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/75/97836d7ec6b9c13b2323e4b70b3e49/.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-rnd-pltf-dev-nextflow-scratch-01/work/42/086624e554e3c97e416447051655b6/NTC_0002_0015_A23MHWWLT4_1/NTC_0002_0015_A23MHWWLT4_1_R1.fastq.gz
  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/42/086624e554e3c97e416447051655b6/NTC_0002_0015_A23MHWWLT4_1/NTC_0002_0015_A23MHWWLT4_1_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/97836d7ec6b9c13b2323e4b70b3e49/.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_0015_A23MHWWLT4_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 1821.436 CPU sec, 67.155 real sec
[M::process] read 5604 sequences (842014 bp) in 0.007 CPU sec, 0.008 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 79, 0, 0)
[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: (138, 207, 340)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 744)
[M::mem_pestat] mean and std.dev: (234.35, 119.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 946)
[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 5604 reads in 12.997 CPU sec, 0.426 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: 5604
overall: 68435431424 mem 1715.954 user 125.336 sys 74.446 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:A23MHWWLT4.NTC_0002_0015_A23MHWWLT4_1.L002\tPU:L002\tSM:NTC_0002_0015_A23MHWWLT4_1\tLB:NTC_0002_0015_A23MHWWLT4_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_0015_A23MHWWLT4_1_R1.fastq.gz NTC_0002_0015_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 74.484 sec; CPU: 1841.293 sec
sorting block 0, #reads = 5798 mem = 3207323 peak = 81911808
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: 414230
output reads: 5798
bam_mem_sort: 1 calls 0.001 user 0.000 sys 0.002 real
bam_write: 1 calls 0.005 user 0.000 sys 0.007 real
execute: 1 calls 0.053 user 0.130 sys 74.629 real
merge_files: 1 calls 0.036 user 0.096 sys 0.151 real
parse_chunk: 1 calls 0.000 user 0.000 sys 0.007 real
read_chunk: 4 calls 0.000 user 0.003 sys 6.857 real
sort_block: 1 calls 0.007 user 0.010 sys 6.869 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.002 real
overall: 270753792 mem 0.169 user 0.215 sys 74.649 real
ls: cannot access '*.cram': No such file or directory