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!

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 on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

BaseRecalibrator Hangs Without Error Message

Hi,

I am using the BaseRecalibrator on a set of 20 samples that have been exome capture sequenced (~35x mapped coverage over 60Mb), and I am getting strange behavior. The BaseRecalibrator hangs after printing the message "Done initializing BAM readers." I've let it go for 16 hours, and nothing has changed. I've tried both single sample and merged BAM files with read groups, and the behavior is the same.

The command I am running is as follows

java -jar GenomeAnalysisTK.jar\
    -T BaseRecalibrator\
    -R reference.fasta\
    --knownSites known_snps.vcf\
    -I alignment.bam\
    --covariate ContextCovariate\
    --covariate CycleCovariate\
    --covariate QualityScoreCovariate\
    --covariate ReadGroupCovariate\
    -o recalibration.table\
    -nct 8

I am using the Java SE runtime version 1.8.0_45 and GATK version 3.5-0-g36282e4 on a 64-bit Linux server.

Is this a matter of just waiting longer, or is there likely to be some problem with my input files? Thank you!

Best Answer

Answers

Sign In or Register to comment.