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 659_eKx-T1-TDNA-1_A23MHWWLT4_1.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 1903.064 CPU sec, 69.979 real sec
[M::process] read 28866 sequences (4081464 bp) in 0.049 CPU sec, 0.052 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 11096, 1, 4)
[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, 229, 332)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 688)
[M::mem_pestat] mean and std.dev: (252.35, 124.79)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 866)
[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 28866 reads in 9.057 CPU sec, 0.304 real sec
os version: Linux 6.12.88
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: 28866
overall: 68430671872 mem 1762.448 user 158.608 sys 79.233 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:A23MHWWLT4.659_eKx-T1-TDNA-1_A23MHWWLT4_1.L008\tPU:L008\tSM:659_eKx-T1-TDNA-1_A23MHWWLT4_1\tLB:659_eKx-T1-TDNA-1_A23MHWWLT4_1\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.64 659_eKx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_eKx-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 79.269 sec; CPU: 1921.059 sec
sorting block 0, #reads = 29079 mem = 14435117 peak = 100761600
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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 2242982
output reads: 29079
bam_mem_sort: 1 calls 0.002 user 0.000 sys 0.008 real
bam_write: 1 calls 0.017 user 0.000 sys 0.010 real
execute: 1 calls 0.060 user 0.126 sys 79.487 real
merge_files: 1 calls 0.032 user 0.102 sys 0.194 real
parse_chunk: 1 calls 0.020 user 0.000 sys 0.028 real
read_chunk: 4 calls 0.000 user 0.018 sys 8.917 real
sort_block: 1 calls 0.018 user 0.042 sys 8.932 real
write_chunk: 1 calls 0.010 user 0.001 sys 0.023 real
overall: 306708480 mem 0.495 user 0.242 sys 79.508 real
ls: cannot access '*.cram': No such file or directory