 575 or Cargill 138.
3. Open a NICE session. Choose one of the non-GPU options that meets your needs for time and RAM usage.
4. Within the NICE session open a terminal
5. In the Terminal: Type: "isub -m 8gb -w 24:00:00" then hit return When prompted enter your MSI account password then hit return Wait for job to start Type: "/home/support/public/smrtanalysis230v2/pacbio_user_setup_230.sh" then hit return. This will set up the pacbio portal files in your home directory under the folder name "smrtanalysis".

Running the PacBio portal (Mesabi queue for genomes < 100 Mbp)

Note: you must request a service unit (SU) allocation on Mesabi before proceeding with these instructions.

1. Open an NICE session (non-GPU session, with more RAM and time for larger genomes).
2. Within the NICE session open a terminal
3. In the Terminal: Type: "ssh -Y login" then enter your MSI account password and hit return to enter the gateway login node. Type: "ssh -Y mesabi" then enter your MSI account password and hit return to enter the HPC system. Type: "qsub -I -l nodes=1:ppn=8,walltime=24:00:00 -X" then hit return. [NOTE: the first -I is a capitol i and the second -l is a lowercase L.] [NOTE2: if you have a larger genome, e.g., > ~30 Mbp, see advanced user tips below] When prompted enter your MSI account password then hit return Wait for job to start Type: "/panfs/roc/pacbio/start_user_portal.sh" then hit return. This will start the portal server going. Copy down the admistrator username/password and URL for use in the next step.
4. In the same Terminal window and isub session: Type: "firefox -no-remote &" then hit return When Firefox opens, enter the URL you copied down in the previous step into the browser address bar. It will look something like this "http://cn0575:8080/smrtportal/". When prompted for your username and password, enter the administrator username/password you copied in the previous step.
5. Do not exit the browser until the job is complete. You can always close out the NICE server and Save your session, reconnecting later as you please. The job will run in the background.
6. When you are all complete be sure to clean up the session by running the following script: Type: "/panfs/roc/pacbio/stop_user_portal.sh" then hit return. Then type "exit" to exit your isub session.

Advanced users hints

Queue speedups

If you installed your PacBio portal prior to September 25, 2015, your portal is probably set up to use the PBS system, which tends to experience serious delays when running on Mesabi. The portal works much better in multi-threaded mode, rather than in cluster mode. So, you'll need to change a few things in a couple of config files. Edit the following 2 files:

$HOME/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/user.smrtpipe.rc
$HOME/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/smrtpipe.rc

change CLUSTER_MANAGER = PBS to CLUSTER_MANAGER = BASH in both of those files.

You can continue to follow the instructions above (mesabi section). When you run 'top', you should now see many processes happening in your local node, and qstat -u USERNAME should only show your single interactive batch job.

Adding more processor cores and memory for genomes > 30 Mbp

By default, we've set up the configuration files to use only 8 processor cores and 24 hours of walltime. But if you have a large genome, you will greatly benefit from increasing these limits, and you may need more memory. On Mesabi, you may request up to 96h of walltime and 32 processor cores on the ram1t nodes (See queue table specs here). To take advantage of these increases, edit the 2 files:

$HOME/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/user.smrtpipe.rc
$HOME/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/smrtpipe.rc

change MAX_THREADS = 8 to MAX_THREADS = 32 in both of those files (assuming 32 is the number of cores you want to use). change TMP = /tmp to TMP = /scratch.global/ to avoid overflowing the memory in /tmp for large genomes.

Then login to mesabi or itasca by ssh-ing to one of those machines and submit a request for an interactive queue submission: "qsub -I -l nodes=1:ppn=32,walltime=96:00:00 -q ram1t -X", for example. Then follow the normal instructions.

Troubleshooting errors

If you get an error in the setup or running of the PacBio server, try the steps once more. If it still fails, try the following:

1. Open an NICE session.
2. Within the NICE session open a terminal
3. In the Terminal: Type: "isub -m 8gb -w 24:00:00" then hit return When prompted enter your MSI account password then hit return Wait for job to start If you wish to save data from previous runs, move or make a copy of your current ~/smrtanalysis directory before proceding to the next step. Type: "/panfs/roc/pacbio/delete_user_portal.sh" then hit return. This will delete your existing portal data and pending jobs. Exit the current isub session by typing: "exit" and retry the steps for running the portal above.
4. If you continue to have problems, send a email to "help@msi.umn.edu", being careful to include "trouble running PacBio portal" in the subject line.

Not a Module

This software is not provided as a module. See the associated documentation for access instructions.