File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/856250258cea4ca30d4b7f34e31bae/.command.log
Size
5.1 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS (negative_somatic_control_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/d72d95d354f9f8d177cde2789f1692/negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/856250258cea4ca30d4b7f34e31bae/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/24c1e6a03a46b83d507556a1dee859/negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/2401ab986fab590fe8c16e53147590/negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/feee377997101861535bd0307528ca/negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/e6522ac977542bb276e925fe7793ed/negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/e065f5d197d4f8f46ccaa00d6cb210/negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/856250258cea4ca30d4b7f34e31bae/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/238f1ae47563581fc5470715dd4672/negative_somatic_control_1.strelka.chr9_110971973-110972217.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/ab/c8482437a885d6a50faab179456263/negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/e288446ef1e4ec49a017b5ac0668b3/negative_somatic_control_1.strelka.chr10_74133927-74134264.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_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --OUTPUT negative_somatic_control_1.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
21:46:50.580 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 21:46:50 GMT 2026] MergeVcfs --INPUT negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --OUTPUT negative_somatic_control_1.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
[Wed Jun 03 21:46:50 GMT 2026] Executing as ?@nf-51856250258cea4ca30d4b7f34e31bae-0af0e-8lmql 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 21:46:50 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=341835776
Tool returned:
0