Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/2f72921688686f79be23f3d97bf8c3/negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/1fffe445f50a0e14bac472df65ad88/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/bf4e77cd7935e064bb644d6d171430/negative_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/fa5bf381de3434bec2bd0f63ffa53a/negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/ef0ce02e01365a2d36ec02a03a5e40/negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/93623dd2914e57054c402fb415136b/negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/badbc58e56a014171c61b7eb9e47f2/negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/2a4c3cd8d7bcc9699bd39f5a911c6f/negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/812513dc71877c1efab743b9eb5255/negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/504d80d3c785555bd86b21f1e38f54/negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/1fffe445f50a0e14bac472df65ad88/.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 negative_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT negative_somatic_control_2.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
15:32:25.372 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 May 27 15:32:25 GMT 2026] MergeVcfs --INPUT negative_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT negative_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 May 27 15:32:25 GMT 2026] Executing as ?@nf-751fffe445f50a0e14bac472df65ad88-0b3f3-r7mpc 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
[Wed May 27 15:32:25 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=127926272
Tool returned:
0