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 Sig_18_tissue.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 2232.091 CPU sec, 77.397 real sec
[M::process] read 125234 sequences (17709222 bp) in 0.233 CPU sec, 0.242 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 47032, 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: (154, 225, 320)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 652)
[M::mem_pestat] mean and std.dev: (246.51, 119.92)
[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 125234 reads in 14.395 CPU sec, 0.498 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125234
overall: 68532150272 mem 2086.294 user 168.109 sys 85.820 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.L007\tPU:L007\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: 85.855 sec; CPU: 2254.406 sec
sorting block 0, #reads = 125460 mem = 59662775 peak = 167673856
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 00050657
  features: bfebfbff 7ffefbff
  extended: d39ff7eb 00000818
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 31 max 96
algo: util-sort
license: sentieon:util=1
output file size: 7062537
output reads: 125460
bam_mem_sort: 1 calls 0.053 user 0.000 sys 0.053 real
bam_write: 1 calls 0.033 user 0.000 sys 0.032 real
execute: 1 calls 0.118 user 0.139 sys 86.338 real
merge_files: 1 calls 0.096 user 0.106 sys 0.370 real
parse_chunk: 2 calls 0.073 user 0.036 sys 0.126 real
read_chunk: 8 calls 0.051 user 0.042 sys 7.856 real
sort_block: 1 calls 0.149 user 0.063 sys 7.815 real
write_chunk: 4 calls 0.020 user 0.011 sys 0.045 real
overall: 492310528 mem 2.086 user 0.403 sys 86.361 real
ls: cannot access '*.cram': No such file or directory