File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/3f2d66a17d4dcdef50ec883a102923/.command.log
Size
5.1 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS (negative_somatic_control_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7ed58e6cd13a5ce32d1a69da085f5a/negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/3f2d66a17d4dcdef50ec883a102923/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/696948a2e52a7da0964e36fc47ef27/negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7a/f27aeded661b4a4a15e985f4ec3c8b/negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/b9da2789d83227c815d3137c507119/negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/078f6a67c67c16a0b82ff17e00e793/negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/58322c2f9c9b0e77b0518b4468b52a/negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/036ed73b411d21a1c6573d400392cf/negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/3f2d66a17d4dcdef50ec883a102923/.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/db/1bca3892e33eee6a2b59c63f05fab7/negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/3f99ecf859218d621858edbfff40bf/negative_somatic_control_1.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 negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT negative_somatic_control_1.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
17:19:45.418 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 17:19:45 GMT 2026] MergeVcfs --INPUT negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT negative_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
[Thu Jun 04 17:19:45 GMT 2026] Executing as ?@nf-b13f2d66a17d4dcdef50ec883a102923-901ea-sftzx 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 17:19:45 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Tool returned:
0
Runtime.totalMemory()=169869312