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_tumor.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 2790.188 CPU sec, 103.034 real sec
[M::process] read 124560 sequences (17940725 bp) in 0.174 CPU sec, 0.174 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 43403, 0, 7)
[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: (181, 272, 392)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 814)
[M::mem_pestat] mean and std.dev: (297.87, 148.80)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1025)
[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 124560 reads in 12.547 CPU sec, 0.423 real sec
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31
algo: bwa-mem
license: sentieon:klib=31
reads: 124560
overall: 68023242752 mem 2461.520 user 350.527 sys 112.811 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_tumor.L004\tPU:L004\tSM:HCC1395_tumor\tLB:HCC1395_tumor\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_tumor_R1.fastq.gz HCC1395_tumor_R2.fastq.gz
[main] Real time: 112.845 sec; CPU: 2812.050 sec
sorting block 0, #reads = 124723 mem = 59715543 peak = 160497664
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: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  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: 7289742
output reads: 124723
bam_mem_sort: 1 calls 0.026 user 0.000 sys 0.033 real
bam_write: 1 calls 0.106 user 0.014 sys 0.119 real
execute: 1 calls 0.077 user 0.108 sys 113.290 real
merge_files: 1 calls 0.057 user 0.088 sys 0.269 real
parse_chunk: 2 calls 0.049 user 0.027 sys 0.080 real
read_chunk: 8 calls 0.037 user 0.088 sys 9.298 real
sort_block: 1 calls 0.168 user 0.121 sys 9.373 real
write_chunk: 4 calls 0.010 user 0.017 sys 0.050 real
overall: 468041728 mem 1.228 user 0.385 sys 113.310 real
ls: cannot access '*.cram': No such file or directory