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/ee/64a973ef0dd65210fd2aacd5733eef/.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/3f/02e57185f37673fe55eed0e31351f7/Sig_18_tissue/Sig_18_tissue_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/64a973ef0dd65210fd2aacd5733eef/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3f/02e57185f37673fe55eed0e31351f7/Sig_18_tissue/Sig_18_tissue_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 Sig_18_tissue.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 1580.383 CPU sec, 54.823 real sec
[M::process] read 125244 sequences (17742351 bp) in 0.165 CPU sec, 0.174 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 46956, 0, 1)
[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: (155, 223, 319)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 647)
[M::mem_pestat] mean and std.dev: (246.06, 119.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 811)
[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 125244 reads in 11.017 CPU sec, 0.378 real sec
os version: Linux 6.12.83
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: 125244
overall: 68517224448 mem 1479.884 user 116.406 sys 60.095 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_tissue.L002\tPU:L002\tSM:Sig_18_tissue\tLB:Sig_18_tissue\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_tissue_R1.fastq.gz Sig_18_tissue_R2.fastq.gz
[main] Real time: 60.131 sec; CPU: 1596.293 sec
sorting block 0, #reads = 125469 mem = 59623350 peak = 168439808
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 192
algo: util-sort
license: sentieon:util=1
output file size: 7030812
output reads: 125469
bam_mem_sort: 1 calls 0.019 user 0.000 sys 0.025 real
bam_write: 1 calls 0.085 user 0.010 sys 0.092 real
execute: 1 calls 0.034 user 0.134 sys 60.500 real
merge_files: 1 calls 0.024 user 0.106 sys 0.244 real
parse_chunk: 2 calls 0.044 user 0.016 sys 0.068 real
read_chunk: 8 calls 0.028 user 0.042 sys 4.829 real
sort_block: 1 calls 0.154 user 0.035 sys 4.865 real
write_chunk: 4 calls 0.000 user 0.020 sys 0.030 real
overall: 476000256 mem 1.117 user 0.302 sys 60.521 real
ls: cannot access '*.cram': No such file or directory