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/fd/1ab7a43bc3fd630eec583a1d057470/NTC_0002_0014_B23KGCJLT4_1/NTC_0002_0014_B23KGCJLT4_1_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/6cea635713f101411207ce672026b5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/1ab7a43bc3fd630eec583a1d057470/NTC_0002_0014_B23KGCJLT4_1/NTC_0002_0014_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/4c/6cea635713f101411207ce672026b5/.command.run
==> 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 NTC_0002_0014_B23KGCJLT4_1.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 1873.330 CPU sec, 82.441 real sec
[M::process] read 1122 sequences (169416 bp) in 0.000 CPU sec, 0.002 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1, 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 1122 reads in 3.214 CPU sec, 0.116 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: 1122
overall: 68422836224 mem 1703.121 user 182.450 sys 91.593 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_0014_B23KGCJLT4_1.L004\tPU:L004\tSM:NTC_0002_0014_B23KGCJLT4_1\tLB:NTC_0002_0014_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_0014_B23KGCJLT4_1_R1.fastq.gz NTC_0002_0014_B23KGCJLT4_1_R2.fastq.gz
[main] Real time: 91.633 sec; CPU: 1885.574 sec
sorting block 0, #reads = 1144 mem = 636672 peak = 75587584
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: 112181
output reads: 1144
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.000 real
bam_write: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.056 user 0.164 sys 91.760 real
merge_files: 1 calls 0.021 user 0.119 sys 0.155 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.001 real
read_chunk: 4 calls 0.001 user 0.003 sys 9.025 real
sort_block: 1 calls 0.002 user 0.000 sys 9.025 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 264581120 mem 0.127 user 0.173 sys 91.786 real
ls: cannot access '*.cram': No such file or directory