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 2562.585 CPU sec, 101.414 real sec
[M::process] read 125588 sequences (18133711 bp) in 0.235 CPU sec, 0.236 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 44648, 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: (188, 284, 407)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 845)
[M::mem_pestat] mean and std.dev: (308.41, 153.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1064)
[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 125588 reads in 16.332 CPU sec, 0.543 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: 125588
overall: 67994988544 mem 2305.613 user 281.708 sys 110.376 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.L005\tPU:L005\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: 110.404 sec; CPU: 2587.324 sec
sorting block 0, #reads = 125732 mem = 59740910 peak = 160534528
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: 7392989
output reads: 125732
bam_mem_sort: 1 calls 0.020 user 0.000 sys 0.029 real
bam_write: 1 calls 0.033 user 0.002 sys 0.026 real
execute: 1 calls 0.090 user 0.136 sys 110.772 real
merge_files: 1 calls 0.066 user 0.103 sys 0.295 real
parse_chunk: 2 calls 0.062 user 0.011 sys 0.077 real
read_chunk: 7 calls 0.017 user 0.057 sys 8.301 real
sort_block: 1 calls 0.082 user 0.061 sys 8.257 real
write_chunk: 3 calls 0.023 user 0.012 sys 0.039 real
overall: 468918272 mem 1.402 user 0.336 sys 110.788 real
ls: cannot access '*.cram': No such file or directory