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/5c/5372a0f53550a8d0a1858f3bc96e64/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/c4e98831a30a7c0afc2fc668203ebf/.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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/c4e98831a30a7c0afc2fc668203ebf/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/5372a0f53550a8d0a1858f3bc96e64/HCC1395_BL/HCC1395_BL_R1.fastq.gz
==> STAGING COMPLETE (7 inputs)

This software is licensed to bgold@natera.com by Sentieon Inc.
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_BL.bam --sam2bam -
This software is licensed to bgold@natera.com by Sentieon Inc.
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 2930.366 CPU sec, 112.261 real sec
[M::process] read 124828 sequences (18022863 bp) in 0.166 CPU sec, 0.175 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44466, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (186, 282, 403)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 837)
[M::mem_pestat] mean and std.dev: (306.65, 153.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1054)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 124828 reads in 35.794 CPU sec, 1.167 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124828
overall: 68032671744 mem 2246.817 user 730.296 sys 124.386 real
[main] Version: 0.7.17-r1188
[main] CMD: /opt/conda/share/sentieon-202308.03-3/libexec/bwa mem -K 100000000 -Y -R @RG\tID:REGRESSION.HCC1395_BL.L006\tPU:L006\tSM:HCC1395_BL\tLB:HCC1395_BL\tDS:s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta\tPL:ILLUMINA -t 31 ./BWAIndex/Homo_sapiens_assembly38.fasta.64 HCC1395_BL_R1.fastq.gz HCC1395_BL_R2.fastq.gz
[main] Real time: 124.415 sec; CPU: 2977.116 sec
sorting block 0, #reads = 124937 mem = 59360983 peak = 160505856
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: util-sort
license: sentieon:util=1
output file size: 7327533
output reads: 124937
bam_mem_sort: 1 calls 0.018 user 0.000 sys 0.026 real
bam_write: 1 calls 0.102 user 0.016 sys 0.110 real
execute: 1 calls 0.085 user 0.165 sys 124.885 real
merge_files: 1 calls 0.062 user 0.146 sys 0.316 real
parse_chunk: 2 calls 0.046 user 0.024 sys 0.080 real
read_chunk: 7 calls 0.020 user 0.046 sys 10.903 real
sort_block: 1 calls 0.138 user 0.080 sys 10.946 real
write_chunk: 3 calls 0.020 user 0.030 sys 0.060 real
overall: 459026432 mem 1.271 user 0.427 sys 124.906 real
ls: cannot access '*.cram': No such file or directory