File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/1dee9e932e382441c08ac29a1673fe/.command.log
Size
2.9 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS (custom_Sig_18_tumor_normal)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/359a0ed1f04c3451c78939ab676afd/custom_Sig_18_tumor_normal.strelka.chr21_5117003-5117331.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/67c4fae7bc73cbfc8d56fc84b2bf51/custom_Sig_18_tumor_normal.strelka.chr21_34799195-34799564.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/1dee9e932e382441c08ac29a1673fe/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/08/272228f2a6fe982ce3fc6b74dd43f9/custom_Sig_18_tumor_normal.strelka.chr21_44102678-44103072.bed.somatic_snvs.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/1dee9e932e382441c08ac29a1673fe/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (6 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 custom_Sig_18_tumor_normal.strelka.chr21_44102678-44103072.bed.somatic_snvs.vcf.gz --INPUT custom_Sig_18_tumor_normal.strelka.chr21_5117003-5117331.bed.somatic_snvs.vcf.gz --INPUT custom_Sig_18_tumor_normal.strelka.chr21_34799195-34799564.bed.somatic_snvs.vcf.gz --OUTPUT custom_Sig_18_tumor_normal.strelka.somatic_snvs.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
20:37:56.539 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 20:37:56 GMT 2026] MergeVcfs --INPUT custom_Sig_18_tumor_normal.strelka.chr21_44102678-44103072.bed.somatic_snvs.vcf.gz --INPUT custom_Sig_18_tumor_normal.strelka.chr21_5117003-5117331.bed.somatic_snvs.vcf.gz --INPUT custom_Sig_18_tumor_normal.strelka.chr21_34799195-34799564.bed.somatic_snvs.vcf.gz --OUTPUT custom_Sig_18_tumor_normal.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 20:37:56 GMT 2026] Executing as ?@nf-a21dee9e932e382441c08ac29a1673fe-aa87f-z9xv8 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 20:37:56 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=358612992
Tool returned:
0