File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/b2e244895daf29192da6642e514deb/.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

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/b2e244895daf29192da6642e514deb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/c6e286c0c08dac984a859e37efe139/germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/168529841e1d7fb51fa2a3e741dcbf/germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/b2e244895daf29192da6642e514deb/.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/e4/987a466acb810f9eb26eaf185f89fc/germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/dbf9ae5058424671301b20df028068/germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/12df46fd5dcc03989face677d41579/germline_control_1.haplotyper.chr1_69091-70008.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.chr14_64122012-64122133.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr1_69091-70008.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 .
16:55:08.855 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 16:55:08 GMT 2026] MergeVcfs --INPUT germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr1_69091-70008.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 16:55:08 GMT 2026] Executing as ?@nf-0fb2e244895daf29192da6642e514deb-d7c75-h2dgb 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 16:55:09 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=186646528
Tool returned:
0