File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/3092ff0aa0457e984bff4b167c4d51/.command.log
Size
5.1 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS (negative_somatic_control_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/eca02bab50d4af8379d8b3f3e17745/negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/ca34ae33503111418f31a7e3ed94ce/negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/3092ff0aa0457e984bff4b167c4d51/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/18f7a401fcc6ed6f49d24f0a3a9dd5/negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/b6ee742f6e49ad0b8c3d002beafe66/negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/3092ff0aa0457e984bff4b167c4d51/.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/39/67eec4051e396a9e56b0be0fa0405f/negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/8875781b95a0cfd0a4fd2dc9b8085d/negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/2f8f35e2e66e7c05a3e1ea6265ee1d/negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/faab0c21807f7326b7e52fa4fa29e8/negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/2a72ae53d22b2a362bf6b56b605c0b/negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.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_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT negative_somatic_control_1.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
17:37:25.268 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 17:37:25 GMT 2026] MergeVcfs --INPUT negative_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_snvs.vcf.gz --INPUT negative_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_snvs.vcf.gz --OUTPUT negative_somatic_control_1.strelka.somatic_snvs.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 17:37:25 GMT 2026] Executing as ?@nf-353092ff0aa0457e984bff4b167c4d51-9bf3f-h6rwr 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 17:37:25 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=333447168
Tool returned:
0