cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/util sort -r Homo_sapiens_assembly38.fasta -t 31 -o Sig_18_tissue.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 1376.176 CPU sec, 49.749 real sec
[M::process] read 125792 sequences (17808231 bp) in 0.171 CPU sec, 0.176 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 47271, 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: (154, 224, 320)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 652)
[M::mem_pestat] mean and std.dev: (246.05, 119.39)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 818)
[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 125792 reads in 19.024 CPU sec, 0.636 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125792
overall: 68512440320 mem 1265.498 user 135.382 sys 56.070 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_tissue.L003\tPU:L003\tSM:Sig_18_tissue\tLB:Sig_18_tissue\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_tissue_R1.fastq.gz Sig_18_tissue_R2.fastq.gz
[main] Real time: 56.170 sec; CPU: 1400.882 sec
sorting block 0, #reads = 126017 mem = 59991631 peak = 168431616
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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 7116343
output reads: 126017
bam_mem_sort: 1 calls 0.025 user 0.000 sys 0.027 real
bam_write: 1 calls 0.097 user 0.000 sys 0.096 real
execute: 1 calls 0.049 user 0.144 sys 56.518 real
merge_files: 1 calls 0.031 user 0.119 sys 0.282 real
parse_chunk: 2 calls 0.065 user 0.009 sys 0.079 real
read_chunk: 8 calls 0.067 user 0.011 sys 5.637 real
sort_block: 1 calls 0.192 user 0.014 sys 5.671 real
write_chunk: 4 calls 0.000 user 0.027 sys 0.046 real
overall: 475992064 mem 1.384 user 0.246 sys 56.616 real
ls: cannot access '*.cram': No such file or directory