File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/efbe37b65923c8953bc5fc5a25de3b/.command.log
Size
2.5 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS (HCC1395_BL)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/c6c19583d7f45f82f68ed89ca3a1ff/HCC1395_BL.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/efbe37b65923c8953bc5fc5a25de3b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/efbe37b65923c8953bc5fc5a25de3b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/de32157441b4354414137b7b901290/HCC1395_BL.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (5 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 HCC1395_BL.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz --INPUT HCC1395_BL.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz --OUTPUT HCC1395_BL.haplotyper.unfiltered.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
20:43:25.966 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
[Mon Jun 08 20:43:25 GMT 2026] MergeVcfs --INPUT HCC1395_BL.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz --INPUT HCC1395_BL.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz --OUTPUT HCC1395_BL.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
[Mon Jun 08 20:43:26 GMT 2026] Executing as ?@nf-d1efbe37b65923c8953bc5fc5a25de3b-f1a09-rh6tm 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
[Mon Jun 08 20:43:26 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=341835776
Tool returned:
0