cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o Sig_18_Blood.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 1768.786 CPU sec, 64.453 real sec
[M::process] read 124888 sequences (18114909 bp) in 0.165 CPU sec, 0.174 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44931, 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: (192, 290, 413)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 855)
[M::mem_pestat] mean and std.dev: (315.53, 156.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1076)
[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 124888 reads in 25.056 CPU sec, 0.827 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: 124888
overall: 68503027712 mem 1619.402 user 180.550 sys 71.394 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.Sig_18_Blood.L008\tPU:L008\tSM:Sig_18_Blood\tLB:Sig_18_Blood\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 Sig_18_Blood_R1.fastq.gz Sig_18_Blood_R2.fastq.gz
[main] Real time: 71.431 sec; CPU: 1799.955 sec
sorting block 0, #reads = 125049 mem = 60110585 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: 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: 7453703
output reads: 125049
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.029 real
bam_write: 1 calls 0.089 user 0.000 sys 0.085 real
execute: 1 calls 0.056 user 0.124 sys 71.811 real
merge_files: 1 calls 0.037 user 0.104 sys 0.252 real
parse_chunk: 2 calls 0.060 user 0.000 sys 0.071 real
read_chunk: 8 calls 0.035 user 0.046 sys 6.059 real
sort_block: 1 calls 0.165 user 0.032 sys 6.090 real
write_chunk: 4 calls 0.003 user 0.026 sys 0.039 real
overall: 483041280 mem 1.250 user 0.306 sys 71.833 real
ls: cannot access '*.cram': No such file or directory