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 NTC_0002_0015_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 2420.955 CPU sec, 94.436 real sec
[M::process] read 5144 sequences (774040 bp) in 0.000 CPU sec, 0.007 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 69, 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: (128, 224, 324)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 716)
[M::mem_pestat] mean and std.dev: (253.04, 158.15)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 912)
[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 5144 reads in 9.500 CPU sec, 0.312 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: 5144
overall: 68111310848 mem 2008.844 user 427.959 sys 101.103 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.NTC_0002_0015_A23MHWWLT4_1.L004\tPU:L004\tSM:NTC_0002_0015_A23MHWWLT4_1\tLB:NTC_0002_0015_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 NTC_0002_0015_A23MHWWLT4_1_R1.fastq.gz NTC_0002_0015_A23MHWWLT4_1_R2.fastq.gz
[main] Real time: 101.130 sec; CPU: 2436.806 sec
sorting block 0, #reads = 5366 mem = 2974907 peak = 75603968
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: 400360
output reads: 5366
bam_mem_sort: 1 calls 0.000 user 0.000 sys 0.002 real
bam_write: 1 calls 0.000 user 0.006 sys 0.004 real
execute: 1 calls 0.041 user 0.129 sys 101.258 real
merge_files: 1 calls 0.023 user 0.098 sys 0.136 real
parse_chunk: 1 calls 0.000 user 0.002 sys 0.005 real
read_chunk: 4 calls 0.002 user 0.000 sys 6.342 real
sort_block: 1 calls 0.002 user 0.010 sys 6.349 real
write_chunk: 1 calls 0.000 user 0.000 sys 0.002 real
overall: 265371648 mem 0.091 user 0.240 sys 101.275 real
ls: cannot access '*.cram': No such file or directory