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.
Read the number of expected bins( 65600) but still had more elements in file with IlluminaBclToFastq
Has this issue (previously reported as https://gatkforums.broadinstitute.org/gatk/discussion/10168/picard-illuminabasecallstosam-clocs-file-issue-more-elements-than-expected ) been fixed? I have just tried using IlluminaBclToFastq in picard tools 2.15.0/java.1.8.0_20 and had this same error: Read the number of expected bins( 65600) but still had more elements in file. However, when I use picard tools version 1.119/java.1.7.0_67 there is no problem and the IlluminaBclToFastq completes without issue. In both cases I use NUM_PROCESSORS=4 . Any ideas? Should I simply upgrade to the newest version of picard tools?