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 1359.625 CPU sec, 46.787 real sec
[M::process] read 124548 sequences (17983515 bp) in 0.244 CPU sec, 0.254 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 44272, 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: (185, 282, 404)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 842)
[M::mem_pestat] mean and std.dev: (306.53, 153.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1061)
[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 124548 reads in 10.093 CPU sec, 0.338 real sec
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124548
overall: 68556685312 mem 1325.518 user 48.975 sys 51.919 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.L003\tPU:L003\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: 51.955 sec; CPU: 1374.496 sec
sorting block 0, #reads = 124708 mem = 59256603 peak = 169172992
uniq header count 1
merging 1 blocks
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 64
algo: util-sort
license: sentieon:util=1
output file size: 7324881
output reads: 124708
bam_mem_sort: 1 calls 0.023 user 0.000 sys 0.025 real
bam_write: 1 calls 0.020 user 0.000 sys 0.020 real
execute: 1 calls 0.085 user 0.091 sys 52.244 real
merge_files: 1 calls 0.069 user 0.060 sys 0.247 real
parse_chunk: 2 calls 0.070 user 0.017 sys 0.099 real
read_chunk: 7 calls 0.011 user 0.041 sys 4.651 real
sort_block: 1 calls 0.075 user 0.043 sys 4.608 real
write_chunk: 3 calls 0.011 user 0.008 sys 0.026 real
overall: 492367872 mem 1.430 user 0.217 sys 52.280 real
ls: cannot access '*.cram': No such file or directory