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/d5/b3d77dc629875035677775fd7229ca/.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/92/c9dd894aa053073f277378895c051f/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/92/c9dd894aa053073f277378895c051f/NTC_0002_0015_A23MHWWLT4_1/NTC_0002_0015_A23MHWWLT4_1_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/b3d77dc629875035677775fd7229ca/.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 1787.492 CPU sec, 65.141 real sec
[M::process] read 5434 sequences (818090 bp) in 0.001 CPU sec, 0.007 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: (168, 247, 351)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 717)
[M::mem_pestat] mean and std.dev: (271.27, 131.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 900)
[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 5434 reads in 10.125 CPU sec, 0.338 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: 5434
overall: 68430688256 mem 1600.046 user 203.669 sys 71.584 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.L008\tPU:L008\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: 71.618 sec; CPU: 1803.718 sec
sorting block 0, #reads = 5627 mem = 3119342 peak = 80334848
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 192
algo: util-sort
license: sentieon:util=1
output file size: 412130
output reads: 5627
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.001 real
bam_write: 1 calls 0.000 user 0.005 sys 0.004 real
execute: 1 calls 0.024 user 0.134 sys 71.739 real
merge_files: 1 calls 0.022 user 0.094 sys 0.132 real
parse_chunk: 1 calls 0.000 user 0.003 sys 0.004 real
read_chunk: 4 calls 0.004 user 0.000 sys 6.099 real
sort_block: 1 calls 0.002 user 0.009 sys 6.105 real
write_chunk: 1 calls 0.000 user 0.001 sys 0.002 real
overall: 268582912 mem 0.196 user 0.114 sys 71.760 real
ls: cannot access '*.cram': No such file or directory