Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/3dba2e9c067a64493f6b1088594be3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/7bd2afe7d8805cc25a22dfff4b1c59/positive_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/8fd9d44764f3ad347c58fdec5a77a4/positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/648216267c49cceaae5cdd058250b9/positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c2/915921feeb27155444fea3f784fd24/positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/420eb84a371cfd942b21c1d4fcd22d/positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/b6cc79071ff3ea7a23f8ec49745409/positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/445dbfa56dc8a66e172429b6beba18/positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/3dba2e9c067a64493f6b1088594be3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/7943787c809884ea01f0e397c8a8fd/positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/b390a1af592e6515cb7505b6222678/positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
==> 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_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT positive_somatic_control_2.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
20:59:17.096 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
[Wed Jun 03 20:59:17 GMT 2026] MergeVcfs --INPUT positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT positive_somatic_control_2.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
[Wed Jun 03 20:59:17 GMT 2026] Executing as ?@nf-903dba2e9c067a64493f6b1088594be3-5bd8e-hjdlq 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
[Wed Jun 03 20:59:17 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=367001600
Tool returned:
0