File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/78bd3b07321c533afd7ac38cd01867/.command.log
Size
5.1 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS (negative_somatic_control_2)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/7221e1d227c1925a0ea3264828db87/negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/78bd3b07321c533afd7ac38cd01867/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/26ff0a781b507d6e40a8f087be8d33/negative_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/6068cdd61e3281b50213f2ead72a46/negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/1116248d979fd0bf733a51fa508a09/negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/0a7ee56efff04559cda9ab0b16ab98/negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/4942d0fdb5b70fe96a466d754d3a48/negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/c713215a03b40d794ef524c0aa2a21/negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c0/0279134524a56b7509714b39d519f1/negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/374ee5957b89bb366503e82b34a936/negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/78bd3b07321c533afd7ac38cd01867/.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.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 --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 --OUTPUT negative_somatic_control_2.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
14:01:33.682 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
[Fri Jun 05 14:01:33 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.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 --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 --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
[Fri Jun 05 14:01:33 GMT 2026] Executing as ?@nf-7278bd3b07321c533afd7ac38cd01867-9c4c1-dgm67 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
[Fri Jun 05 14:01:34 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=178257920
Tool returned:
0