Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/d3ff6b39a6c49e17c7faa6904ddc3a/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  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/2a/93921f4e4311cef957f1947aacbe01/.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/2a/93921f4e4311cef957f1947aacbe01/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/d3ff6b39a6c49e17c7faa6904ddc3a/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 1683.162 CPU sec, 59.256 real sec
[M::process] read 124904 sequences (18031367 bp) in 0.169 CPU sec, 0.177 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 44581, 0, 3)
[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, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 840)
[M::mem_pestat] mean and std.dev: (307.00, 153.31)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1058)
[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 124904 reads in 23.332 CPU sec, 0.779 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: 124904
overall: 68474712064 mem 1552.792 user 159.437 sys 65.782 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.L007\tPU:L007\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: 65.830 sec; CPU: 1712.232 sec
sorting block 0, #reads = 125063 mem = 59373495 peak = 166821888
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: 7316072
output reads: 125063
bam_mem_sort: 1 calls 0.028 user 0.000 sys 0.028 real
bam_write: 1 calls 0.046 user 0.000 sys 0.047 real
execute: 1 calls 0.110 user 0.068 sys 66.145 real
merge_files: 1 calls 0.088 user 0.052 sys 0.261 real
parse_chunk: 2 calls 0.023 user 0.034 sys 0.072 real
read_chunk: 7 calls 0.055 user 0.011 sys 5.694 real
sort_block: 1 calls 0.117 user 0.032 sys 5.679 real
write_chunk: 3 calls 0.022 user 0.006 sys 0.032 real
overall: 460779520 mem 1.377 user 0.226 sys 66.200 real
ls: cannot access '*.cram': No such file or directory