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/3c/ccdbed10220a45ffeadd32c67f5396/Sig_18_Blood/Sig_18_Blood_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/732d4935dddd58c49115de19032ed3/.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/ee/732d4935dddd58c49115de19032ed3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/ccdbed10220a45ffeadd32c67f5396/Sig_18_Blood/Sig_18_Blood_R2.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 Sig_18_Blood.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 1584.968 CPU sec, 57.945 real sec
[M::process] read 124888 sequences (18114909 bp) in 0.213 CPU sec, 0.220 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44931, 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: (192, 290, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 855)
[M::mem_pestat] mean and std.dev: (315.53, 156.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1076)
[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 124888 reads in 28.585 CPU sec, 0.946 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124888
overall: 68526673920 mem 1460.998 user 159.244 sys 65.592 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.Sig_18_Blood.L008\tPU:L008\tSM:Sig_18_Blood\tLB:Sig_18_Blood\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 Sig_18_Blood_R1.fastq.gz Sig_18_Blood_R2.fastq.gz
[main] Real time: 65.624 sec; CPU: 1620.244 sec
sorting block 0, #reads = 125049 mem = 60110585 peak = 168034304
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000606a6
  features: 1f8bfbff fffa320b
  extended: f1bf07ab 00407f5a
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 31 max 128
algo: util-sort
license: sentieon:util=1
output file size: 7453703
output reads: 125049
bam_mem_sort: 1 calls 0.042 user 0.000 sys 0.043 real
bam_write: 1 calls 0.052 user 0.026 sys 0.080 real
execute: 1 calls 0.074 user 0.132 sys 66.073 real
merge_files: 1 calls 0.057 user 0.105 sys 0.304 real
parse_chunk: 2 calls 0.069 user 0.007 sys 0.087 real
read_chunk: 8 calls 0.025 user 0.069 sys 6.627 real
sort_block: 1 calls 0.143 user 0.077 sys 6.643 real
write_chunk: 4 calls 0.016 user 0.006 sys 0.041 real
overall: 490754048 mem 1.703 user 0.385 sys 66.092 real
ls: cannot access '*.cram': No such file or directory