Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/fca5f3616ff3dba5a32398ee041269/positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/eef38f9c21f03574808a9826d09a9d/positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/fa4002120ec1bb6b834499ee271ec4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/8cc3eda70d4bbb870c9ef518893427/positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/37c0936fa3ee992c1c99a5d66a0867/positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/2154b96e1a48c032c52691e704859b/positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/40a6a0efb3bd199195761e433e350f/positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/fa4002120ec1bb6b834499ee271ec4/.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/cc/e0e5f55c6892143c58dfd1c5d70ce5/positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/dd8361f096f0652257d7634f006daf/positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/3b0c8e3edeac43e1d66ef606d3fff5/positive_somatic_control_2.strelka.chr19_15162349-15162662.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 positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT positive_somatic_control_2.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
16:55:08.211 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 16:55:08 GMT 2026] MergeVcfs --INPUT positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT positive_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
[Thu Jun 04 16:55:08 GMT 2026] Executing as ?@nf-1afa4002120ec1bb6b834499ee271ec4-47dbe-qrmv9 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 16:55:08 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Tool returned:
0
Runtime.totalMemory()=178257920