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/2f/812f543c73ed00d9fb245712d9b3a9/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/ae81e06d8938fad2c8e725d03a23ba/.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/aa/ae81e06d8938fad2c8e725d03a23ba/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/812f543c73ed00d9fb245712d9b3a9/HCC1395_BL/HCC1395_BL_R1.fastq.gz
==> STAGING COMPLETE (7 inputs)

This software is licensed to bgold@natera.com by Sentieon Inc.
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o HCC1395_BL.bam --sam2bam -
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 1361.552 CPU sec, 46.899 real sec
[M::process] read 124904 sequences (18031367 bp) in 0.184 CPU sec, 0.191 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 44581, 0, 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: (186, 282, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 840)
[M::mem_pestat] mean and std.dev: (307.00, 153.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1058)
[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 124904 reads in 9.679 CPU sec, 0.327 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: 124904
overall: 68558794752 mem 1327.723 user 48.270 sys 51.998 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.HCC1395_BL.L007\tPU:L007\tSM:HCC1395_BL\tLB:HCC1395_BL\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 HCC1395_BL_R1.fastq.gz HCC1395_BL_R2.fastq.gz
[main] Real time: 52.029 sec; CPU: 1375.996 sec
sorting block 0, #reads = 125063 mem = 59373495 peak = 169701376
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: 7316072
output reads: 125063
bam_mem_sort: 1 calls 0.016 user 0.000 sys 0.025 real
bam_write: 1 calls 0.028 user 0.000 sys 0.021 real
execute: 1 calls 0.055 user 0.134 sys 52.355 real
merge_files: 1 calls 0.039 user 0.111 sys 0.264 real
parse_chunk: 2 calls 0.059 user 0.019 sys 0.085 real
read_chunk: 7 calls 0.004 user 0.057 sys 4.702 real
sort_block: 1 calls 0.079 user 0.049 sys 4.657 real
write_chunk: 3 calls 0.010 user 0.017 sys 0.033 real
overall: 496119808 mem 1.362 user 0.305 sys 52.373 real
ls: cannot access '*.cram': No such file or directory