Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/7797af8302a8f26e69c3e29f326378/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  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/5d/c51aab4bf4056af585f0083a156c68/Sig_18_tissue/Sig_18_tissue_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/7797af8302a8f26e69c3e29f326378/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/c51aab4bf4056af585f0083a156c68/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 2303.447 CPU sec, 93.859 real sec
[M::process] read 124960 sequences (17676029 bp) in 0.167 CPU sec, 0.171 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 46672, 3, 3)
[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: (154, 223, 320)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 652)
[M::mem_pestat] mean and std.dev: (246.09, 119.65)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 818)
[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 124960 reads in 13.978 CPU sec, 0.465 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: 124960
overall: 68256038912 mem 2032.065 user 293.654 sys 102.621 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.L006\tPU:L006\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: 102.648 sec; CPU: 2325.722 sec
sorting block 0, #reads = 125203 mem = 59559176 peak = 163663872
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: 7072948
output reads: 125203
bam_mem_sort: 1 calls 0.028 user 0.001 sys 0.030 real
bam_write: 1 calls 0.082 user 0.014 sys 0.097 real
execute: 1 calls 0.038 user 0.158 sys 103.058 real
merge_files: 1 calls 0.021 user 0.133 sys 0.261 real
parse_chunk: 2 calls 0.044 user 0.033 sys 0.081 real
read_chunk: 8 calls 0.015 user 0.063 sys 8.238 real
sort_block: 1 calls 0.128 user 0.082 sys 8.286 real
write_chunk: 4 calls 0.000 user 0.031 sys 0.034 real
overall: 474005504 mem 1.155 user 0.368 sys 103.075 real
ls: cannot access '*.cram': No such file or directory