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 2697.945 CPU sec, 108.508 real sec
[M::process] read 124828 sequences (18022863 bp) in 0.172 CPU sec, 0.178 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 44466, 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: (186, 282, 403)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 837)
[M::mem_pestat] mean and std.dev: (306.65, 153.17)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1054)
[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 124828 reads in 22.847 CPU sec, 0.749 real sec
os version: Linux 6.12.83
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: 124828
overall: 68139646976 mem 2162.690 user 566.440 sys 117.605 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.L006\tPU:L006\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: 117.652 sec; CPU: 2729.133 sec
sorting block 0, #reads = 124937 mem = 59360983 peak = 160493568
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 7327533
output reads: 124937
bam_mem_sort: 1 calls 0.024 user 0.000 sys 0.027 real
bam_write: 1 calls 0.081 user 0.009 sys 0.089 real
execute: 1 calls 0.045 user 0.151 sys 118.016 real
merge_files: 1 calls 0.033 user 0.119 sys 0.264 real
parse_chunk: 2 calls 0.033 user 0.031 sys 0.074 real
read_chunk: 7 calls 0.037 user 0.046 sys 8.281 real
sort_block: 1 calls 0.142 user 0.047 sys 8.313 real
write_chunk: 3 calls 0.011 user 0.023 sys 0.039 real
overall: 460820480 mem 1.274 user 0.298 sys 118.065 real
ls: cannot access '*.cram': No such file or directory