Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/261a047028d4af4c7e6ca8a8d2ba00/positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/0da2daeadc2db307135a0ee8c830d5/positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/b85cc05e14f4a6c269988f242c02ef/positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/b2bac87c27fd07aed858bdea31588d/positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/2b2e864409034cfd470b17f20b2c6d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/6d40a6182e59667e8e6c6b9c415686/positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/aa8b40963adf6651389f4b0b0f2575/positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/c9e91507588a2419aec7d9a3f81937/positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/ac06c7e104ef09f7c0028f174c8c40/positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/2b2e864409034cfd470b17f20b2c6d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/62/6e1ef8385cc04ea3c9036c4657229c/positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz
  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.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT positive_somatic_control_1.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
05:37:13.482 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
[Thu May 28 05:37:13 GMT 2026] MergeVcfs --INPUT positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT positive_somatic_control_1.strelka.somatic_snvs.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
[Thu May 28 05:37:13 GMT 2026] Executing as ?@nf-832b2e864409034cfd470b17f20b2c6d-59a5f-w7frd on Linux 6.12.83 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
[Thu May 28 05:37:13 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=199229440
Tool returned:
0