File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/0ff2fcbe6927865e4ecdc0d7466222/.command.log
Size
5.1 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS (pos_somatic_016)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/c9deeb8f2f10f764aa5c69df71da5f/pos_somatic_016.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/fcc3d62690840639b8561faf33bcdb/pos_somatic_016.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/0ff2fcbe6927865e4ecdc0d7466222/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/62c06550cd1ecf11dc3f96594d4563/pos_somatic_016.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/1efe9b793874593be2bca4a54b6152/pos_somatic_016.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/4c906012365fa159433be7acd47685/pos_somatic_016.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/60a42d05b1fe2c2fd427a182c9dffd/pos_somatic_016.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/246a760a2fc89b94b65003734d2166/pos_somatic_016.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/0ff2fcbe6927865e4ecdc0d7466222/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/c8ffdeceb7523baff6ff57ca20a070/pos_somatic_016.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/01e70d7266814544de6e76f7e5c2bf/pos_somatic_016.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  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 pos_somatic_016.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --OUTPUT pos_somatic_016.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
19:56:42.651 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 19:56:42 GMT 2026] MergeVcfs --INPUT pos_somatic_016.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT pos_somatic_016.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --OUTPUT pos_somatic_016.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 19:56:42 GMT 2026] Executing as ?@nf-0c0ff2fcbe6927865e4ecdc0d7466222-80f89-lw9kn 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
INFO	2026-06-04 19:56:43	MergeVcfs	Processed        10,000 records.  Elapsed time: 00:00:00s.  Time for last 10,000:    0s.  Last read position: chr6:31,723,754
INFO	2026-06-04 19:56:43	MergeVcfs	Processed        20,000 records.  Elapsed time: 00:00:00s.  Time for last 10,000:    0s.  Last read position: chr12:122,855,583
[Thu Jun 04 19:56:43 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=226492416
Tool returned:
0