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/0a/74aeb7f69ceded08e0bdff53f6372b/.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/6d/e409ea2e15e7ca672e8cce2cc1b855/Sig_18_tissue/Sig_18_tissue_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/74aeb7f69ceded08e0bdff53f6372b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/e409ea2e15e7ca672e8cce2cc1b855/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 1363.002 CPU sec, 46.895 real sec
[M::process] read 125154 sequences (17709424 bp) in 0.204 CPU sec, 0.206 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 46750, 1, 2)
[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: (153, 224, 319)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 651)
[M::mem_pestat] mean and std.dev: (245.57, 119.23)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 817)
[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 125154 reads in 11.090 CPU sec, 0.371 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125154
overall: 68558823424 mem 1329.003 user 49.921 sys 52.114 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.L001\tPU:L001\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: 52.159 sec; CPU: 1378.926 sec
sorting block 0, #reads = 125386 mem = 59501897 peak = 169820160
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: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 64
algo: util-sort
license: sentieon:util=1
output file size: 7015338
output reads: 125386
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.026 real
bam_write: 1 calls 0.021 user 0.000 sys 0.018 real
execute: 1 calls 0.036 user 0.140 sys 52.448 real
merge_files: 1 calls 0.016 user 0.115 sys 0.254 real
parse_chunk: 2 calls 0.046 user 0.018 sys 0.080 real
read_chunk: 7 calls 0.029 user 0.026 sys 4.760 real
sort_block: 1 calls 0.082 user 0.038 sys 4.714 real
write_chunk: 3 calls 0.000 user 0.015 sys 0.026 real
overall: 493711360 mem 1.357 user 0.248 sys 52.488 real
ls: cannot access '*.cram': No such file or directory