Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/2264c4e7816caf1d67ccb261b5c637/positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/17000b8f125aa90aada83ceb19baa5/positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/0dc76c699bd59c420b985816715eb4/positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/318d1e43635ee8dd11e513d5607008/positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/5079b03476c67258990bfd12113d2f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/fcea1fb81584c536e4ce18be19ca61/positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6df77d3bd92942a90ff14809d8189e/positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/6b3013e9d9b82eec558f6b032b640e/positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/601772304568b45fff9fce446c2b06/positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/c3f48e42b42f75a3f3cee7607d1f51/positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/5079b03476c67258990bfd12113d2f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (12 inputs)

Using GATK jar /usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-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 -Xmx3276M -XX:-UsePerfData -jar /usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar MergeVcfs --INPUT positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT positive_somatic_control_1.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
22:18:20.322 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.5.0.0-0/gatk-package-4.5.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 22:18:20 GMT 2026] MergeVcfs --INPUT positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT positive_somatic_control_1.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR . --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX true --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Mon Jun 08 22:18:20 GMT 2026] Executing as ?@nf-ab5079b03476c67258990bfd12113d2f-61840-tmq59 on Linux 6.12.88 amd64; OpenJDK 64-Bit Server VM 17.0.10-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.5.0.0
[Mon Jun 08 22:18:20 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=360710144
Tool returned:
0