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/56/642a392ca013205e9aeb3b4ee11882/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/0a27ec53a5ecc1864e6b9ebccd005a/.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/95/0a27ec53a5ecc1864e6b9ebccd005a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/642a392ca013205e9aeb3b4ee11882/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 2014.835 CPU sec, 71.472 real sec
[M::process] read 125268 sequences (18081190 bp) in 0.242 CPU sec, 0.249 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 44781, 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: (185, 281, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (306.22, 154.08)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1061)
[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 125268 reads in 19.913 CPU sec, 0.655 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: 125268
overall: 68454191104 mem 1859.937 user 182.725 sys 80.046 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.L008\tPU:L008\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: 80.078 sec; CPU: 2042.664 sec
sorting block 0, #reads = 125405 mem = 59527015 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: 7353993
output reads: 125405
bam_mem_sort: 1 calls 0.033 user 0.000 sys 0.036 real
bam_write: 1 calls 0.091 user 0.000 sys 0.089 real
execute: 1 calls 0.093 user 0.152 sys 80.552 real
merge_files: 1 calls 0.081 user 0.118 sys 0.329 real
parse_chunk: 2 calls 0.035 user 0.033 sys 0.079 real
read_chunk: 7 calls 0.042 user 0.033 sys 7.810 real
sort_block: 1 calls 0.160 user 0.053 sys 7.826 real
write_chunk: 3 calls 0.030 user 0.010 sys 0.045 real
overall: 446402560 mem 1.600 user 0.339 sys 80.571 real
ls: cannot access '*.cram': No such file or directory