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/33/4b97d9b9a9bbacd34e65d2e6bd998e/Sig_18_Blood/Sig_18_Blood_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/e56c456c96c7bbba8532e483b97490/.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/80/e56c456c96c7bbba8532e483b97490/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/4b97d9b9a9bbacd34e65d2e6bd998e/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 1621.715 CPU sec, 57.226 real sec
[M::process] read 125346 sequences (18175258 bp) in 0.169 CPU sec, 0.177 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 45082, 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: (192, 292, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (316.67, 156.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1100)
[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 125346 reads in 24.881 CPU sec, 0.833 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125346
overall: 68518780928 mem 1489.040 user 163.468 sys 63.971 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.L004\tPU:L004\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: 64.010 sec; CPU: 1652.510 sec
sorting block 0, #reads = 125458 mem = 60226619 peak = 165253120
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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 7445623
output reads: 125458
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.029 real
bam_write: 1 calls 0.087 user 0.019 sys 0.099 real
execute: 1 calls 0.040 user 0.129 sys 64.396 real
merge_files: 1 calls 0.040 user 0.090 sys 0.245 real
parse_chunk: 2 calls 0.039 user 0.014 sys 0.070 real
read_chunk: 8 calls 0.047 user 0.035 sys 5.854 real
sort_block: 1 calls 0.153 user 0.051 sys 5.898 real
write_chunk: 4 calls 0.000 user 0.018 sys 0.030 real
overall: 482398208 mem 1.268 user 0.262 sys 64.415 real
ls: cannot access '*.cram': No such file or directory