File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/4e96c8e1c888593741ef2c533b208e/.command.log
Size
3.5 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS (germline_control_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/4e96c8e1c888593741ef2c533b208e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/1fadc4b877c588261657929a2269c0/germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/9d207621ff3899f540127c08a1a4a9/germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/4e96c8e1c888593741ef2c533b208e/.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/b0/64a791bcfe36427882d7b2a34ab5da/germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/c22ace01d2c582d39f4f1535772d60/germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/926f2b46766d05d3599d14dfdc7cf0/germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz
==> STAGING COMPLETE (8 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 germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz --OUTPUT germline_control_1.haplotyper.unfiltered.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
17:04:37.975 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 17:04:38 GMT 2026] MergeVcfs --INPUT germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz --OUTPUT germline_control_1.haplotyper.unfiltered.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 17:04:38 GMT 2026] Executing as ?@nf-994e96c8e1c888593741ef2c533b208e-9662c-x6g4d 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 17:04:38 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=115343360
Tool returned:
0