Test out the preview version of the next GKL (DO NOT MERGE)

[droazen]

Test out the preview version of the GKL, containing the new native PDHMM.

The jar was build using Java 1.8 and contains AVX optimized binaries for Linux hosts and not optimized binaries for Mac (Intel CPUs)

Example code showing how to call into the PDHMM is here: https://github.com/Intel-HLS/GKL/blob/master/src/test/java/com/intel/gkl/pdhmm/IntelPDHMMUnitTest.java

[droazen]

@jamesemery Here's the branch we discussed -- see my notes above.

[jamesemery]

A command line that triggered the crash in our testing:

gatk HaplotypeCaller -R /cromwell_root/gcp-public-data--broad-references/hg38/v0/dragen_reference/Homo_sapiens_assembly38_masked.fasta -I gs://broad-dsde-methods-dragen/reprocessed_data_v3.7.5_masked/CH1_CHM13_WGS1/CH1_CHM13_WGS1.bam -L /cromwell_root/fc-971fd540-210c-4e5a-87ce-d3f8c91c7557/submissions/0586864c-d263-4797-89f1-b517e487ad2a/VariantCalling/b177671c-e96b-433e-824a-f9d641184e75/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/109scattered.interval_list -O CH1_CHM13_WGS1.vcf.gz --pileup-detection --pileup-detection-absolute-alt-depth 0 --pileup-detection-bad-read-tolerance 0.4 --pileup-detection-enable-indel-pileup-calling --pileup-detection-active-region-phred-threshold 3.0 --use-pdhmm -contamination 0.0 -G StandardAnnotation -G StandardHCAnnotation --dragen-mode --disable-spanning-event-genotyping --dragstr-params-path /cromwell_root/fc-971fd540-210c-4e5a-87ce-d3f8c91c7557/submissions/0586864c-d263-4797-89f1-b517e487ad2a/VariantCalling/b177671c-e96b-433e-824a-f9d641184e75/call-DragstrAutoCalibration/CH1_CHM13_WGS1.bam.dragstr -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90

--dragstr-params-path /cromwell_root/fc-971fd540-210c-4e5a-87ce-d3f8c91c7557/submissions/0586864c-d263-4797-89f1-b517e487ad2a/VariantCalling/b177671c-e96b-433e-824a-f9d641184e75/call-DragstrAutoCalibration/CH1_CHM13_WGS1.bam.dragstr is likely optional

-L is optional and any interval will likely work to reproduce the error.

[gatk-bot]

Github actions tests reported job failures from actions build 10011498561 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	17.0.6+10	10011498561.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10012664149 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	17.0.6+10	10012664149.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10063197705 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	17.0.6+10	10063197705.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10063916773 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	17.0.6+10	10063916773.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10063991760 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	17.0.6+10	10063991760.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10078507648 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	10078507648.10	logs
variantcalling	17.0.6+10	10078507648.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10099458986 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	10099458986.10	logs
variantcalling	17.0.6+10	10099458986.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10099827390 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	10099827390.10	logs
variantcalling	17.0.6+10	10099827390.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10099861078 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	10099861078.10	logs
variantcalling	17.0.6+10	10099861078.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10114843161 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	10114843161.10	logs
variantcalling	17.0.6+10	10114843161.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10146103273 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	10146103273.10	logs
variantcalling	17.0.6+10	10146103273.2	logs

[gatk-bot]

Github actions tests reported job failures from actions build 10306895203 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
cloud	17.0.6+10	10306895203.10	logs
unit	17.0.6+10	10306895203.12	logs
integration	17.0.6+10	10306895203.11	logs
unit	17.0.6+10	10306895203.1	logs
variantcalling	17.0.6+10	10306895203.2	logs
integration	17.0.6+10	10306895203.0	logs