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/31/20903647f1ea0b9d9d1940b5fd3c98/Sig_18_Blood/Sig_18_Blood_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/6d7cc8ee020bb865b86ec16ac59782/.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/1c/6d7cc8ee020bb865b86ec16ac59782/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/20903647f1ea0b9d9d1940b5fd3c98/Sig_18_Blood/Sig_18_Blood_R2.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_Blood.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 1694.441 CPU sec, 60.670 real sec
[M::process] read 124736 sequences (18072176 bp) in 0.173 CPU sec, 0.176 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44863, 0, 1)
[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: (189, 289, 417)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (315.26, 157.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1101)
[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 124736 reads in 21.752 CPU sec, 0.718 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: 124736
overall: 68504604672 mem 1566.383 user 155.747 sys 67.328 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_Blood.L007\tPU:L007\tSM:Sig_18_Blood\tLB:Sig_18_Blood\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_Blood_R1.fastq.gz Sig_18_Blood_R2.fastq.gz
[main] Real time: 67.365 sec; CPU: 1722.134 sec
sorting block 0, #reads = 124877 mem = 60037142 peak = 166850560
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 192
algo: util-sort
license: sentieon:util=1
output file size: 7455819
output reads: 124877
bam_mem_sort: 1 calls 0.030 user 0.000 sys 0.030 real
bam_write: 1 calls 0.022 user 0.011 sys 0.035 real
execute: 1 calls 0.027 user 0.164 sys 67.718 real
merge_files: 1 calls 0.017 user 0.134 sys 0.275 real
parse_chunk: 2 calls 0.064 user 0.010 sys 0.092 real
read_chunk: 8 calls 0.039 user 0.058 sys 5.891 real
sort_block: 1 calls 0.082 user 0.062 sys 5.859 real
write_chunk: 4 calls 0.000 user 0.031 sys 0.035 real
overall: 476061696 mem 1.400 user 0.384 sys 67.738 real
ls: cannot access '*.cram': No such file or directory