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/a0/4746f92f1df612670333c5c4dc11ed/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/e36173e90c1aa3e5ef47f7c4f510f4/NTC_0002_0010_B23KGCJLT4_1/NTC_0002_0010_B23KGCJLT4_1_R2.fastq.gz
  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/3e/e36173e90c1aa3e5ef47f7c4f510f4/NTC_0002_0010_B23KGCJLT4_1/NTC_0002_0010_B23KGCJLT4_1_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/4746f92f1df612670333c5c4dc11ed/.command.run
==> STAGING COMPLETE (7 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o NTC_0002_0010_B23KGCJLT4_1.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 1819.157 CPU sec, 70.129 real sec
[M::process] read 992 sequences (149664 bp) in 0.000 CPU sec, 0.001 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 2, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[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 992 reads in 2.051 CPU sec, 0.074 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 992
overall: 68421214208 mem 1674.548 user 152.776 sys 76.327 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:B23KGCJLT4.NTC_0002_0010_B23KGCJLT4_1.L006\tPU:L006\tSM:NTC_0002_0010_B23KGCJLT4_1\tLB:NTC_0002_0010_B23KGCJLT4_1\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 NTC_0002_0010_B23KGCJLT4_1_R1.fastq.gz NTC_0002_0010_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 76.364 sec; CPU: 1827.327 sec
sorting block 0, #reads = 1043 mem = 581552 peak = 77160448
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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 108822
output reads: 1043
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.004 user 0.000 sys 0.003 real
execute: 1 calls 0.035 user 0.133 sys 76.474 real
merge_files: 1 calls 0.020 user 0.101 sys 0.129 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.001 real
read_chunk: 4 calls 0.001 user 0.003 sys 6.121 real
sort_block: 1 calls 0.005 user 0.000 sys 6.122 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 267493376 mem 0.088 user 0.140 sys 76.495 real
ls: cannot access '*.cram': No such file or directory