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/fd/5d3ac4d9f62d2ba567dd2f849da5b1/Sig_18_Blood/Sig_18_Blood_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/9ea75918c79b7a0bf61749e7459cd8/.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/ad/9ea75918c79b7a0bf61749e7459cd8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/5d3ac4d9f62d2ba567dd2f849da5b1/Sig_18_Blood/Sig_18_Blood_R2.fastq.gz
==> STAGING COMPLETE (7 inputs)

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.
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 1987.745 CPU sec, 79.016 real sec
[M::process] read 125394 sequences (18178356 bp) in 0.204 CPU sec, 0.214 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 45026, 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: (191, 291, 414)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 860)
[M::mem_pestat] mean and std.dev: (315.20, 156.87)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1083)
[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 125394 reads in 22.437 CPU sec, 0.735 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125394
overall: 68410232832 mem 1781.196 user 235.602 sys 86.383 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.L001\tPU:L001\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: 86.426 sec; CPU: 2016.801 sec
sorting block 0, #reads = 125537 mem = 60403849 peak = 165273600
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 7527494
output reads: 125537
bam_mem_sort: 1 calls 0.022 user 0.000 sys 0.027 real
bam_write: 1 calls 0.017 user 0.010 sys 0.021 real
execute: 1 calls 0.061 user 0.148 sys 86.782 real
merge_files: 1 calls 0.037 user 0.124 sys 0.300 real
parse_chunk: 2 calls 0.050 user 0.031 sys 0.090 real
read_chunk: 8 calls 0.022 user 0.057 sys 6.556 real
sort_block: 1 calls 0.068 user 0.089 sys 6.507 real
write_chunk: 4 calls 0.009 user 0.008 sys 0.030 real
overall: 478793728 mem 1.562 user 0.312 sys 86.818 real
ls: cannot access '*.cram': No such file or directory