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/04/0398c61a052c4bd860bdf964851a1a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/3550fa2c6e667c37f3eb00ff6cf14b/659_Lx-T1-TDNA-1_A23MHWWLT4_1/659_Lx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz
  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/04/0398c61a052c4bd860bdf964851a1a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/3550fa2c6e667c37f3eb00ff6cf14b/659_Lx-T1-TDNA-1_A23MHWWLT4_1/659_Lx-T1-TDNA-1_A23MHWWLT4_1_R2.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 659_Lx-T1-TDNA-1_A23MHWWLT4_1.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 1829.963 CPU sec, 67.088 real sec
[M::process] read 64532 sequences (8863395 bp) in 0.075 CPU sec, 0.084 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 24591, 7, 11)
[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: (129, 179, 254)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 504)
[M::mem_pestat] mean and std.dev: (198.91, 92.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 629)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (497, 501, 627)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (237, 887)
[M::mem_pestat] mean and std.dev: (489.12, 112.45)
[M::mem_pestat] low and high boundaries for proper pairs: (39, 1017)
[M::mem_pestat] skip orientation RR
[M::mem_process_seqs] Processed 64532 reads in 13.889 CPU sec, 0.463 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: 64532
overall: 68425969664 mem 1699.611 user 151.010 sys 74.331 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:A23MHWWLT4.659_Lx-T1-TDNA-1_A23MHWWLT4_1.L001\tPU:L001\tSM:659_Lx-T1-TDNA-1_A23MHWWLT4_1\tLB:659_Lx-T1-TDNA-1_A23MHWWLT4_1\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.64 659_Lx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_Lx-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 74.366 sec; CPU: 1850.623 sec
sorting block 0, #reads = 65198 mem = 32255193 peak = 136937472
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 192
algo: util-sort
license: sentieon:util=1
output file size: 4945001
output reads: 65198
bam_mem_sort: 1 calls 0.009 user 0.000 sys 0.015 real
bam_write: 1 calls 0.041 user 0.002 sys 0.038 real
execute: 1 calls 0.046 user 0.121 sys 74.645 real
merge_files: 1 calls 0.031 user 0.095 sys 0.205 real
parse_chunk: 1 calls 0.036 user 0.009 sys 0.045 real
read_chunk: 5 calls 0.018 user 0.018 sys 6.774 real
sort_block: 1 calls 0.096 user 0.029 sys 6.794 real
write_chunk: 2 calls 0.000 user 0.010 sys 0.016 real
overall: 363261952 mem 0.833 user 0.246 sys 74.666 real
ls: cannot access '*.cram': No such file or directory