Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Hi, may in know is HaplotypeCaller from version3.6 same as version4.1?
wlai
Member ✭
There is --nct for HaplotypeCaller in v3.6 to help me speed up the analysis. May i know can if i could replace the HaplotypeCaller from 4.1 to 3.6?
Best Answers
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SChaluvadi
admin
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SChaluvadi
admin
Hello @wlai - Sorry for the delayed response. It seems that this error has been seen due to insufficient memory allocated for the process. Would you be able to re-try by increasing memory? Here is a forum discussion with the same error and the user's solution listed as well for reference?
Answers
@wlai
The GATK 4 release promotes the use of Sparktools as the primary method of threading. Each tool that is supported by Spark contains the suffix "Spark". HaplotypeCallerSpark for example, is the Spark version of HaplotypeCaller in GATK 4.0. You can use this tool if you wish to perform threading with HaplotypeCaller.
@wlai
There has been work done with HaplotypeCallerSpark so that it now matches the output of regular HaplotypeCaller. You can use the parameter
--strictto invoke this behavior but please note that there are still modifications being made to improve performance as listed in this ticket.Thanks for the reply. I have another problem for a while when i run genomicsDBImport.
Is it okay to ask it at here or in a question?
The problem:
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A USER ERROR has occurred: Couldn't read file. Error was: Failure while waiting for FeatureReader to initialize with exception: org.broadinstitute.hellbender.exceptions.UserException: Failed to create reader from file:///mnt1/WES_analysis/./LBrun7/LB94.g.vcf.gz
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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
My command:
gatk --java-options "-Xmx4g -Xms4g" -DGATK_STACKTRACE_ON_USER_EXCEPTION=true GenomicsDBImport --genomicsdb-workspace-path my_database -L chr1 --sample-name-map LBrun-map --batch-size 20 --tmp-dir ./tmp --reader-threads 2
Using GATK jar /home/cruadmin01/installations/gatk-4.0.12.0/gatk-package-4.0.12.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx4g -Xms4g -jar /home/cruadmin01/installations/gatk-4.0.12.0/gatk-package-4.0.12.0-local.jar -DGATK_STACKTRACE_ON_USER_EXCEPTION=true GenomicsDBImport --genomicsdb-workspace-path my_database -L chr1 --sample-name-map LBrun-map --batch-size 20 --tmp-dir ./tmp --reader-threads 2
***********************************************************************
A USER ERROR has occurred: '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' is not a valid command.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
So, I couldnt run GenomicsDBimport and i cant see the Stacktrace. May i have some advice from you to regarding this? Thank you.
Hello @wlai - Sorry for the delayed response. It seems that this error has been seen due to insufficient memory allocated for the process. Would you be able to re-try by increasing memory? Here is a forum discussion with the same error and the user's solution listed as well for reference?