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/fe/be3d7bfb5026afd3675816ee5bf0a8/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/1984d8eac5163e45df14b90d0e855a/.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/91/1984d8eac5163e45df14b90d0e855a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/be3d7bfb5026afd3675816ee5bf0a8/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 1566.959 CPU sec, 60.727 real sec
[M::process] read 125588 sequences (18133711 bp) in 0.208 CPU sec, 0.216 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 44648, 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: (188, 284, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (308.41, 153.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1064)
[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 125588 reads in 12.634 CPU sec, 0.423 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: 125588
overall: 68485726208 mem 1415.019 user 171.359 sys 67.950 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.L005\tPU:L005\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: 67.987 sec; CPU: 1586.381 sec
sorting block 0, #reads = 125732 mem = 59740910 peak = 165224448
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 192
algo: util-sort
license: sentieon:util=1
output file size: 7392989
output reads: 125732
bam_mem_sort: 1 calls 0.028 user 0.000 sys 0.031 real
bam_write: 1 calls 0.027 user 0.000 sys 0.024 real
execute: 1 calls 0.062 user 0.156 sys 68.359 real
merge_files: 1 calls 0.039 user 0.133 sys 0.306 real
parse_chunk: 2 calls 0.075 user 0.009 sys 0.093 real
read_chunk: 7 calls 0.005 user 0.070 sys 6.720 real
sort_block: 1 calls 0.100 user 0.060 sys 6.678 real
write_chunk: 3 calls 0.010 user 0.018 sys 0.032 real
overall: 471912448 mem 1.506 user 0.359 sys 68.392 real
ls: cannot access '*.cram': No such file or directory