Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/8a8571420b0810cf69ba4e1c8a81c5/negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/c384998f41e35452be9121ad5fce21/negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/ec85929338f2738aec41ad514d15d7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/d4288bfe6f93e93bf4c1411e997ef0/negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/48aec8acf21faefec642710cf69ebd/negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/ec85929338f2738aec41ad514d15d7/.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/e3/601eba435d6b2dc018de4c17790d8e/negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/9af9453f569eb37dc8b3305c970d4e/negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/0051934782328300101f0efd8715d4/negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/4f9e5655d61759e100cca020dc1cf3/negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/2870669be14269a3300f86ad20b349/negative_somatic_control_1.strelka.chr12_102480219-102480663.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 negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --OUTPUT negative_somatic_control_1.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
16:55:47.521 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 16:55:47 GMT 2026] MergeVcfs --INPUT negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --OUTPUT negative_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 16:55:47 GMT 2026] Executing as ?@nf-a2ec85929338f2738aec41ad514d15d7-858a6-86r68 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()=197132288
Tool returned:
0