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/5d/d97e28426f76b50e4b35e0f687e9ef/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/074c78fa2af42f4ecba9e0a18baead/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/b7/074c78fa2af42f4ecba9e0a18baead/NTC_0002_0010_B23KGCJLT4_1/NTC_0002_0010_B23KGCJLT4_1_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/d97e28426f76b50e4b35e0f687e9ef/.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 1856.250 CPU sec, 64.266 real sec
[M::process] read 976 sequences (146990 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 976 reads in 2.167 CPU sec, 0.076 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: 976
overall: 68498296832 mem 1720.121 user 143.646 sys 69.700 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.L007\tPU:L007\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: 69.737 sec; CPU: 1863.770 sec
sorting block 0, #reads = 1015 mem = 566974 peak = 77168640
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: 108054
output reads: 1015
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.004 user 0.000 sys 0.004 real
execute: 1 calls 0.079 user 0.086 sys 69.856 real
merge_files: 1 calls 0.052 user 0.069 sys 0.133 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.001 real
read_chunk: 4 calls 0.001 user 0.003 sys 5.359 real
sort_block: 1 calls 0.006 user 0.000 sys 5.361 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 265191424 mem 0.123 user 0.107 sys 69.876 real
ls: cannot access '*.cram': No such file or directory