.. _docs_faq_new_users: .. spelling:word-list:: alliancecan Niagra GMail qsub sbatch phred bp fastqc New Users --------- .. include:: /common/new_gp_wizard.txt .. contents:: :local: :depth: 1 ---- To create a `new CCDB/DRAC account`_, what should I fill in the form field: 'position'? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. image:: /img/faq/ccdb-position-formfield.png **Response** Choose an appropriate option in the form, for example: .. code-block:: bash external collaborator For the CCRI field, use your sponsor's `Digital Research Alliance of Canada `_, formerly Compute Canada (CCDB), Role Identifier (CCRI) as input. The CCRI has a structure similar to this: `abc-123-01`. What email ID should I use if I am an external collaborator? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ **Response** GMail or your work ID should be fine as long as you provide the name of your institution (or college in case of students). My account is activated. How do I learn more about Compute Canada Servers and resources available? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ **Response** See `Digital Research Alliance Documentation `_. .. caution:: `Digital Research Alliance of Canada (DRAC) `_ was formerly known as Compute Canada (CCDB). My account is activated but I cannot login into |key_ccdb_server_name| server or any other node such as |other_ccdb_server_names|? What is wrong? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ **Response** Check out the current CCDB server status `here `_. Many a times, not being able to log in might just be due to system unavailability. Please note that if you try to log in 3 or more times consecutively with a wrong password, your account gets deactivated and your IP address might get blacklisted. You would need to write to `Digital Research Alliance Support`_ to get that reversed. What is the best place to report GenPipes bugs? +++++++++++++++++++++++++++++++++++++++++++++++ **Response** .. tab-set:: .. tab-item:: GenPipes v6.x The preferred way to report GenPipes bugs is on our GitHub issue page : https://github.com/c3g/GenPipes/issues. .. tab-item:: GenPipes v5.x The preferred way to report GenPipes bugs is on our Bitbucket issue page : https://bitbucket.org/mugqic/genpipes/issues. You can always reach us by email at mailto:pipelines@computationalgenomics.ca or use `Google Group for GenPipes `_ for any requests. For more details, visit :ref:`GenPipes Support` and :ref:`GenPipes Channels` page in this documentation. I was trying to use `GenPipes deployed in a Docker Container`_. What value should I use? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ **Response** You can use the "latest" tag or one of the tags listed at `GenPipes Docker Hub: `_. If you omit the Docker will use "latest" by default. How do I run GenPipes locally in my infrastructure using a containerized setup? Is a scheduler setup necessary? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ GenPipes pipelines use scheduler's calls (qsub, sbatch) for submitting genomic analysis compute jobs. If you plan to use GenPipes locally using your infrastructure, inside a container, you need to run the GenPipes pipeline python scripts using the "batch mode" option. For local containerized versions of GenPipes, this is the preferred way of running the pipelines, if you don't have access to a scheduler locally such as SLURM or PBS. This is how you can run GenPipes pipelines such as :ref:`DNA Sequencing Pipeline`, refer to the command below: .. code-block:: bash user@machine:~$ genpipes dnaseq -c dnaseq.base.ini dnaseq.batch.ini -j batch -r your-readsets.tsv -d your-design.tsv -s 1-34 -t mugqic -g genpipes-file-script.sh user@machine:~$ bash genpipes-file-script.sh Please note, there is a disadvantage to running GenPipes Pipelines without a scheduler. In the batch mode, which is configured using the "-j batch" option, all the jobs would run as a batch, one after another, on a single node. If your server is powerful enough, this might be your preferable option. Otherwise, if you would like to take advantage of GenPipes' job scheduling capabilities, you need to install a job scheduler locally in your infrastructure so that GenPipes can work effectively. We recommend SLURM scheduler for GenPipes. GenPipes 3.4 RNA Sequencing Pipeline moved from using Trimmomatic to Skewer. Why? What does this change mean for GenPipes users? ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ In addition to why, there are additional queries that we received. So we will respond to all of these together: In RNA-seq skewer, a. What does the untrimmed read pairs available after processing refer to? b. If a large proportion of the reads are untrimmed does this mean the adapter sequence is wrong and how to troubleshoot this issue? **Why the switch?** The switch from trimmomatic to skewer was based on benchmarking. Skewer had improved F1 score across numerous truth sets over trimmomatic. **Untrimmed Reads and Troubleshooting** Untrimmed read pairs refers to read pairs which did not require quality 3' trimming i.e. the quality was above 25 phred score or were above the size selection criteria of 50 bp after trimming and/or adapter removal. Typically when the fastqc are generated after sequencing the adapters are removed, but in some cases the adapter remains. You can use fastqc on the raw reads to visualize the proportion of these. Also if you are unsure check that the adapters you are using are inline with sequencer and libraries you are using. .. _new CCDB/DRAC account: https://ccdb.alliancecan.ca/account_application .. _GenPipes deployed in a Docker Container: https://genpipes.readthedocs.io/en/latest/deploy/dep_gp_container.html .. _Digital Research Alliance Support: mailto:support@alliancecan.ca