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 2255.307 CPU sec, 81.572 real sec
[M::process] read 124478 sequences (17924843 bp) in 0.171 CPU sec, 0.175 real sec...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 43537, 0, 2)
[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: (180, 274, 394)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 822)
[M::mem_pestat] mean and std.dev: (298.63, 150.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1036)
[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 124478 reads in 27.231 CPU sec, 0.925 real sec
os version: Linux 6.12.88
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: 124478
overall: 68300107776 mem 1947.434 user 344.937 sys 92.340 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.L001\tPU:L001\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: 92.377 sec; CPU: 2292.375 sec
sorting block 0, #reads = 124658 mem = 59579630 peak = 160505856
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: 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: 7258879
output reads: 124658
bam_mem_sort: 1 calls 0.025 user 0.000 sys 0.034 real
bam_write: 1 calls 0.092 user 0.008 sys 0.096 real
execute: 1 calls 0.065 user 0.140 sys 92.813 real
merge_files: 1 calls 0.060 user 0.104 sys 0.291 real
parse_chunk: 2 calls 0.057 user 0.038 sys 0.102 real
read_chunk: 7 calls 0.014 user 0.048 sys 9.800 real
sort_block: 1 calls 0.137 user 0.069 sys 9.831 real
write_chunk: 3 calls 0.026 user 0.015 sys 0.064 real
overall: 450908160 mem 1.376 user 0.366 sys 92.834 real
ls: cannot access '*.cram': No such file or directory