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_Blood.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 1957.282 CPU sec, 71.647 real sec
[M::process] read 125346 sequences (18175258 bp) in 0.214 CPU sec, 0.217 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 45082, 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, 292, 419)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 873)
[M::mem_pestat] mean and std.dev: (316.67, 156.91)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1100)
[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 125346 reads in 24.249 CPU sec, 0.803 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: 125346
overall: 68429099008 mem 1798.190 user 190.086 sys 79.217 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.L004\tPU:L004\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: 79.254 sec; CPU: 1988.278 sec
sorting block 0, #reads = 125458 mem = 60226619 peak = 166821888
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: 7445623
output reads: 125458
bam_mem_sort: 1 calls 0.019 user 0.000 sys 0.028 real
bam_write: 1 calls 0.027 user 0.000 sys 0.024 real
execute: 1 calls 0.040 user 0.191 sys 79.644 real
merge_files: 1 calls 0.023 user 0.148 sys 0.317 real
parse_chunk: 2 calls 0.058 user 0.028 sys 0.090 real
read_chunk: 8 calls 0.035 user 0.041 sys 6.682 real
sort_block: 1 calls 0.086 user 0.060 sys 6.629 real
write_chunk: 4 calls 0.000 user 0.027 sys 0.033 real
overall: 482164736 mem 1.481 user 0.426 sys 79.665 real
ls: cannot access '*.cram': No such file or directory