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/fa/c836151604bf952cb212ddd9058f75/.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/17/fe84a83c2a45bb5b98a01f7b8cd09a/Sig_18_tissue/Sig_18_tissue_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/c836151604bf952cb212ddd9058f75/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/fe84a83c2a45bb5b98a01f7b8cd09a/Sig_18_tissue/Sig_18_tissue_R1.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_tissue.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 1348.129 CPU sec, 47.211 real sec
[M::process] read 124960 sequences (17676029 bp) in 0.168 CPU sec, 0.173 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 9.363 CPU sec, 0.322 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124960
overall: 68509323264 mem 1268.368 user 94.296 sys 52.714 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: 52.753 sec; CPU: 1362.666 sec
sorting block 0, #reads = 125203 mem = 59559176 peak = 166817792
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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 7072948
output reads: 125203
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.025 real
bam_write: 1 calls 0.109 user 0.000 sys 0.110 real
execute: 1 calls 0.073 user 0.118 sys 53.177 real
merge_files: 1 calls 0.051 user 0.098 sys 0.272 real
parse_chunk: 2 calls 0.037 user 0.029 sys 0.081 real
read_chunk: 8 calls 0.016 user 0.058 sys 5.127 real
sort_block: 1 calls 0.151 user 0.067 sys 5.176 real
write_chunk: 4 calls 0.006 user 0.024 sys 0.048 real
overall: 473690112 mem 1.313 user 0.251 sys 53.196 real
ls: cannot access '*.cram': No such file or directory