File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/83b3919c1c87d18c2de9185aebb5b5/.command.log
Size
4.8 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS (neg_somatic_009)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/946525fa5ec7fe1b733ac7814067fb/neg_somatic_009.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/7224a0a07c512d643c6689f3ebd0ca/neg_somatic_009.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/83b3919c1c87d18c2de9185aebb5b5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/49ff13df03ac161e721cfc4aef63d5/neg_somatic_009.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/7d3188f73f2ad9a2485b9c5ccb6b9a/neg_somatic_009.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/fa87029faf0c213cef1baba6872395/neg_somatic_009.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/46d415dc0447bc34f29618a098b5f0/neg_somatic_009.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/1344c7ca07a73a1e62c733b7186df0/neg_somatic_009.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/ee7e143c0763c3cf14dfe31a118d3b/neg_somatic_009.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/83b3919c1c87d18c2de9185aebb5b5/.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/da/af6bfcb314de131ff433065a97dfe9/neg_somatic_009.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 neg_somatic_009.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --OUTPUT neg_somatic_009.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
19:38:45.979 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 19:38:46 GMT 2026] MergeVcfs --INPUT neg_somatic_009.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT neg_somatic_009.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --OUTPUT neg_somatic_009.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
[Thu Jun 04 19:38:46 GMT 2026] Executing as ?@nf-3b83b3919c1c87d18c2de9185aebb5b5-181ba-fppgq 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 19:38:47 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=253755392
Tool returned:
0