While the course home page serves as an organizational template for what you have done in the course, there are always going to be differences between what was on the webpage and what you did. Here we will create a document that will highlight exactly what tutorials you did to go along with the home page. Additionally, throughout the course you have been running anything of substance (ie programs and scripts) on iDev nodes, but as mentioned several times, using the idev nodes is not how you will typically want to interact with TACC. Note that there is actually very little "tutorial/code/command" on this page. Instead this is a more detailed review of key ideas, with commands at the end to collect useful things to archive .


This tutorial aims to:

  1. Review theory of TACC's job submission architecture.
  2. Review conda use and theory.
  3. Theory of what makes a good tool.
  4. Transfer important files back to your computer, including reminder of what you have done in the course.



There is often confusion about differences between the different types of compute nodes (development vs normal) and how the reservation we've been using this week allowed us to with the tutorials  though the idev node which while great for learning, troubleshooting, and testing (at least in some cases),as compared to how you will use the job submission system for actual analysis of your work. The stampede2 user guide includes some great information that tries to speak to people both well versed in computer science and those that aren't. They provide the following figure to describe how the resources at stampede2 are laid out which while accurate and helpful doesn't describe 3 key things that I always find helpful to think about:

  1. How the head node or login node are shared between all users
  2. Explain the different queues that are available and how their choice effects you
  3. Differences between idev sessions and submitted jobs

A few years ago this course began using  similar figure that highlights the things that I think are important (specifically the 3 things I feel the above doesn't convey), and label things with the terms I use to think about them. As mentioned several times, my background is biology, not computer science, and ultimately I think slightly inaccurate descriptive terms may help clear up some of the confusion.

Different Queues

The stamapede2 user guide has detailed information about the queues and what the limits are, but similar to the figures above, as a biologist the information in those tables isn't really what I tend to think about. Instead I think about the queues as follows:

QueueMax TimePurpose/when to use
normal48this is my default queue, while 48 hours is the max time, I can only think of 2 instances I have ever needed to request more than 24 hours. Remember I work mostly with bacteria and up to 100s of millions of reads across dozens-400 samples at a time typically so your experience may vary.
development2Short jobs that I need output from, to start a larger job. In particular, read trimming (always) and FastQC/MultiQC (if more than 25ish samples or 50ish millions of reads)
largemem*48Recently working with collaborator on sequencing project with very deep coverage, majority of reads related to a host organism, and minority of reads related to a poorly characterized bacteria. This required a the largemem node for a complex mapping command, and subsequent assembly attempts.
"other"?I know there are other queues that are available, but have never had need to figure out what they are or found nodes above to be lacking. As described in the read QC tutorial with not knowing about the 'zgrep' command it is possible or even probable that using one of the other queues would be more efficient, but I doubt it as the normal queue is for typical things, and the other queues are more specialty services addressing specific issues (turn around time, memory, etc).

*largemem queue was on ls5, does not have equivalent in stampede2. Frontera has ultra large memory nodes (2-4x those available on LS5). If you running into memory problems (large assemblies), you may want to consult with someone at tacc https://portal.tacc.utexas.edu/tacc-consulting to verify if frontera is where you should be working.

idev Vs submitted job

Submitting a job to the queue is my (and should be your) default position for several reasons:

  1. Nearly all of the jobs I run take at least 30-60 minutes when running a reasonable number of samples, and most take at least double that. During that time, nothing happens that needs my intervention or input, the computer does the work for me. So running in an interactive mode where I can see output in real time would be a terrible use of my time.
  2. I make routine use of redirecting the output and errors to log files with the >& command used in several of the advanced tutorials (Breseq, fastp, structural variants, and several others) so I can view information from the run after the run is done or has had an error. (more on the >& below).
  3. I am always working with multiple samples, and running multiple samples at the same time on a single node. This means even if I wanted to see what was going on, I wouldn't be able to decipher what lines came from what specific samples.

There are times that I do use idev nodes:

  1. Jobs that I have submitted, keep failing early, but not immediately.
    1. Launch idev, start command wait to see where it goes wrong and troubleshoot as it happens with restarting command, watching it crash, editing something (commands file, novel script,  using fewer reads, etc) repeat.
  2. Job doesn't seem to be launching correctly as jobs.
    1. As we have seen throughout the course, the compute nodes are NOT the head node (corral-repl access), sometimes logging into an idev node helps clarify what is going wrong by using which, tab completion etc.
    2. Suspect and hope that installing programs exclusively (or as close to it as possible) via conda will help limit this.
  3. I have several jobs to run in a row that I know will take <5-10 minutes each, but require sequential intervention. 
    1. Specifically a pipeline for a bunch of plasmid sequencing the lab does that the analysis has 7 steps including: read trimming, breseq analysis, compare table generation, spades alignment, spades comparison, overall run statistics, and organization of results into different groups for individual researchers in the lab. Since they are sequential, submitting them as 7 different jobs that finish so quickly just isn't practical.
  4. Working with a new analysis program and downsampled data still triggers a TACC warning to get off the head node. (Warning message shown below)

If idev is so rare why did we use it in the class:

First, running in interactive mode gives you some comparison of how different programs work. Think back on your runs this week, what programs/commands printed information to the screen that had useful information (read trimming, read mapping come to my mind), what programs didn't (mpileup, indexing, file conversions), and what programs had large amounts of information but wasn't directly needed or evaluated (breseq, spades). This may help you decide when there are things you want to capture and when you should expect empty files.

Second, it speeds the class up. No matter what output is generated when you execute a command, you get your command prompt back when the command is done, and you can immediately interrogate the results rather than waiting and guessing when your job starts, and when it finishes.

Finally, throughout the course we made use of the reservation system which allowed us to skip the queue and immediately get an idev session or job running. In previous years where reservations weren't possible tutorials were planned around a:

  • "hurry up and get the job started its going to sit for some amount of time in the queue"
  • "ok let me tell you about those commands that are sitting around waiting to run" 
  • "DRAT! there is a typo in your commands file! edit that command and go back to the end of the queue while we talk about the results you can't actually see"

I hope you can see that using idev nodes has enabled each of you to accomplish more tutorials than previous years while hopefully learning more. Generally, the feedback from students who have taken the course under this type of format has been positive, so if you find that you are overly reliant on idev nodes or have a hard time transitioning to submitting jobs, I'd love to hear the feedback so I can attempt to modify things further. 

Good citizenship on the head node

When you log into stampede2 using ssh you are connected to what is known as the login node or "the head node". There are several different head nodes, but they are shared by everyone that is logged into lonestar (not just in this class, or from campus, or even from Texas, but everywhere in the world). Anything you type onto the command line has to be executed by the head node. The longer something takes to complete, or the more it will slow down you and everybody else. Get enough people running large jobs on the head node all at once (say a classroom full of summer school students) and stampede2 can actually crash leaving nobody able to execute commands or even log in for minutes -> hours -> even days if something goes really wrong. To try to avoid crashes, TACC tries to monitor things and proactively stop things before they get too out of hand. If you guess wrong on if something should be run on the head node, you may eventually see a message like the one pasted below. If you do, it's not the end of the world, but repeated messages will become revoked TACC access and emails where you have to explain what you are doing to TACC and your PI and how you are going to fix it and avoid it in the future.  

Example of how you learn you shouldn't have been on the head node
Message from root@login1.ls4.tacc.utexas.edu on pts/127 at 09:16 ...
Please do not run scripts or programs that require more than a few minutes of
CPU time on the login nodes.  Your current running process below has been
killed and must be submitted to the queues, for usage policy see
If you have any questions regarding this, please submit a consulting ticket.

Recall this is the type of message that I have gotten when working with downsampled data on the head node and lead me to start an idev session to figure out what is going on.

Submitting jobs to the queue 

Every job you submit will have 2 parts:

  1. A file with the commands you want to run
  2. A control file that interacts with the queue system to do all the computer science stuff of executing the commands.

Access to nodes (regardless of what queue they are in) is controlled by a "Queue Manager" program. You can personify the Queue Manager program as: Heimdall in Thor, a more polite version of Gandalf in lord of the rings when dealing with with the balrog, the troll from the billy goats gruff tail, or any other "gatekeeper" type. Regardless of how nerdy your personification choice is, the Queue Manager has an interesting caveat: you can only interact with it using the  sbatch command. "sbatch filename.slurm" tells the que manager to run a set of job(s) based on information in filename.slurm (i.e. how many nodes you need, how long you need them for, how to charge your allocation, etc). The Queue manager doesn't care WHAT you are running, only HOW you want to run it.

The easiest way I have found to deal with slurm files is by copying a .slurm file into the directory I am running my job from and editing the relevant parts. This is exactly what you have been walked through when you have submitted jobs in tutorials rather than run them interactively.

Slurm file

Recall that we have copied the GVA.launcher.slurm file into many of our optional tutorial directories on scratch.

GVA.launcher.slurm file contents
# Simple SLURM script for submitting multiple serial
# jobs (e.g. parametric studies) using a script wrapper
# to launch the jobs.
# To use, build the launcher executable and your
# serial application(s) and place them in your WORKDIR
# directory.  Then, edit the CONTROL_FILE to specify 
# each executable per process.
#         <------ Setup Parameters ------>
#SBATCH -J jobName              # More descriptive the better
#SBATCH -n 1                    # number of tasks to run at once (68 max recommend, 272 absolute max)
#SBATCH -N 1                    # number of nodes (68 cores, 272 threads per node)
#SBATCH -p normal               # normal is most common queue
#SBATCH -o Queue_job.o%j        # autogenerate log files with name format
#SBATCH -t 12:00:00             # time in hh:mm:ss format
##SBATCH --mail-user=ADD        # uncomment and add email to recieve emails from TACC about job status
##SBATCH --mail-type=all        # what emails to send
#SBATCH -A UT-2015-05-18        # charge SUs to class account

export LAUNCHER_JOB_FILE=commands

16#SBATCH -J jobNameUse detailed names if you expect to have multiple jobs on queue system at once. Helps with the showq -u  command
17#SBATCH -n 1How many tasks to run at once. 68 suggested max if working with 1 Node, 136 if working with 2,  204 if working with 3, etc
18#SBATCH -N 1How many nodes do you want to request at once. The more nodes you request here, the longer it will take for your job to start
19#SBATCH -p normalDiscussed above. VERY rare personally to use other on stampede2
21#SBATCH -t 12:00:00How long for the job to run. Rare for me to request more than 12 hours. The longer you request, the longer it is likely for your job to start. If you request too short, job won't finish, likely have to resubmit job starting over, and will take at least twice as long overall.
22,23##SBATCH --mail-user=ADD
##SBATCH --mail-type=all
Where to send emails and what emails to send. What email options: all, begin, end, fail.

If you at least turn on "end" your email will slowly accumulate how long different programs/analysis is taking to complete will help you estimate line 21 better over time
31export LAUNCHER_JOB_FILE=commandsReplace "commands" with exact name of commands file (see below for comment on naming commands/slurm files).

Commands files

How does Dan make commands files?

  1. In several tutorials (MultiQC, fastp, Advanced Breseq) I gave example command line for loops that can be used to generate commands files for large numbers of samples. 
  2. Often I use a python script to generate files like this, as I am more fluent in python coding than I am in bash/command line scripting.
  3. Sometimes I generate some commands in Excel 
    1. An example might be a formula of '="breseq -j 6 -p -r Ref.gbk -o Run_output/" & A1 & " " & B1 & " " & C1 & " >& runLogs/" & A1' with sample name in A1, read1 in B1 and read2 in C1.
  4. In a program like BBedit/notepad to copy paste the same command multiple times and change it as appropriate then paste the text directly into a nano editor on TACC.
  5. In the introduction tutorial, several alternative text editor programs were mentioned with different ssh connectivity

Use of the '>&' symbology 

Adding >& symbol to the end of a command followed by a file name is very useful. This results in redirecting what would normally print to the screen as either the standard output and the standard error streams to a file that follows. This can be very useful for determining where/why a particular sample failed as it sorts it into a specific file based on the sample being analyzed. This behavior is demonstrated in the fastp tutorial as well as the advanced breseq tutorial.

The same information will be found in the .o<jobID> and .e<jobID>, but the output and error streams will be mixed together among all simultaneously running commands. 

Naming conventions

Preferred naming convention

I suggest and try to conform to the idea that all commands files should be named something descriptive followed by a _ or a. and then the word commands. The same description should also be used as a prefix to the .slurm file. This enables me to easily and obviously associate commands with the conditions they were run in TACC on. The down side is that this then leads to more jobs failing because i have a typo between the commands file name, and what is listed on line 31 of the slurm file.

My bad habit naming convention

Alternatively, you can use no description and just have all slurm files called 'launcher.slurm' and all commands be in a file named 'commands'. This cuts down on what you have to edit in the slurm file and makes it much easier to avoid typos (note you could still accidentally name your commands file 'cmmmands'). The downside here is that when you are optimizing either computer conditions (slurm file) or command options (commands file) it can be hard to keep track of what your progress has been, especially if you step away from your analysis for more than a few days.

Launching the job

Once you have your slurm file with all your options set, your commands file full of the commands you want to run, and you've got everything named according to whatever convention you are using its time to actually submit the job. As the class has almost exclusively focused on giving access to commands via conda (more on conda itself below), it is critical that you remember the next step:

conda activate environment_name

When the job is submitted to the queue a snapshot of your $PATH (more below), all currently available programs, and current directory architecture is sent along with your commands file. This means if you have installed say fastp on a conda environment, but you do not activate that environment, you will get an error ... not when you submit the job, but when the job tries to run. Remember, the queue system doesn't care WHAT you are trying to run, it assumes you wrote commands that will work. Perhaps it is because I'm still a recent convert to the relatively new tool that is conda, but failure to activate my conda environment (or activating the wrong one) is the #2 most common cause of submitted jobs failing.

Whats the #3 most common cause of submitted jobs failing? That honor goes to the italic "current" in reference to the directory architecture. As mentioned in a few of the tutorials, some programs will create directories that do not exist if you list that directory as part of an output filename or output directory. Others do not. As mentioned in those tutorials, making all your own directories will never cause a command to fail, hoping or assuming the program is capable of creating directories will cause all the programs that can't to fail. Often I forget this fact until I run the sbatch command, and then I forget that adding the new directory after the job is submitted doesn't fix the problem.

Remember the different uses of mkdir
mkdir folder1 folder2 folder3  # will make 3 different folders
mkdir -p folder1/folder2/folder3  #will make folder3 inside of folder2 inside of folder1
mkdir -p folder 1/ folder 2/ folder 3  #will make 4 different folders at the same level. They will be named 1 2 3 and folder

For those wondering what the #1 most common reason submitted jobs fail for Dan is

It was mentioned back on Monday when you didn't have any more context on it beyond taking my word for it. The #1 reason commands fail is because of typos, as I know several have experienced this week first hand. 

Once you have your directories created and have access to the conda environment you want its time to launch the job.

sbatch launcher.slurm

Interrogating the launcher queue

Once your job is submitted you often want to check on the status of it. Things that you are specifically interested in checking/learning:

  1. Did your job actually start or is it still waiting in the queue? You care about this because jobs are expected to run for some time (minutes-hours), jobs that have problems (such as typos) only run for seconds to minutes. There is something relieving knowing the job is running. Until the time remaining on the job starts to tick down to 0 and you begin to worry you didn't give the job enough time.
  2. How long until the job times out? This is useful if you have a multistep analysis, and you are debating if you can/should try to get the next step in the queue before the end of the day, or when you can check in to find finished data (assuming no errors or timeout). Note that the count down is strictly a ticking clock with whatever value you had in your slurm file, NOT an estimation of how long it will take until the command finishes running.
  3. How long the job has been waiting in the queue? In my work, wait times that go past 18ish hours begin to suggest that something is going wrong at TACC, or my slurm file is wrong (maybe i requested -n 1 -N 68 ... 1 command running across 68 nodes, instead of -n 68 -N 1 ... 68 commands running at the same time on a single node).

Some of the common commands that you can run and what they will do or tell you:




showq -u

Shows only your jobs

Shows all of your currently submitted jobs, a state of:

"qw" means it is still queued and has not run yet

"r" means it is currently running

scancel <job-ID>

Delete a submitted job before it is finished running

note: you can only get the job-ID by using showq -u

There is no confirmation here, so be sure you are deleting the correct job.

There is nothing worse than deleting a job that has sat a long time by accident because you forgot something on a job you just submitted.


You are a nosy person and want to see everyone that has submitted a job

Typically a huge list of jobs, and not actually informative

SUs on TACC and allocations

SUs or "service units" are a currency TACC uses to control access and encourage everyone to engage in the best behaviors. We have not spoken much about them, as they are provided as part of the class. These are an exhaustible resource (though they can be replenished via the allocation management pages on the user portal or contacting people at TACC). Giving every command its own node, is probably wasteful unless you are having memory issues.

For information on applying for an allocation at TACC, visit https://portal.tacc.utexas.edu/allocations-overview. It is my understanding (which may be flawed) that this is a very easy process for UT faculty, and possibly more difficult for external academic researchers, but still be possible (potentially requiring you to go through https://portal.xsede.org/submit-request#/login which is linked from the allocations overview page above). In my experience, the people at TACC are awesome at helping people through these types of processes and ticket requests through the TACC user portal are a great way to start the process. If there is an actual bar from allowing you (or more likely your PI), I suspect the people at TACC have much more detailed information about alternative resources.

Each job (including idev sessions) uses SUs at a given rate. SUs are deducted from your balance based on the time, type, and number of nodes you occupy, NOT the time requested.  More information can be found here. This represents an additional reason submitting a job is better practice than idev nodes most of the time: they cost less. Not because they are charged differently, but rather, a submitted job is charged based on exactly how long the commands take to execute while idev sessions have waiting between executing commands and you must remember to log out at the end of it to stop the billing.

Recall from today's presentation that you will be left on the allocation through at least the end of July, and probably the end of August. If you are removed from the allocation and are still trying to work with the tutorials, please reach out and we will see if we can add you back to them.


As noted on the first day. This is only the second year that this course has been taught using conda environments. Overall I think this has gone exceptionally well, and significantly better than last year. Feedback on this in the post class survey would be greatly appreciated if you have any thoughts on how you would have rather seen conda presented especially if you disagree and feel that the use of conda was a negative thing in the course. Additional tips on how to make better use of conda can be found here.

Things to remember about conda moving forward

Some things I suspect you will want to remember as you begin creating your own environments and working with new tools:

  1. It is often much easier to install new tools in independent environments rather than forcing everything to work in harmony. If you are trying a new program, and are unsure if you will continue to use it, it should 100% go in its own environment until you have a better understanding of it.
  2. Tools and their installation instructions can be found at https://anaconda.org/. There are tools for way more programs than I had expected, if you are interested in a new program you should 100% be checking if it available through anaconda.
  3. Most of the tools installed into conda environments in this class came from the "bioconda" channel and behind the scenes required (or were made easier) by the "conda-forge" channel. If you are tiered of adding all the -c bioconda -c conda-forge calls to your new environments, it is possible to add these channels to the default channel list the conda uses. Information on how to do this can be found in the conda user guide here https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
  4. Conflicts and downgrading/upgrading packages can lead to problems, some of this can be avoided by specifying all programs that you want in an environment at the same time rather than adding them sequentially. Recall that we did this for several of our environments including: GVA-ReadPreProcessing GVA-ReadQC GVA-SNV
  5. "Solving environment failed" messages are expected and ignored when installing new packages provided conflicts or up/downgrading packages don't crop up after.
  6. Finally, a useful cheat sheet covering both the functions we have used in class (changing environments, creating new environments, removing tools and environments, listing tools in a given environment, etc) and those not covered in the class can be found here: https://docs.conda.io/projects/conda/en/4.6.0/_downloads/52a95608c49671267e40c689e0bc00ca/conda-cheatsheet.pdf

Transferring conda

All week we have talked about the strength of being able to transfer conda environments not just between computers but also between operating systems. While I will give you commands below to copy your environment files to another machine, a blog post with some more information about a few different ways of doing this and why you might choose one way over another can be found at https://www.anaconda.com/blog/moving-conda-environments. The ability to transfer environments not just among machines but also between people opens up some possibilities that you may not have thought of yet:

  1. The ability to have a lab wide conda environment file or share a conda environment with other people in your lab to make sure that everyone is working from the same starting point and with tools that should work. I can tell you a sizable portion of the time I spend in lab helping other members is devoted to dealing with accessing programs. Being able to just share a conda environment file with them significantly improves this.
  2. In the section dealing with selecting tools, I talk a bit about publishing, and how some papers struggle to define exactly what they did computationally with enough detail to be able to make use of the analysis they did in looking at my own work. Conda environments are increasingly being shared as part of supplemental information not just in/for publications about computational based programs, but for any paper involving command line analysis. I hope that this trend continues, and that you see the value in doing such things and contribute to it.
  3. As mentioned early in class, your laptop is not going to be capable of performing the majority of the analysis you are going to want to do. That being said, sometimes we have to work with what we have, or it can be useful to look at or build things on your local machine before transferring the analysis to TACC. Downstream analysis often requires working with python/R/etc to generate figures for publication. Putting required visualization packages into a single environment (or given number of environments) can aid in publication reproducibility/interaction as mentioned above.
Command to get the environments that you have used in class ready to export to your local machine for storage, or use elsewhere
for pathway in $(for conda_env in `conda env list`;do echo $conda_env|grep "^/.*miniconda3\/envs";done); do env_name=$(echo $pathway|sed 's/.*\///');echo $env_name;conda activate $env_name;conda list;done > list_of_envrionments_used_in_GVA2022_and_packages_installed.txt
for pathway in $(for conda_env in `conda env list`;do echo $conda_env|grep "^/.*miniconda3\/envs";done); do env_name=$(echo $pathway|sed 's/.*\///');echo $env_name;conda activate $env_name;conda env export > $env_name.yml;done
mkdir GVA2022_conda_files
mv *.yml GVA2022_conda_files
mv list_of_envrionments_used_in_GVA2022_and_packages_installed.txt GVA2022_conda_files
tar -czvf GVA2022_conda_files.tar.gz GVA2022_conda_files/

Using the scp tutorial you can now transfer the GVA2022_conda_files.tar.gz file back to your computer

What to do when conda is lacking

Lacking could mean several different things:

  • The program you want to use isn't available on conda
    • Typically we become aware of new programs from literature, and it is rare to allow publication without documenting where code can be found. This is even more true for program based publications.
  • Conda environments taking too long to solve.
    • Split the environment into parts such that all programs are not being installed together
    • Specify versions of key programs to cut down on the solution space (time) conda has to work through
    • Specify all programs at the time of environment creation
    • consider switching to mamba
  • Conda tells you there is no viable solution 
    • consider switching to mamba
    • install fewer programs in a single environment

So what is mamba? mamba is a "drop in solution" for conda that is faster/more efficient. Functionally, this means that you install mamba via conda, and then just always type mamba anywhere you would otherwise type conda. Additional information about  be found here: https://bioconda.github.io/faqs.html. A more detailed discussion/description of mamba can be found here. Mamba is likely going to be taking the place in next year's course due to recent revelations that a few programs can be installed via mamba that conda can not.

A warning about $PATH variable

One of the nice things about the conda system is that it handles changing your path or adding executable files to your path for you. In previous years, anything not loaded through TACC's module system had to either be moved into your path, or your path modified to include them. Because of how broadly we have used conda, important discussions about the dangers and problems modifying your $PATH variable have not come up. Briefly putting them here as I'd feel very guilty not listing it somewhere for you to review if you ran into problems down the road with it.

Your $PATH variable is a list of locations on the computer that the command line searches through when you enter a command. 

  • When you type a command, only locations that are in your PATH variable are searched for an executable command matching that name.
  • When the command is found in your PATH, the computer immediately substitutes the location it was found for the short command name you entered, and stops searching.
  • This means that things that are early in your path are always searched first. In some extreme circumstances if you add a bunch of locations with lots of files to the front of your PATH, you can actually slow down your entire computer, so try to limit the path variable to only look in directories containing executable files.
  • You can manually manipulate your $PATH variable, usually in your .bashrc file in your home directory.
  • One of the most important lessons you can ever learn

    Anytime you manipulate your PATH variable you always want to make sure that you include $PATH on the right side of the equation somewhere separated by : either before it, after it, or on both sides of it if you want it in the middle of 2 different locations. As we are explaining right now, there are reasons and times to put it in different relative places, but if you fail to include it (or include a typo in it by calling it say $PTAH) you can actually remove access to all existing commands including the most basic things like "ls" "mkdir" "cd".

Tool selection

What makes a good tool?

  1. It does the job it is supposed to, and gets you closer to answering your biological question.
  2. Others in your field are using it.
    1. Science can't be all follow the leader, but there is strength in numbers.
  3. It has its own tutorials, and sample data available.
    1. Virtually guaranteed to increase the speed you understand how to use the tool, making it easier to optimize the command in my own experience.
  4. Detailed documentation is available.
    1. This is different than being published. Papers published about tools detail what the tool is good for, how it works, and often this is framed around something biological they are describing/investigating/etc. Documentation describes how to USE the tool.
  5. Community forums/active users/developers who are actively developing the tool
    1. Suggests there are places to go to ask questions and get answers relating to the tool
    2. Active development can often be found in "change logs, version histories, or readme" files/tabs/sections of websites.
  6. It is published.
    1. Not strictly required, but tools that are peer reviewed are more likely to be of a higher quality.
  7. It is easy to install
  8. It is fast

What makes a bad tool?

  1. It is not widely used/downloaded.
    1. Even I consider myself a novice at best when it comes to computational analysis. I rely on others who are more versed in the computer science, biostatistics, etc to evaluate  tools.
    2. If you try to publish using a tool that is not common to the field or worse that none of the reviewers have ever heard of, you will deal with it in the review process, including potentially having to redo analysis with better accepted/common tools as a condition of publication
  2. Difficult to install
  3. Lack example command on command line to model your work after
  4. Lack command line help detailing what options are expected/available
  5. Present in a paper but no github/website/forum.
    1. Broadly this suggests not actively being developed, and increasing likelihood you will have difficulties getting answers to questions or help if there are problems.

Program Versions

What version should I use?

  1. Any version that works to get you closer to answering the biological question that does not have a newer version that "fixes bugs/errors associated with" the version you want to use for the options you are selecting.
    1. Most new versions deal with expanding features, or some kind of speed/memory improvement. Very few new versions result in producing different results.
    2. Generally the bigger the value change, the bigger the change to the program. Changing from version 1 to version 2 is a very big change. version 1.1 to 1.2 less big 1.1.5 to 1.1.6 smaller still etc. There is a lot of wiggle room in this.
  2. Version similar to that which others are publishing about.
    1. If field is publishing using gatk version 4.0 and you have to cite gatk version 2.0 those are very different.
  3. A single version for all analysis in a single paper, or at least section of the methods.
    1. Personally I am incredibly frustrated with papers that say something like "versions x to y of toy Z were used". This is going to make it very hard to figure out how to mimic their analysis, repeat their analysis, evaluate their analysis.
      1. Not listing a version of a computational program is even worse.
      2. Not citing a paper as tools request is worse still.
    2. The bad things listed above are also associated with papers that do not detail what actual commands were used in analysis, again making it harder to mimic their analysis.
    3. If you do decide to update the version of a program, repeat the analysis you have already done.
      1. You should be conducting your analysis in such a way that you can repeat the analysis for exactly this reason.

When should you probably upgrade versions?

  • Results you have don't make sense, can't be validated, or are inconsistent.
  • A major bug effecting analysis is repaired.
    • Can be difficult to determine what the effect a version change will have. If the documentation calls it a "major bug" or describes something that impacts your analysis.
    • Forums of some of the better programs will break down what changes a little better and most will respond to any inquiries of "do I need to update".
    • If looking for help on an error or problem with the program and lots of answers deal with mentioning specific versions being wrong/bad/the source of the problem and you are using that version (even if you don't think you are having problems).
  • An existing pipeline no longer works with new sample/data/improvement.
  • Has new feature you want to try.
    • Probably a good idea to test this in separate environment.
  • Staring work on a new project/paper or new analysis in an on going project/paper that uses the same tool.

Transferring files

The majority of the files we have worked with have been in our $SCRATCH space. Recall that files on $SCRATCH can be deleted after a period of inactivity. Below is a list of things that you SHOULD copy to your $HOME or $WORK space.

Collecting class information via job submission


Navigate to the $SCRATCH directory before doing the following.

Commands to get to the where the data is and launch nano editor
cds  # move to your scratch directory
nano commands
Sample commands that can be pasted into nano
echo "My name is _____ and todays date is:" > GVA2022.output.txt
date >> GVA2022.output.txt
echo "I have just demonstrated that I know how to redirect output to a new file, and to append things to an already created file. Or at least thats what I think I did" >> GVA2022.output.txt
echo "i'm going to test this by counting the number of lines in the file that I am writing to. So if the next line reads 4 I remember I'm on the right track" >> GVA2022.output.txt
wc -l GVA2022.output.txt >> GVA2022.output.txt
echo "I know that normally i would be typing commands on each line of this file, that would be executed on a compute node instead of the head node so that my programs run faster, in parallel, and do not slow down others or risk my tacc account being locked out" >> GVA2022.output.txt
echo "i'm currently in my scratch directory on stampede2. there are 2 main ways of getting here: cds and cd $SCRATCH" >>GVA2022.output.txt
pwd >> GVA2022.output.txt
echo "over the last week I've conducted multiple different types of analysis on a variety of sample types and under different conditions. Each of the exercises was taken from the website https://wikis.utexas.edu/display/bioiteam/Genome+Variant+Analysis+Course+2022" >> GVA2022.output.txt
echo "using the ls command i'm now going to try to remind you (my future self) of what tutorials I did" >> GVA2022.output.txt
ls -1 >> GVA2022.output.txt
echo "the contents of those directories (representing the data i downloaded and the work i did) are as follows: ">> GVA2022.output.txt
find . >> GVA2022.output.txt
echo "the commands that i have run on the headnode are: " >> GVA2022.output.txt
history >> GVA2022.output.txt
echo "the contents of this, my commands file are: ">>GVA2022.output.txt
cat commands >> GVA2022.output.txt
echo "I will next create a what_i_did_at_GVA2022.slurm file that will run for 15 minutes" >> GVA2022.output.txt
echo "and i will send this job to the queue using the the command: sbatch what_i_did_at_GVA2022.slurm" >> GVA2022.output.txt
Use wc -l command to verify the number of lines in your commands file.
wc -l commands

If you get a number larger than 19 edit your commands file with nano so each command is a single line as they appear above. Several of the lines are likely long enough that they will wrap when you paste them in nano and cause problems

Modify your slurm file
cp /corral-repl/utexas/BioITeam/gva_course/GVA2022.launcher.slurm what_i_did_at_GVA2022.slurm
nano what_i_did_at_GVA2022.slurm

As stated above things we want to change are:

Line numberAs isTo be

#SBATCH -J jobName

#SBATCH -J end_of_class

#SBATCH -t 12:00:00

#SBATCH -t 0:10:00

Again use ctl-o and ctl-x to save the file and exit.

submit job
sbatch what_i_did_at_GVA2022.slurm

Evaluating your job submission

Based on our example you may have expected 1 new file to have been created during the job submission (GVA2022.output.txt), but instead you will find 2 extra files as follows: what_i_did_at_GVA2022.e(job-ID), and what_i_did_at_GVA2022.o(job-ID). When things have worked well, these files are typically ignored. When your job fails, these files offer insight into the why so you can fix things and resubmit. 

Many times while working with NGS data you will find yourself with intermediate files. Two of the more difficult challenges of analysis can be trying to decide what files you want to keep, and remembering what each intermediate file represents. Your commands files can serve as a quick reminder of what you did so you can always go back and reproduce the data. Using arbitrary endings (.out in this case) can serve as a way to remind you what type of file you are looking at. Since we've learned that the scratch directory is not backed up and is purged, see if you can turn your intermediate files into a single final file using the cat command, and copy the new final file, the .slurm file you created, and the 3 extra files to work. This way you should be able to come back and regenerate all the intermediate files if needed, and also see your final product.

make a single final file using the cat command and copy to a useful work directory
# remember that things after the # sign are ignored by bash
cat GVA2022.output.txt > end_of_class_job_submission.final.output
mkdir $WORK/GVA2022
mkdir $WORK/GVA2021/end_of_course_summary/  # each directory must be made in order to avoid getting a no such file or directory error
cp end_of_class_job_submission.final.output $WORK/GVA2022/end_of_course_summary/
cp what_i_did* $WORK/GVA2022/end_of_course_summary/  # note this grabs the 2 output files generated by tacc about your job run as well as the .slurm file you created to tell it how to run your commands file
cp commands $WORK/GVA2022/end_of_course_summary/

Copy paste alternative to transfer

As we have seen several times in class, many output files are comma, or space, or tab delimited . While this type of formatting is often required for downstream applications, it can make it very difficult to look at if you are just trying to get a feel for what is going on. One solution to this is often to copy from the terminal screen to Excel. Sometimes Excel will recognize the delimiter character and each chunk of data will go into its own Excell cell. Other times each line goes in column A (or worse the entire copy paste goes into cell A1. For reasons unknown to me, using the text editor BBEdit (formerly known as text wrangler, not to be confused with any association to TACC's naming conventions) as an intermediate can automatically convert tab (and some space) delimited text to the invisible tab characters Excel expects, and if not (or if it uses comma delimiters), BBEdit's find/replace interface is capable of working with the same regular expressions you are increasingly becoming familiar with from the command line programs (sed, grep, awk). While there is a paid version of BBEdit I have never even bothered using their free 30 day trial.

Additional use for BBEdit

BBEdit is also a very lightweight plain text editor. This means that it is capable of opening large files (such as genbank references) without huge amounts of buffering or "destination" formatting issues that something like microsoft word would have. https://www.barebones.com/products/bbedit/. If in your own work you find an alternative that seems to do much of the same functionality as described here, I would love to hear about it.

Helpful cheat sheets

cheat sheets are a common thing produced by people for common commands they want to use but don't always remember the exact formatting for or needed options. Here are a list of cheat sheets that may be helpful and what they are helpful for. They should at least provide you with the scope different cheat sheets are produced, if you find one lacking there are others that may have something you are looking for and can be found pretty quickly using google.

Return to GVA2022 to work on any additional tutorials you are interested in.

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