Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/63fe072cd1a3266a4732d8bf7934c5/negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/d65c277075f40b12a126e40c040099/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/b5d0cc914c7d697ea70bece5b0050b/negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/ac492d61e0dfc5cad07256a1c4d7a7/negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/4d5fa890a536365a4dd8added98120/negative_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/153a93fb501dd641af1e3637c1e5b7/negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/33c485c585f69553975defb9f0282b/negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/d65c277075f40b12a126e40c040099/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/d6619eb3626fc89f9d868e5113ea16/negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/7298874873e471d35e790c1cde8739/negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  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/e5/2c6cb864af49f1dbacb3575632ce57/negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.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_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT negative_somatic_control_2.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
22:20:13.347 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
[Mon Jun 08 22:20:13 GMT 2026] MergeVcfs --INPUT negative_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT negative_somatic_control_2.strelka.somatic_indels.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
[Mon Jun 08 22:20:13 GMT 2026] Executing as ?@nf-67d65c277075f40b12a126e40c040099-afdb6-nxqgx 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
[Mon Jun 08 22:20:13 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=320864256
Tool returned:
0