Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/3635c092701047f5d7b33871d49390/positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/76961641a91958fd74d79f628b171a/positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/9091b606a653aca62f4442b4d2fbf2/positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/199af2584434d7864363d297762b2f/positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/6cf805b23e9c2a6b479cc8302349d5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/7975ae91673545578b7bf0857a3349/positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/6143d845be0eaa4e372521c5d7fe46/positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/1188cffcc9b8c7e44f5e1f3670d784/positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/8a98062ab566c54cc3df9594260ef6/positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/6cf805b23e9c2a6b479cc8302349d5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/5aac92d929ee27d0b8c55598a82e4f/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.chr19_15162349-15162662.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.chr1_68991-70108.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 --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --OUTPUT positive_somatic_control_1.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
16:55:46.702 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 Jun 04 16:55:46 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.chr19_15162349-15162662.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.chr1_68991-70108.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 --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.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 Jun 04 16:55:46 GMT 2026] Executing as ?@nf-bf6cf805b23e9c2a6b479cc8302349d5-46a68-4jk2d 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
[Thu Jun 04 16:55:47 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=192937984
Tool returned:
0