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/d0/b0120c2ec844ac347e1a181f05e7ab/HCC1395_BL/HCC1395_BL_R2.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/0bc6762a3bbedbefac84c02690c106/.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/b8/0bc6762a3bbedbefac84c02690c106/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/b0120c2ec844ac347e1a181f05e7ab/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 2040.485 CPU sec, 75.960 real sec
[M::process] read 124548 sequences (17983515 bp) in 0.210 CPU sec, 0.211 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 44272, 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: (185, 282, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (306.53, 153.44)
[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 124548 reads in 11.940 CPU sec, 0.397 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124548
overall: 68419670016 mem 1901.220 user 158.970 sys 84.136 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.L003\tPU:L003\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: 84.178 sec; CPU: 2060.192 sec
sorting block 0, #reads = 124708 mem = 59256603 peak = 165277696
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: util-sort
license: sentieon:util=1
output file size: 7324881
output reads: 124708
bam_mem_sort: 1 calls 0.027 user 0.000 sys 0.031 real
bam_write: 1 calls 0.016 user 0.011 sys 0.044 real
execute: 1 calls 0.042 user 0.190 sys 84.593 real
merge_files: 1 calls 0.020 user 0.160 sys 0.326 real
parse_chunk: 2 calls 0.115 user 0.019 sys 0.137 real
read_chunk: 7 calls 0.027 user 0.053 sys 7.716 real
sort_block: 1 calls 0.104 user 0.054 sys 7.686 real
write_chunk: 3 calls 0.000 user 0.030 sys 0.036 real
overall: 463626240 mem 1.617 user 0.430 sys 84.630 real
ls: cannot access '*.cram': No such file or directory