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Test-drive the GATK tools and Best Practices pipelines on Terra
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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?