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/51/d2a6653c947807646d7249a6f58cc6/Sig_18_Blood/Sig_18_Blood_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b0c640d1c25177eecbadc2635792ef/.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/20/b0c640d1c25177eecbadc2635792ef/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/d2a6653c947807646d7249a6f58cc6/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 1595.336 CPU sec, 62.733 real sec
[M::process] read 125394 sequences (18178356 bp) in 0.216 CPU sec, 0.216 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 21.544 CPU sec, 0.724 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: 68479410176 mem 1429.411 user 194.169 sys 70.164 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: 70.196 sec; CPU: 1623.583 sec
sorting block 0, #reads = 125537 mem = 60403849 peak = 166821888
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 0.020 user 0.000 sys 0.027 real
bam_write: 1 calls 0.020 user 0.008 sys 0.021 real
execute: 1 calls 0.047 user 0.165 sys 70.567 real
merge_files: 1 calls 0.024 user 0.140 sys 0.306 real
parse_chunk: 2 calls 0.074 user 0.000 sys 0.092 real
read_chunk: 8 calls 0.000 user 0.064 sys 6.632 real
sort_block: 1 calls 0.080 user 0.059 sys 6.575 real
write_chunk: 4 calls 0.000 user 0.028 sys 0.031 real
overall: 480088064 mem 1.516 user 0.353 sys 70.591 real
ls: cannot access '*.cram': No such file or directory