File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/945407c2b95b088273ef8a676f22f6/.command.log
Size
4.8 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_INDELS (neg_somatic_004)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/945407c2b95b088273ef8a676f22f6/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/25d7c5ccd2c6e128dc01ccaf8532e0/neg_somatic_004.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/0bce29a55909f5aaf3874013b7c7a8/neg_somatic_004.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/90174de269c3edddd843212f89e211/neg_somatic_004.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/5f7e017ba8878f7c6dafbcfcd7e9a8/neg_somatic_004.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/dc6ca5ad3f0187587d8a29b9b84fdf/neg_somatic_004.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/1132bc93da474e111017dea37b7a34/neg_somatic_004.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/945407c2b95b088273ef8a676f22f6/.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/9a/d8058f41f15b39b7a7b87855564504/neg_somatic_004.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/06bce178a71eac6b73b1da556bb28b/neg_somatic_004.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/78356e2f865be8e2a556976906a970/neg_somatic_004.strelka.chr10_74133927-74134264.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 neg_somatic_004.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --OUTPUT neg_somatic_004.strelka.somatic_indels.vcf.gz --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict --TMP_DIR .
19:37:41.725 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 19:37:41 GMT 2026] MergeVcfs --INPUT neg_somatic_004.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT neg_somatic_004.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --OUTPUT neg_somatic_004.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 19:37:41 GMT 2026] Executing as ?@nf-1c945407c2b95b088273ef8a676f22f6-9a4f9-fjl4j 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 19:37:42 GMT 2026] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=222298112
Tool returned:
0