Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/c6ee0df836af2ce0b6040bcbb1e235/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/c6ee0df836af2ce0b6040bcbb1e235/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/1b780e82228e825cb40abaea84a098/HCC1395_tumor.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/foresight_clarity_targets_hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/1b780e82228e825cb40abaea84a098/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
==> STAGING COMPLETE (8 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i HCC1395_tumor.md.bam --algo HsMetricAlgo --targets_list targets/foresight_clarity_targets_hg38.bed --baits_list baits/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed HCC1395_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
No more license available for sentieon:Metrics
progress 5% @chr1:161000001, elapsed 60.0s, est remaining 1140.9s, peak mem 100MB, user 0.2s, sys 0.4s, output queue size 1
progress 10% @chr2:47000001, elapsed 60.1s, est remaining 540.6s, peak mem 100MB, user 0.3s, sys 0.9s, output queue size 26
progress 15% @chr2:236000001, elapsed 60.1s, est remaining 340.5s, peak mem 100MB, user 0.4s, sys 1.6s, output queue size 19
progress 20% @chr3:158000001, elapsed 60.1s, est remaining 240.5s, peak mem 100MB, user 0.5s, sys 2.2s, output queue size 14
progress 25% @chr4:118000001, elapsed 60.1s, est remaining 180.4s, peak mem 100MB, user 0.6s, sys 2.7s, output queue size 25
progress 30% @chr5:88000001, elapsed 60.2s, est remaining 140.4s, peak mem 100MB, user 0.8s, sys 3.4s, output queue size 23
progress 35% @chr6:69000001, elapsed 60.2s, est remaining 111.8s, peak mem 100MB, user 0.9s, sys 3.9s, output queue size 21
progress 40% @chr7:59000001, elapsed 60.2s, est remaining 90.3s, peak mem 100MB, user 1.0s, sys 4.5s, output queue size 12
progress 45% @chr8:57000001, elapsed 60.2s, est remaining 73.6s, peak mem 100MB, user 1.3s, sys 5.0s, output queue size 3
progress 50% @chr9:73000001, elapsed 60.3s, est remaining 60.3s, peak mem 100MB, user 1.3s, sys 5.6s, output queue size 15
progress 55% @chr10:90000001, elapsed 60.3s, est remaining 49.3s, peak mem 100MB, user 1.5s, sys 6.0s, output queue size 5
progress 60% @chr11:122000001, elapsed 60.3s, est remaining 40.2s, peak mem 100MB, user 1.7s, sys 6.6s, output queue size 3
progress 65% @chr13:9000001, elapsed 60.3s, est remaining 32.5s, peak mem 100MB, user 1.8s, sys 7.3s, output queue size 6
progress 70% @chr14:63000001, elapsed 60.3s, est remaining 25.9s, peak mem 100MB, user 1.9s, sys 7.8s, output queue size 7
progress 75% @chr16:13000001, elapsed 60.4s, est remaining 20.1s, peak mem 100MB, user 1.9s, sys 8.3s, output queue size 21
progress 80% @chr18:1, elapsed 60.4s, est remaining 15.1s, peak mem 100MB, user 2.1s, sys 8.9s, output queue size 4
progress 85% @chr20:21000001, elapsed 60.4s, est remaining 10.7s, peak mem 100MB, user 2.2s, sys 9.6s, output queue size 1
progress 90% @chrX:33000001, elapsed 60.5s, est remaining 6.7s, peak mem 129MB, user 2.6s, sys 10.0s, output queue size 114
progress 95% @chrY:34000001, elapsed 60.5s, est remaining 3.2s, peak mem 145MB, user 3.0s, sys 10.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 60.8s, est remaining 0.0s, peak mem 166MB, user 4.0s, sys 11.5s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: HsMetricAlgo
license: sentieon:Metrics=31
input file size: 50813910
reads: 1001320
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1.204 user 5.901 sys 7.529 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.004 user 0.003 sys 60.793 real
idle: 61 calls 0.011 user 0.018 sys 38.413 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 174874624 mem 4.294 user 12.190 sys 62.001 real