File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/0bf37d6d0694502a8174cba618ec88/.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/d1/2e8e7362a0be0bdfdde3a1fe22a477/negative_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/0bf37d6d0694502a8174cba618ec88/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/7e372414ca6136858b7b8f76129240/negative_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/77b89721bb0caebd8063fd6bfea220/negative_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/40b07f9a5449227b18a2c2f8895ccd/negative_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/c9e2697a659bed6ea0dbd22ba65779/negative_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/778f5c4109dedc322c5b22fb115619/negative_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/d3b6afaaf303949f121fe85f260ae2/negative_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/32b1e3d114be61c2d0add3ad0b0f54/negative_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/650f48823f268cd55c80149438bd63/negative_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/0bf37d6d0694502a8174cba618ec88/.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 .
20:59:16.922 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 Jun 03 20:59:16 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 Jun 03 20:59:16 GMT 2026] Executing as ?@nf-850bf37d6d0694502a8174cba618ec88-55352-q7wg9 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
[Wed Jun 03 20:59:17 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=144703488
Tool returned:
0