File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/57c9974798795051caa1eff4010629/.command.log
Size
5.1 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS (positive_somatic_control_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/b7ba67cd642e595adc151b4eb56c4c/positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/29bbcc9d8cb688b0e8a287a2f08029/positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/1f0365e92a8c9e1eb3987a173396f4/positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/96690a5ac6cdff8256d2628693cf82/positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/57c9974798795051caa1eff4010629/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/98e4aafe9bfc7479e7dbcc3aa563c3/positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/196d089fe141cd7387374d5cefb524/positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/07b7b4f5579bd5a614924ab8b55f8d/positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/9f3157c5bd665f6063d1419fe2dc98/positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/ee983d89b915920183c28a16f1cde4/positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/57c9974798795051caa1eff4010629/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> 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 positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --OUTPUT positive_somatic_control_1.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
22:21:29.711 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 22:21:29 GMT 2026] MergeVcfs --INPUT positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --OUTPUT positive_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
[Mon Jun 08 22:21:29 GMT 2026] Executing as ?@nf-6a57c9974798795051caa1eff4010629-b4f1d-thbpn 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 22:21:30 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=293601280
Tool returned:
0