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/97/bc840ff228e1c2d6d77a23aff2ba70/.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/79/83a2710b26978b0a620a3d35f48e4e/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/97/bc840ff228e1c2d6d77a23aff2ba70/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/83a2710b26978b0a620a3d35f48e4e/HCC1395_tumor/HCC1395_tumor_R1.fastq.gz
==> STAGING COMPLETE (7 inputs)

This software is licensed to bgold@natera.com by Sentieon Inc.
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.
version: sentieon-genomics-202308.03
[M::bwa_idx_load_from_disk] read 3171 ALT contigs
[M::main_mem] bwa index loaded in 1648.785 CPU sec, 60.212 real sec
[M::process] read 125052 sequences (17995734 bp) in 0.161 CPU sec, 0.171 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 43482, 0, 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, 393)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 819)
[M::mem_pestat] mean and std.dev: (297.47, 149.74)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1032)
[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 125052 reads in 21.213 CPU sec, 0.706 real sec
os version: Linux 6.12.83
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: 125052
overall: 68501491712 mem 1502.506 user 173.138 sys 66.565 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.L006\tPU:L006\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: 66.600 sec; CPU: 1675.646 sec
sorting block 0, #reads = 125216 mem = 59825649 peak = 168439808
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 7277935
output reads: 125216
bam_mem_sort: 1 calls 0.022 user 0.000 sys 0.030 real
bam_write: 1 calls 0.095 user 0.007 sys 0.094 real
execute: 1 calls 0.054 user 0.116 sys 66.980 real
merge_files: 1 calls 0.038 user 0.091 sys 0.244 real
parse_chunk: 2 calls 0.047 user 0.005 sys 0.069 real
read_chunk: 8 calls 0.031 user 0.046 sys 5.594 real
sort_block: 1 calls 0.149 user 0.050 sys 5.633 real
write_chunk: 4 calls 0.006 user 0.019 sys 0.035 real
overall: 483258368 mem 1.131 user 0.366 sys 67.002 real
ls: cannot access '*.cram': No such file or directory