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/05/2c7627608eaf9c7b4bdcd56eed3122/.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/ae/8bd134deadad043006cafe4da3c1c3/HCC1395_tumor/HCC1395_tumor_R2.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/05/2c7627608eaf9c7b4bdcd56eed3122/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/8bd134deadad043006cafe4da3c1c3/HCC1395_tumor/HCC1395_tumor_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_tumor.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 1965.779 CPU sec, 68.040 real sec
[M::process] read 125124 sequences (17999868 bp) in 0.180 CPU sec, 0.183 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 43763, 1, 2)
[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: (180, 272, 391)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 813)
[M::mem_pestat] mean and std.dev: (296.95, 149.26)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1024)
[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 125124 reads in 17.400 CPU sec, 0.585 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: 125124
overall: 68403859456 mem 1848.011 user 142.584 sys 76.044 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_tumor.L007\tPU:L007\tSM:HCC1395_tumor\tLB:HCC1395_tumor\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_tumor_R1.fastq.gz HCC1395_tumor_R2.fastq.gz
[main] Real time: 76.075 sec; CPU: 1990.599 sec
sorting block 0, #reads = 125293 mem = 59924104 peak = 157360128
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: 7303558
output reads: 125293
bam_mem_sort: 1 calls 0.035 user 0.000 sys 0.042 real
bam_write: 1 calls 0.063 user 0.009 sys 0.065 real
execute: 1 calls 0.062 user 0.165 sys 76.544 real
merge_files: 1 calls 0.042 user 0.135 sys 0.338 real
parse_chunk: 2 calls 0.061 user 0.008 sys 0.083 real
read_chunk: 8 calls 0.029 user 0.080 sys 7.398 real
sort_block: 1 calls 0.148 user 0.059 sys 7.379 real
write_chunk: 4 calls 0.012 user 0.028 sys 0.058 real
overall: 403931136 mem 1.532 user 0.418 sys 76.563 real
ls: cannot access '*.cram': No such file or directory