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/eb/13c374dd7beaa84f6ebbdd037716f2/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/8b7d39ff769b789c12dc083d6c5ea2/.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/59/8b7d39ff769b789c12dc083d6c5ea2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/13c374dd7beaa84f6ebbdd037716f2/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 1557.561 CPU sec, 56.049 real sec
[M::process] read 124700 sequences (17992902 bp) in 0.213 CPU sec, 0.215 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 44507, 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: (186, 282, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 849)
[M::mem_pestat] mean and std.dev: (307.31, 153.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1070)
[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 124700 reads in 19.342 CPU sec, 0.639 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: 124700
overall: 68481056768 mem 1435.543 user 146.923 sys 62.264 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.L002\tPU:L002\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: 62.295 sec; CPU: 1582.470 sec
sorting block 0, #reads = 124816 mem = 59282090 peak = 165273600
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: 7313733
output reads: 124816
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.032 real
bam_write: 1 calls 0.037 user 0.000 sys 0.028 real
execute: 1 calls 0.087 user 0.143 sys 62.711 real
merge_files: 1 calls 0.057 user 0.123 sys 0.330 real
parse_chunk: 2 calls 0.072 user 0.009 sys 0.097 real
read_chunk: 7 calls 0.013 user 0.062 sys 5.513 real
sort_block: 1 calls 0.101 user 0.054 sys 5.457 real
write_chunk: 3 calls 0.015 user 0.004 sys 0.040 real
overall: 471281664 mem 1.835 user 0.320 sys 62.728 real
ls: cannot access '*.cram': No such file or directory