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/7d/7a4b3329a396792628d700c077dba9/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/3052ba45f07c88db69a7f08cb69ae9/.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/7d/7a4b3329a396792628d700c077dba9/HCC1395_BL/HCC1395_BL_R1.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/3052ba45f07c88db69a7f08cb69ae9/.command.run
==> 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 1593.353 CPU sec, 56.145 real sec
[M::process] read 124700 sequences (17992902 bp) in 0.172 CPU sec, 0.180 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 44507, 0, 1)
[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, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 849)
[M::mem_pestat] mean and std.dev: (307.31, 153.98)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1070)
[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 124700 reads in 11.572 CPU sec, 0.400 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: 124700
overall: 68523466752 mem 1477.007 user 133.758 sys 62.385 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.L002\tPU:L002\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: 62.458 sec; CPU: 1610.768 sec
sorting block 0, #reads = 124816 mem = 59282090 peak = 168386560
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: 7313733
output reads: 124816
bam_mem_sort: 1 calls 0.025 user 0.000 sys 0.027 real
bam_write: 1 calls 0.091 user 0.002 sys 0.097 real
execute: 1 calls 0.088 user 0.080 sys 62.807 real
merge_files: 1 calls 0.065 user 0.063 sys 0.242 real
parse_chunk: 2 calls 0.037 user 0.027 sys 0.069 real
read_chunk: 7 calls 0.050 user 0.036 sys 5.774 real
sort_block: 1 calls 0.144 user 0.054 sys 5.814 real
write_chunk: 3 calls 0.012 user 0.004 sys 0.029 real
overall: 471912448 mem 1.267 user 0.229 sys 62.857 real
ls: cannot access '*.cram': No such file or directory