File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/577bb3c3af543114e04dbef3fb6a8e/.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_2)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/b064f8a76d620172adb894eb7b73db/positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bc/c1e99592be14499b7e11a84014955e/positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/577bb3c3af543114e04dbef3fb6a8e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/f988f51a662e899706e33267860537/positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/ca413dbeb7a138ea4c0c436b80f580/positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/f470c3121e77dd7b67f0256a574f8a/positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/5888ae167f060cadc4808ddb3994e4/positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/577bb3c3af543114e04dbef3fb6a8e/.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/56/5123e3deafff7a3fcfb40316c272b0/positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/65d2a9345e97a134eb15bc01b67beb/positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/2cfe80fdfacff14a2834c30ac65d54/positive_somatic_control_2.strelka.chr19_15162349-15162662.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 positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT positive_somatic_control_2.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
17:19:43.293 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 17:19:43 GMT 2026] MergeVcfs --INPUT positive_somatic_control_2.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT positive_somatic_control_2.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --OUTPUT positive_somatic_control_2.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 17:19:43 GMT 2026] Executing as ?@nf-b0577bb3c3af543114e04dbef3fb6a8e-1529e-b54bh 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 17:19:43 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=180355072
Tool returned:
0