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/90/e2e4769a8c1d5f69f1949a3174e662/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/6eede871c2c3491aa6c913043f062d/D0000162_22q/D0000162_22q_R1.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/c5/6eede871c2c3491aa6c913043f062d/D0000162_22q/D0000162_22q_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/e2e4769a8c1d5f69f1949a3174e662/.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 D0000162_22q.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 2362.048 CPU sec, 85.186 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 0
overall: 68158496768 mem 2011.019 user 361.298 sys 95.443 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:20260529_LH00995_0049_B23YT2HLT4.D0000162_22q.L007\tPU:L007\tSM:D0000162_22q\tLB:D0000162_22q\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 D0000162_22q_R1.fastq.gz D0000162_22q_R2.fastq.gz
[main] Real time: 95.478 sec; CPU: 2372.321 sec
sorting block 0, #reads = 0 mem = 0 peak = 75599872
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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: util-sort
license: sentieon:util=1
output file size: 37898
output reads: 0
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.001 user 0.000 sys 0.002 real
execute: 1 calls 0.062 user 0.123 sys 95.628 real
merge_files: 1 calls 0.029 user 0.107 sys 0.140 real
read_chunk: 2 calls 0.000 user 0.000 sys 0.002 real
sort_block: 1 calls 0.001 user 0.000 sys 0.003 real
overall: 262762496 mem 0.082 user 0.144 sys 95.648 real
ls: cannot access '*.cram': No such file or directory