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/e3/dfb732597e79114eb9c5563b02c6ce/Sig_18_Blood/Sig_18_Blood_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/9d3b6095b14323d77a7a48247c9ade/.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/ce/9d3b6095b14323d77a7a48247c9ade/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/dfb732597e79114eb9c5563b02c6ce/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 2871.564 CPU sec, 114.738 real sec
[M::process] read 125180 sequences (18146427 bp) in 0.178 CPU sec, 0.181 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44859, 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, 289, 415)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 863)
[M::mem_pestat] mean and std.dev: (315.14, 156.56)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1087)
[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 125180 reads in 28.950 CPU sec, 0.948 real sec
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
algo: bwa-mem
license: sentieon:klib=31
reads: 125180
overall: 67957223424 mem 2266.366 user 641.610 sys 123.152 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.L003\tPU:L003\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: 123.184 sec; CPU: 2907.978 sec
sorting block 0, #reads = 125327 mem = 60250287 peak = 163577856
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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 7480298
output reads: 125327
bam_mem_sort: 1 calls 0.026 user 0.000 sys 0.032 real
bam_write: 1 calls 0.090 user 0.000 sys 0.088 real
execute: 1 calls 0.063 user 0.127 sys 123.589 real
merge_files: 1 calls 0.055 user 0.093 sys 0.265 real
parse_chunk: 2 calls 0.052 user 0.040 sys 0.103 real
read_chunk: 8 calls 0.018 user 0.064 sys 7.403 real
sort_block: 1 calls 0.135 user 0.067 sys 7.439 real
write_chunk: 4 calls 0.011 user 0.012 sys 0.035 real
overall: 476401664 mem 1.249 user 0.413 sys 123.607 real
ls: cannot access '*.cram': No such file or directory