Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/16d69c2c0e57babc7ebb1b0b423dc2/neg_somatic_000.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/779c3ae4d546f38e85ea76c59a8d4e/neg_somatic_000.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/600b5bba8838c91cadae10a4e03cb0/neg_somatic_000.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/e71ce792963ef64fa167549f11aee8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/d38ab7c6773ddb408b7dbc9aaf5fe0/neg_somatic_000.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/d1dd0f4bbde7103b87eb240aa750c3/neg_somatic_000.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/806be3ac89e3f571191b6829c0b5c0/neg_somatic_000.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/e71ce792963ef64fa167549f11aee8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/5bbd8745d006045b1350b5f8c75829/neg_somatic_000.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/f9bfb11c1df0ad7288a05f834a95ec/neg_somatic_000.strelka.chr4_22420786-22421189.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/d2/58c2fdca8b37a3683b7e3dd42f9422/neg_somatic_000.strelka.chr12_102480219-102480663.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 neg_somatic_000.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --OUTPUT neg_somatic_000.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
19:38:40.150 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 19:38:40 GMT 2026] MergeVcfs --INPUT neg_somatic_000.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT neg_somatic_000.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --OUTPUT neg_somatic_000.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
[Thu Jun 04 19:38:40 GMT 2026] Executing as ?@nf-73e71ce792963ef64fa167549f11aee8-e823c-q2rvc 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 19:38:40 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=264241152
Tool returned:
0