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/da/37b940406e49dc3ae66494bd85b87a/Sig_18_Blood/Sig_18_Blood_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/a300a282ca2b62105a409dc9525395/.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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/a300a282ca2b62105a409dc9525395/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/37b940406e49dc3ae66494bd85b87a/Sig_18_Blood/Sig_18_Blood_R2.fastq.gz
==> STAGING COMPLETE (7 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o Sig_18_Blood.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 1388.909 CPU sec, 48.960 real sec
[M::process] read 124874 sequences (18107705 bp) in 0.172 CPU sec, 0.175 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44963, 0, 1)
[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: (191, 290, 414)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 860)
[M::mem_pestat] mean and std.dev: (315.00, 156.49)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1083)
[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 124874 reads in 10.296 CPU sec, 0.344 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: 124874
overall: 68479459328 mem 1309.581 user 95.538 sys 55.221 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:REGRESSION.Sig_18_Blood.L005\tPU:L005\tSM:Sig_18_Blood\tLB:Sig_18_Blood\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 Sig_18_Blood_R1.fastq.gz Sig_18_Blood_R2.fastq.gz
[main] Real time: 55.288 sec; CPU: 1405.122 sec
sorting block 0, #reads = 125029 mem = 60136694 peak = 165285888
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: 7482925
output reads: 125029
bam_mem_sort: 1 calls 0.018 user 0.000 sys 0.027 real
bam_write: 1 calls 0.108 user 0.012 sys 0.115 real
execute: 1 calls 0.069 user 0.131 sys 55.682 real
merge_files: 1 calls 0.044 user 0.113 sys 0.299 real
parse_chunk: 2 calls 0.061 user 0.007 sys 0.074 real
read_chunk: 8 calls 0.018 user 0.040 sys 5.879 real
sort_block: 1 calls 0.170 user 0.047 sys 5.919 real
write_chunk: 4 calls 0.008 user 0.024 sys 0.054 real
overall: 475693056 mem 1.413 user 0.303 sys 55.764 real
ls: cannot access '*.cram': No such file or directory