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 1902.660 CPU sec, 79.715 real sec
[M::process] read 125588 sequences (18133711 bp) in 0.257 CPU sec, 0.258 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 15.204 CPU sec, 0.511 real sec
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa3203
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 125588
overall: 68554539008 mem 1752.879 user 174.447 sys 89.703 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: 89.738 sec; CPU: 1927.330 sec
sorting block 0, #reads = 125732 mem = 59740910 peak = 169582592
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 00050657
  features: 1f8bfbff fffa3203
  extended: d19f47ab 00000018
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz
threads: 31 max 64
algo: util-sort
license: sentieon:util=1
output file size: 7392989
output reads: 125732
bam_mem_sort: 1 calls 0.039 user 0.001 sys 0.046 real
bam_write: 1 calls 0.032 user 0.010 sys 0.036 real
execute: 1 calls 0.068 user 0.228 sys 90.256 real
merge_files: 1 calls 0.040 user 0.193 sys 0.406 real
parse_chunk: 2 calls 0.100 user 0.027 sys 0.130 real
read_chunk: 7 calls 0.062 user 0.035 sys 9.401 real
sort_block: 1 calls 0.162 user 0.048 sys 9.350 real
write_chunk: 3 calls 0.010 user 0.028 sys 0.055 real
overall: 494026752 mem 2.291 user 0.443 sys 90.280 real
ls: cannot access '*.cram': No such file or directory