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/5f/9f52db9a598e6d395639b38b8cb90b/.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/90/a25460bbffc406cc04c27c846eeefd/Sig_18_tissue/Sig_18_tissue_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/9f52db9a598e6d395639b38b8cb90b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/a25460bbffc406cc04c27c846eeefd/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 2245.742 CPU sec, 82.049 real sec
[M::process] read 124902 sequences (17673402 bp) in 0.178 CPU sec, 0.188 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 19.976 CPU sec, 0.657 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124902
overall: 68127043584 mem 1842.295 user 428.751 sys 88.043 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: 88.152 sec; CPU: 2271.049 sec
sorting block 0, #reads = 125142 mem = 59607517 peak = 163688448
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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 7084194
output reads: 125142
bam_mem_sort: 1 calls 0.028 user 0.000 sys 0.029 real
bam_write: 1 calls 0.098 user 0.000 sys 0.100 real
execute: 1 calls 0.061 user 0.130 sys 88.463 real
merge_files: 1 calls 0.035 user 0.112 sys 0.266 real
parse_chunk: 2 calls 0.028 user 0.037 sys 0.075 real
read_chunk: 8 calls 0.056 user 0.019 sys 5.267 real
sort_block: 1 calls 0.176 user 0.029 sys 5.310 real
write_chunk: 4 calls 0.011 user 0.022 sys 0.049 real
overall: 453828608 mem 1.319 user 0.263 sys 88.581 real
ls: cannot access '*.cram': No such file or directory