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/52/54180bc5f76aa27effdec571f41094/.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/5d/dfb2c4ffa7fccc5409a7962f8fc8fc/Sig_18_tissue/Sig_18_tissue_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/54180bc5f76aa27effdec571f41094/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/dfb2c4ffa7fccc5409a7962f8fc8fc/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 1658.214 CPU sec, 59.199 real sec
[M::process] read 124902 sequences (17673402 bp) in 0.163 CPU sec, 0.172 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 46778, 1, 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, 224, 320)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 652)
[M::mem_pestat] mean and std.dev: (245.77, 118.86)
[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 124902 reads in 22.056 CPU sec, 0.725 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: 124902
overall: 68510953472 mem 1516.834 user 169.750 sys 66.241 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.L004\tPU:L004\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: 66.278 sec; CPU: 1686.587 sec
sorting block 0, #reads = 125142 mem = 59607517 peak = 166821888
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: 7084194
output reads: 125142
bam_mem_sort: 1 calls 0.024 user 0.000 sys 0.026 real
bam_write: 1 calls 0.082 user 0.000 sys 0.081 real
execute: 1 calls 0.065 user 0.114 sys 66.647 real
merge_files: 1 calls 0.047 user 0.090 sys 0.253 real
parse_chunk: 2 calls 0.047 user 0.008 sys 0.069 real
read_chunk: 8 calls 0.041 user 0.022 sys 6.263 real
sort_block: 1 calls 0.158 user 0.022 sys 6.284 real
write_chunk: 4 calls 0.015 user 0.010 sys 0.036 real
overall: 476925952 mem 1.236 user 0.233 sys 66.670 real
ls: cannot access '*.cram': No such file or directory