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_Lx-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 3103.807 CPU sec, 128.305 real sec
[M::process] read 64872 sequences (8919612 bp) in 0.080 CPU sec, 0.089 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 24707, 4, 7)
[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: (130, 181, 256)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 508)
[M::mem_pestat] mean and std.dev: (199.74, 92.93)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 634)
[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 64872 reads in 45.426 CPU sec, 1.501 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 64872
overall: 68048408576 mem 2282.788 user 879.554 sys 142.954 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_Lx-T1-TDNA-1_A23MHWWLT4_1.L007\tPU:L007\tSM:659_Lx-T1-TDNA-1_A23MHWWLT4_1\tLB:659_Lx-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_Lx-T1-TDNA-1_A23MHWWLT4_1_R1.fastq.gz 659_Lx-T1-TDNA-1_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 142.982 sec; CPU: 3162.344 sec
sorting block 0, #reads = 65569 mem = 32487775 peak = 129048576
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: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  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: 5053913
output reads: 65569
bam_mem_sort: 1 calls 0.013 user 0.000 sys 0.018 real
bam_write: 1 calls 0.015 user 0.010 sys 0.022 real
execute: 1 calls 0.078 user 0.111 sys 143.270 real
merge_files: 1 calls 0.062 user 0.082 sys 0.224 real
parse_chunk: 1 calls 0.016 user 0.024 sys 0.048 real
read_chunk: 5 calls 0.008 user 0.037 sys 13.120 real
sort_block: 1 calls 0.055 user 0.064 sys 13.129 real
write_chunk: 2 calls 0.008 user 0.003 sys 0.017 real
overall: 316710912 mem 0.873 user 0.314 sys 143.295 real
ls: cannot access '*.cram': No such file or directory