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/26/0782e182e32ad5dae8eabed4e5286a/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/0f55b4388e06ce63d811e32548e1b9/.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/ed/0f55b4388e06ce63d811e32548e1b9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/0782e182e32ad5dae8eabed4e5286a/HCC1395_BL/HCC1395_BL_R1.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 HCC1395_BL.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 2070.883 CPU sec, 74.047 real sec
[M::process] read 124828 sequences (18022863 bp) in 0.167 CPU sec, 0.177 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44466, 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: (186, 282, 403)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 837)
[M::mem_pestat] mean and std.dev: (306.65, 153.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1054)
[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 124828 reads in 37.446 CPU sec, 1.232 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: 124828
overall: 68444753920 mem 1784.614 user 333.520 sys 85.082 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.HCC1395_BL.L006\tPU:L006\tSM:HCC1395_BL\tLB:HCC1395_BL\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 HCC1395_BL_R1.fastq.gz HCC1395_BL_R2.fastq.gz
[main] Real time: 85.151 sec; CPU: 2118.137 sec
sorting block 0, #reads = 124937 mem = 59360983 peak = 160505856
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 384
algo: util-sort
license: sentieon:util=1
output file size: 7327533
output reads: 124937
bam_mem_sort: 1 calls 0.022 user 0.000 sys 0.029 real
bam_write: 1 calls 0.119 user 0.000 sys 0.121 real
execute: 1 calls 0.053 user 0.131 sys 85.557 real
merge_files: 1 calls 0.041 user 0.100 sys 0.266 real
parse_chunk: 2 calls 0.055 user 0.008 sys 0.079 real
read_chunk: 7 calls 0.045 user 0.036 sys 9.744 real
sort_block: 1 calls 0.198 user 0.042 sys 9.812 real
write_chunk: 3 calls 0.013 user 0.013 sys 0.049 real
overall: 454033408 mem 1.292 user 0.271 sys 85.610 real
ls: cannot access '*.cram': No such file or directory