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 HCC1395_BL.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 2631.014 CPU sec, 92.832 real sec
[M::process] read 124548 sequences (17983515 bp) in 0.170 CPU sec, 0.176 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 44272, 0, 1)
[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: (185, 282, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (306.53, 153.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1061)
[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 124548 reads in 23.899 CPU sec, 0.785 real sec
os version: Linux 6.12.83
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: 124548
overall: 68237131776 mem 2201.716 user 460.403 sys 100.861 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.HCC1395_BL.L003\tPU:L003\tSM:HCC1395_BL\tLB:HCC1395_BL\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 HCC1395_BL_R1.fastq.gz HCC1395_BL_R2.fastq.gz
[main] Real time: 101.179 sec; CPU: 2662.121 sec
sorting block 0, #reads = 124708 mem = 59256603 peak = 163606528
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 384
algo: util-sort
license: sentieon:util=1
output file size: 7324881
output reads: 124708
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.026 real
bam_write: 1 calls 0.075 user 0.009 sys 0.083 real
execute: 1 calls 0.066 user 0.135 sys 101.588 real
merge_files: 1 calls 0.041 user 0.117 sys 0.284 real
parse_chunk: 2 calls 0.046 user 0.015 sys 0.072 real
read_chunk: 7 calls 0.014 user 0.067 sys 7.479 real
sort_block: 1 calls 0.127 user 0.083 sys 7.489 real
write_chunk: 3 calls 0.012 user 0.032 sys 0.065 real
overall: 446091264 mem 1.301 user 0.410 sys 101.606 real
ls: cannot access '*.cram': No such file or directory