File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/3f4c5eb87a12ccbe0da711fc51921f/.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/47/25e39b187256f944849d0430c61c21/positive_somatic_control_1.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/2a8dbcb349f5fe11a03765f00f5900/positive_somatic_control_1.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/a16f763405c7fe916b5709eb3ab66f/positive_somatic_control_1.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f6/ce0661f0f36636ced1c2d05da448f7/positive_somatic_control_1.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/3f4c5eb87a12ccbe0da711fc51921f/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/a8f1c37590a75474e25d9423c1faba/positive_somatic_control_1.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/3aad7862a3f30d6d1ddc242a29cf5a/positive_somatic_control_1.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/5c933895f2fdf8b2eb23679da47a3d/positive_somatic_control_1.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/4fb9d531d673a63b168ca10574045f/positive_somatic_control_1.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/967cf8127e253e56aabdd1c1bc87fb/positive_somatic_control_1.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/3f4c5eb87a12ccbe0da711fc51921f/.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.chr12_102480219-102480663.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.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr10_74133927-74134264.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.chr20_14085521-14085828.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 --OUTPUT positive_somatic_control_1.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
19:44:14.667 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 19:44:14 GMT 2026] MergeVcfs --INPUT positive_somatic_control_1.strelka.chr12_102480219-102480663.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.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_1.strelka.chr10_74133927-74134264.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.chr20_14085521-14085828.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 --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
[Thu Jun 04 19:44:14 GMT 2026] Executing as ?@nf-5f3f4c5eb87a12ccbe0da711fc51921f-d6fdb-vthmz 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 19:44:15 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=130023424
Tool returned:
0