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/da/210c748167c24a247b317f093f0bb4/.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/8c/9642204284cafdac57a9d2883cd811/Sig_18_tissue/Sig_18_tissue_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/210c748167c24a247b317f093f0bb4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/9642204284cafdac57a9d2883cd811/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 2619.835 CPU sec, 101.049 real sec
[M::process] read 125154 sequences (17709424 bp) in 0.170 CPU sec, 0.173 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 22.118 CPU sec, 0.730 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: 125154
overall: 67960315904 mem 2244.581 user 403.596 sys 108.013 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: 108.053 sec; CPU: 2648.181 sec
sorting block 0, #reads = 125386 mem = 59501897 peak = 163651584
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: 7015338
output reads: 125386
bam_mem_sort: 1 calls 0.035 user 0.000 sys 0.037 real
bam_write: 1 calls 0.043 user 0.003 sys 0.045 real
execute: 1 calls 0.040 user 0.159 sys 108.446 real
merge_files: 1 calls 0.038 user 0.116 sys 0.284 real
parse_chunk: 2 calls 0.069 user 0.008 sys 0.087 real
read_chunk: 7 calls 0.035 user 0.054 sys 6.192 real
sort_block: 1 calls 0.131 user 0.059 sys 6.187 real
write_chunk: 3 calls 0.008 user 0.024 sys 0.037 real
overall: 472625152 mem 1.285 user 0.418 sys 108.467 real
ls: cannot access '*.cram': No such file or directory