Run GATK older version by docker images
Why?
GATK versions before 4.1.0.0 and 4.1.1.0 has big differences. There is some problem download and run gatk v4.1.0 directly.
Hightlights of the 4.1.1.0 release:
Major updates to Mutect2, including completely overhauled filtering and smarter handling of overlapping read pairs.
Regular approach to download gatk
System: Ubuntu 20.04.5 LTS It turned out it works ok on macOS 12.4
wget https://github.com/broadinstitute/gatk/releases/download/4.1.0.0/gatk-4.1.0.0.zip
unzip gatk-4.1.0.0.zip
Issue
# Test run
PATH_TO_gatk/gatk-4.1.0.0/gatk Mutect2
gatk:80: SyntaxWarning: "is" with a literal. Did you mean "=="?
if len(args) is 0 or (len(args) is 1 and (args[0] == "--help" or args[0] == "-h")):
No local jar was found, please build one by running
PATH_TO_gatk/gatk-4.1.0.0/gradlew localJar
or
export GATK_LOCAL_JAR=path_to_local_jar
PATH_TO_gatk/gatk-4.1.0.0/gradlew localJar
FAILURE: Build failed with an exception. * What went wrong: Task 'localJar' not found in root project 'ybao2'. * Try: Run gradlew tasks to get a list of available tasks. Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights. * Get more help at https://help.gradle.org BUILD FAILED in 3s
According to online resource, this issue is related to dependency mismatch between gradle and java. Tried couple times to resolve it by upgrading gradle version but didn't work.
Download gatk-4.1.0.0 docker images
sudo docker pull broadinstitute/gatk:4.1.0.0
Issue
# Activate docker to run Mutect2 tumor only mode
sudo docker run -t broadinstitute/gatk:4.1.0.0 gatk Mutect2 -R $REF.fa \
-I $tumor.bam \
-tumor $tumor.name \
--disable-read-filter MateOnSameContigOrNoMappedMateReadFilter \
-O $out.vcf.gz
A USER ERROR has occurred: The specified fasta file (file:///PATH_TO_REF.fa) does not exist.
This issue related to that there is no access to server files while using docker images.
Following online instructions [1], try to grand docker images with server folder access by:
docker run -v /Users/YOUR_USER_NAME/mydata:/mnt/mydata myimage
Now, /mnt/mydata inside the container will have access to /Users/YOUR_USER_NAME/mydata on my host. [1:1]
However, this attempt ended with the same error.
Solution
After brainstorming/googling with my advisor, (Thanks!), this would work:
# Grand docker image access to your folder FOLDER_YOU_NEED_ON_SERVER
sudo docker run -v FOLDER_YOU_NEED_ON_SERVER:FOLDER_YOU_NEED_ON_SERVER broadinstitute/gatk:4.1.0.0 gatk Mutect2 -R $REF.fa \
-I $tumor.bam \
-tumor $tumor.name \
--disable-read-filter MateOnSameContigOrNoMappedMateReadFilter \
-O $out.vcf.gz
Bonus
Great! Now if you want to wrap the gatk Mutect2 calls into a bash file and submit to slurm, you may face this issue:
sudo: a terminal is required to read the password; either use the -S option to read from standard input or configure an askpass helper
In your terminal, if you do docker run hello-world, you will face some issue related to permission, which requires sudo.
Solution
Assuming that you have sudo rights, you can do:[2]
sudo groupadd docker
sudo usermod -aG docker YOUR_USER_NAME
su - YOUR_USER_NAME
docker run hello-world
If you still face the permission issue, you may need to reload reboot your shell process and possibly even restart your computer [3]
sudo reboot
Hello from Docker!
This message shows that your installation appears to be working correctly.
To generate this message, Docker took the following steps:
1. The Docker client contacted the Docker daemon.
2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
(amd64)
3. The Docker daemon created a new container from that image which runs the
executable that produces the output you are currently reading.
4. The Docker daemon streamed that output to the Docker client, which sent it
to your terminal.
To try something more ambitious, you can run an Ubuntu container with:
$ docker run -it ubuntu bash
Share images, automate workflows, and more with a free Docker ID:
https://hub.docker.com/
For more examples and ideas, visit:
https://docs.docker.com/get-started/